Question: How To Get Sra Informations Given A Pubmed Id?
0
gravatar for Hanfei Sun
6.9 years ago by
Hanfei Sun60
Boston
Hanfei Sun60 wrote:

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) ?

geo sra pubmed • 3.5k views
ADD COMMENTlink modified 6.9 years ago by Rm8.0k • written 6.9 years ago by Hanfei Sun60

can you give us a pmid for a test please.

ADD REPLYlink written 6.9 years ago by Pierre Lindenbaum129k
2
gravatar for Rm
6.9 years ago by
Rm8.0k
Danville, PA
Rm8.0k wrote:

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)

ADD COMMENTlink written 6.9 years ago by Rm8.0k

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.

ADD REPLYlink written 6.9 years ago by Neilfws48k
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