Retrieve bioproject IDs and SRA IDs from PMIDs?

[Jigyasa3]

Hey all,

I have a list of PMIDs for which I want to extract the Bio project ID and SRA IDs. I was unable to find anything in the documentation for the same. Any suggestions?

Looking forward to your replies!

[vkkodali]

You can use elink for this. For example:

esearch -db pubmed -query '33179728[uid]' | elink -target bioproject
esearch -db pubmed -query '33179728[uid]' | elink -target sra

For a database of interest, you can find all the links by running:

einfo -db pubmed | xtract -pattern Link -element Name,Description,DbTo

Alternately, they are all listed here: https://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html

[Jigyasa3]

Hey @vkkodali,

Thank you for replying! I am using the elink to get bioproject id from sra id. I want to go from sra to pubmed id. But when I try the following code(s), I get an empty output even though manual search shows that there is a corresponding pubmed id associated with the bioproject.

esearch -db sra -query 'ERS1266396' | elink -target pubmed | efetch -format uid

esearch -db bioproject -query 'PRJEB14911' | elink -target pubmed | efetch -format uid

[vkkodali]

This SRA accession and the BioProject are not linked to a PubMed article. You can tell this by looking for PubMed in the list of databases with "Related Information" at the top right corner on this page. A similar section appears for the SRA accession here and lacks a link to PubMed. Though there is a DOI link to a publication in the PRJEB14911 page, this connection is unknown to Entrez.