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338,300 | 62,980,538 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,301 | 29,725,300 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,302 | 62,980,473 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,303 | 62,980,467 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,304 | 62,980,460 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,305 | 29,725,319 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,306 | 62,980,466 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,307 | 62,980,481 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,308 | 29,725,252 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,309 | 62,980,564 | 2,916 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,310 | 35,510,371 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,311 | 62,980,462 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,312 | 62,980,461 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,313 | 62,980,458 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,314 | 62,980,546 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,315 | 62,980,515 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,316 | 62,980,558 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,317 | 62,980,550 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,318 | 62,980,553 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,319 | 62,980,556 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,320 | 62,980,544 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,321 | 62,980,542 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,322 | 62,980,485 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,323 | 62,980,527 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,324 | 62,980,506 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,325 | 62,980,532 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,326 | 62,980,528 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,327 | 62,980,533 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,328 | 29,725,279 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,329 | 62,980,562 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,330 | 62,980,510 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,331 | 62,980,590 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,332 | 29,725,249 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,333 | 62,980,608 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,334 | 62,980,523 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,335 | 62,980,514 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,336 | 62,980,518 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,337 | 62,980,507 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,338 | 62,980,610 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,339 | 62,980,596 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,340 | 62,980,617 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,341 | 62,980,519 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,342 | 62,980,603 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,343 | 62,980,503 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,344 | 62,980,598 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,345 | 62,980,530 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,346 | 62,980,607 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,347 | 62,980,592 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,348 | 62,980,604 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,349 | 62,980,620 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,350 | 62,980,537 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,351 | 62,980,634 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,352 | 62,980,616 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,353 | 62,980,597 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,354 | 62,980,591 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,355 | 62,980,586 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,356 | 62,980,594 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,357 | 62,980,653 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,358 | 62,980,600 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,359 | 62,980,585 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,360 | 62,980,517 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,361 | 62,980,581 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,362 | 62,980,571 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,363 | 62,980,565 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,364 | 62,980,582 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,365 | 62,980,570 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,366 | 62,980,652 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,367 | 62,980,649 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,368 | 62,980,654 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,369 | 62,980,642 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,370 | 62,980,636 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,371 | 62,980,657 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,372 | 62,980,638 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,373 | 62,980,667 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,374 | 62,980,660 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,375 | 62,980,643 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,376 | 62,980,629 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,377 | 62,980,611 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,378 | 62,980,605 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,379 | 62,980,673 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,380 | 62,980,686 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,381 | 62,980,623 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,382 | 62,980,606 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,383 | 62,980,694 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,384 | 62,980,621 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,385 | 29,725,277 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,386 | 62,980,628 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,387 | 62,980,698 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,388 | 62,980,711 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,389 | 62,980,704 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,390 | 62,980,561 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,391 | 62,980,717 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,392 | 62,980,724 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,393 | 62,980,718 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,394 | 62,980,692 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,395 | 62,980,703 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,396 | 62,980,700 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,397 | 62,980,645 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,398 | 62,980,504 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900 |
338,399 | 62,980,688 | 2,918 |
In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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