anchor.diff:  Papers that qualify for inclusion in the Catalog are identified through weekly PubMed searches.
   They then undergo two levels of curation.
   First all data, including association information for SNPs, traits and general information about the study, are extracted by one curator.
  -A second curator then performs an additional round of curation to double-check the accuracy and consistency of all the information.
  -Finally, an automated pipeline run at the NCBI performs checks for missing information, such as SNP identifiers, resolution of the citation in PubMed, existence of SNPs in dbSNP, confirmation of gene names vs. NCBI's Gene database, confirmation that the reported SNP and gene are in the same chromosomal region, as well as adding additional information such as the SNP's base pair and cytogenetic location in the current human genome reference assembly.
  -This information is then used for queries and in the production of the karyotype diagram.
  +A second curator then performs an additional round of curation to double-check the accuracy and consistency of all the information. Finally, an automated pipeline performs validation of the extracted data, see the <<mapping, Quality control and SNP mapping section>> below for more details. This information is then used for queries and in the production of the diagram.
   
   
   == Full Description of Methods
  
positive.code: 
  For each identified SNP, we extract:
  
  * REPORTED GENE: Gene(s) reported by the author; "Intergenic" is used to denote a reported intergenic location (or lack of gene if it appeared that gene information was sought); “NR” is used to denote that no gene location information was reported.
  * STRONGEST SNP-RISK ALLELE: SNP(s) most strongly associated with trait + risk/effect allele (? for unknown risk allele). May also refer to a haplotype.
  * SNPS: Strongest SNP; If a haplotype is reported above, this field may include more than one rs number (multiple SNPs comprising the haplotype). Multiple SNPs may also be included if proxy SNPs are reported.
  * RISK ALLELE FREQUENCY: Reported risk/effect allele frequency associated with strongest SNP in controls (if not available among all controls, among the control group with the largest sample size). If the associated locus is a haplotype the haplotype frequency will be extracted.
  * P-VALUE: Reported p-value for strongest SNP risk allele. Note that p-values are rounded to 1 significant digit (for example, a published p- value of 4.8 x 10-7 is rounded to 5 x 10-7).
  * PVALUE_MLOG: -log(p-value)
  * P-VALUE (TEXT): Information describing context of p-value (e.g. females, smokers).
  * OR or BETA: Reported odds ratio or beta-coefficient associated with strongest SNP risk allele. Note that if an OR <1 is reported this is inverted, along with the reported allele, so that all ORs included in the Catalog are >1. Appropriate unit and increase/decrease are included for beta coefficients.
  * 95% CI (TEXT): Reported 95% confidence interval associated with strongest SNP risk allele, along with unit in the case of beta-coefficients. If 95% CIs are not published, we estimate these using the standard error, where available.
  
negative.code: 
  The ancestry is derived from the ancestry descriptors used in the publication. Country of recruitment is extracted if an author states the country of recruitment of the samples. It is not assumed from an ancestry identifier or from a cohort name. Where a country of recruitment but no ancestry is provided, published population demographic information, such as the https://www.cia.gov/library/publications/the-world-factbook/[CIA World Factbook] is consulted.
  
  ==== [[mapping]]Quality control and SNP mapping
  
  An automated pipeline adds additional SNP specific information associated with the rsID extracted. This information includes the SNP's base pair and cytogenetic location(s) in the current human genome reference assembly, mapped genes, mapped gene distance’s and positioning, and SNP function. This information is then used for queries of the search interface and in the production of the diagram. The pipeline also performs checks for consistency and missing information, such as SNP identifiers, existence of SNPs in dbSNP, validation of gene names and confirmation that the reported SNP and gene are in the same chromosomal region. This information is retrieved using the link:http://www.ensembl.org/info/docs/api/index.html[Ensembl API] and the source of the data is both Ensembl and NCBI.
  
  Additional information added by this pipeline. Capitalised titles correspond to column headings in tab delimited file:
  
  * REGION: Cytogenetic region associated with rs number.
  * CHR_ID: Chromosome number associated with rs number.
  * CHR_POS: +++Chromosomal position, in base pairs, associated with rs number.+++
  * MAPPED GENE(S): Gene(s) mapped to the strongest SNP. If the SNP is located within a gene, that gene is listed, with multiple overlapping genes separated by “;”. If the SNP is intergenic, the upstream and downstream genes are listed, separated by “-”.
  * UPSTREAM_GENE_ID: Entrez Gene ID for nearest upstream gene to rs number, if not within gene.
  * DOWNSTREAM_GENE_ID: Entrez Gene ID for nearest downstream gene to rs number, if not within gene.
  