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Finding the paper published from the SRA run riles

Hey folks, i have used this code to download a my query

esearch -db sra -query '("BACTERIA_NAME"[Organism] OR BACTERIA_NAME[All Fields]) AND "BACTERIA_NAME"[orgn] AND ("strategy wgs"[Properties] AND "library layout paired"[Properties] AND "filetype fastq"[Properties])' | efetch -format runinfo -mode text > first_file.tsv

now i have a bunch of SRA file but i would like to look for their respective published paper. how do i do it?

best ~scholar aldre

sra
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updated by GenoMax GenoMax • written by scholaraspect2008 • scholaraspect2008

I think your command is not really returning anything?

esearch -db sra -query '("BACTERIA_NAME"[Organism] OR BACTERIA_NAME[All Fields]) AND "BACTERIA_NAME"[orgn] AND ("strategy wgs"[Properties] AND "library layout paired"[Properties] AND "filetype fastq"[Properties])' 
<ENTREZ_DIRECT>
  <Db>sra</Db>
  <WebEnv>MCID_65818b6aa1b3ae3e6450690c</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>0</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>
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updated by GenoMax GenoMax • written by Raony Guimarães Raony Guimarães 
esearch -db sra -query '("Staphylococcus aureus"[Organism] OR Staphylococcus aureus[All Fields]) AND "Staphylococcus aureus"[orgn] AND ("strategy wgs"[Properties] AND "library layout paired"[Properties] AND "filetype fastq"[Properties])' | efetch -format runinfo -mode text > first_file.tsv

I use "BACTERIA_NAME" to make sure it is general enough for people in from different background to understand, but I was wrong, i created more confusion sorry

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updated by GenoMax GenoMax • written by scholaraspect2008 • scholaraspect2008

The linking between the SRA record and PubMed is not always there. Onus is probably on the submitters to indicate when an accession is published. PubMed may do some linking back but it does not seem to be fool proof.

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written by GenoMax GenoMax

2 answers

The pubmed IDs are empty because the submitters never updated it:

enter image description here

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written by Raony Guimarães Raony Guimarães

With EntrezDirect this will work when the information is present. Generally with new SRA numbers the data is likely to be unpublished when it is first publicly available.

Here is an older example that works.

$ esearch -db sra -query SRR14673325 | elink -target pubmed | efetch -format docsum | xtract -pattern DocumentSummary -element FullJournalName,ELocationID
Nature communications   doi: 10.1038/s41467-022-35713-4
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written by GenoMax GenoMax

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