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How To Get Sra Informations Given A Pubmed Id?

I know I can use elink to get the related GSE ID and GSM ID given a Pubmed ID. However, I found some papers have put their data on SRA but not on GEO, which I can't find the related data from a Pubmed ID. Does anyone have ideas about how to get SRA informations routinely given a Pubmed ID (For example, this Pubmed ID: 23664764) ?

pubmed sra geo
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updated by Rm Rm • written by Hanfei Sun • Hanfei Sun

1 answer

Try NCBIs LinkOut

For example: retrieving SRA records from PubMed ID: 21054605 , Try this:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=sra&id=21054605

Databases Available for Linking

Links can be made from the following NCBI databases to outside resources. When entering the database in the <Database> element, use the Db abbreviation, rather than the database name.
Database Name    Db Abbreviation
http://www​.ncbi.nlm.nih.gov/bioproject    BioProject
http://www​.ncbi.nlm.nih.gov/cdd    Conserved Domains
http://www​.ncbi.nlm.nih.gov/gene    Gene
http://www​.ncbi.nlm.nih.gov/nucleotide    Nucleotide
http://www​.ncbi.nlm.nih.gov/est    NucEST
http://www​.ncbi.nlm.nih.gov/gss    NucGSS
http://www​.ncbi.nlm.nih.gov/pubmed    PubMed
http://www​.ncbi.nlm.nih.gov/pccompound    PubChem Compound
http://www​.ncbi.nlm.nih.gov/protein    Protein
http://www​.ncbi.nlm.nih.gov/taxonomy    Taxonomy

If you are interested in providing LinkOut links to other NCBI databases not listed in the above table, please write to info@ncbi.nlm.nih.gov to express your interest to the relevant groups at NCBI.

NCBI_Linkout_Technology well explained here

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=sra&db=pubmed&id=23664764

Some how Pubmed Id you provided (23664764) does not resulted in SRA linkout: (either its not up dated or i might have missed it)

• 159 views • link
written by Rm Rm

This is the correct answer. If you don't see related data it's either because NCBI have not yet processed it, or it's not available.

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written by Neilfws Neilfws

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