This is a test version of Biostars. For the public version, visit https://www.biostars.org.
NCBI esearch for cited papers with public SRA data

I'm interested in finding all recent (>=2017/01/01) papers with at least 5 citations and open associated SRA data in Entrez. Can someone provide an automated strategy for this?

esearch entrez ncbi sra
• 2,534 views • link
written by Jeremy Leipzig 2.3K

A search along the lines of (not satisfying 5+ citations criteria)

esearch -db pubmed -query "RNA-seq" -mindate 2017 | elink -target SRA | efetch -format runinfo

brings info about 

SRR7340453,2018-06-22 16:22:41,2018-06-14 09:48:42,10042435,3012730500,10042435,300,1206,,https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007168/SRR7340453,SRX4214143,,RNA-Seq,cDNA,TRANSCRIPTOMIC,PAIRED,0,0,ILLUMINA,Illumina HiSeq 4000,SRP149374,PRJNA473835,2,473835,SRS3416763,SAMN09425664,simple,9606,Homo sapiens,GSM3190040,,,,,,,no,,,,,GEO,SRA712926,,public,7934A5DBFA3D2E7224FA0551CBA11A26,406CF9116FF27AF5FEB7D4F677CF58C7
SRR7340454,2018-06-22 16:22:41,2018-06-14 09:50:43,10518061,2103612200,10518061,200,872,,https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRR/007168/SRR7340454,SRX4214143,,RNA-Seq,cDNA,TRANSCRIPTOMIC,PAIRED,0,0,ILLUMINA,Illumina HiSeq 4000,SRP149374,PRJNA473835,2,473835,SRS3416763,SAMN09425664,simple,9606,Homo sapiens,GSM3190040,,,,,,,no,,,,,GEO,SRA712926,,public,348A0047FC17857E1CE031F35FA0201F,A6964DB50484A54986E31E39469F1589
• 0 views • link
written by GenoMax 16K

This python script can automate the process but it'll throw an error when get_sra_ids(pmid) encounters an article with no linked SRA ids because of missing [u'LinkSetDb'][0][u'Link'] tag on those entries. The same may happen with get_citations(pmid) .

• 0 views • link
written by Arup Ghosh 402

0 answers

No answers yet.

Log in to answer this question.

More posts like this