Return the Title and URL of ~100 pubmed queries to a flat file
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5.2 years ago
Vincent Laufer ★ 1.4k

There are ~100 SNPs associated with RA at genome wide significance.

If you enter in just the SNP ID into pubmed, you can sometimes find links to other papers describing a functional effect of the variant.

Individually submitting 100 requests is tedious, so I thought there is probably a "batch submit" button Entrez or EUtilz tool to do this.

However, I was not able to get what options I could find to work. Batch Entrez - NCBI, unless I am mistaken, does not allow you to go from rsID list --> citation list. Instead, what I am looking for is something like dbSNP Batch Query, but that hits the pubmed dbase instead of dbSNP.

How might one submit a list of the form

rs12140275 rs2476601 rs624988 rs2228145 rs2317230 rs4656942 ....

and receive back a flat file, or webpage, etc. containing the title and URL of each study? If I had that, I could scan through very quickly. Thanks in advance.

pubmed batch query • 1.1k views
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You could try NCBI Unix e-utils.

esearch -db snp -query rs12140275|elink -batch -target pubmed|efetch -format abstract
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5.2 years ago

You can query pubmed using Biopython. There are some posts about this here on the forum as well as in the Biopython cookbook. Let me know if you need any assistance setting it up.

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thank you, will check it out.

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