What is the recognized way to reference accession data (.sra files) from NCBI as a URI? I would like to assign a URL/URI to accession runs (i.e. SRR IDs) from the NCBI short read archive.

In program listings, I used to list them as ftp:// URLs, because they were available on their servers as such, e.g. SRR3418242:

ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR341/SRR3418242/SRR3418242.sra


But this approach is deprecated, plus, not all runs are available this way anymore. The now recommended approach is to use sra-tools to download the data. This tool takes the SRR Ids directly, i.e. prefetch "SRR3418242", and resolves them to one of many possible locations (home directory, http, etc).

Is there an official URI scheme that can be used to reference accession runs from the short-read-archive ? I would like to disambiguate them from other types of files and URLs (S3 keys, http, file). For file manifests, spreadsheets, and publications, is there something similar to srr://SRR3418242?
The nomenclature is no longer being followed as NCBI is moving all the files to S3/Google cloud. pysradb allows you to fetch the metadata and get the URLs for each individual SRR. See examples in this notebook.

You can also download an entire project by doing:

pysradb download -p &lt;SRP&gt;