Query based on PMIDs
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3.1 years ago
Deepak Tanwar ★ 4.2k

Hello!

I have a list of PMIDs and would like to query GEOquery and SRAdb to see if there is data submitted from these papers, and if submitted, I would like to download.

As I haven't received any response on https://support.bioconductor.org/p/115547/, I am posting my question here.

geoquery sradb • 834 views
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3.1 years ago
Ahill ★ 1.9k

The NCBI elink utility will take a list of PMIDs as input and map to GEO GDS, or SRA accessions. For example, here are 2 PMIDs that each have one associated GEO GDS:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=gds&id=15772128&id=24808371

This call returns the GDS IDs corresponding to each PMID. To search in SRA, use db=sra instead of db=gds.

You'd then use the returned GEO GDS or SRA IDs to retrieve data from GEO or SRA. To do this you could use R GEOquery or perhaps the SRA toolkit.

Depending on your data/application you could script the steps above.

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