Question

Webtool For Fetching Pmids From Blast?

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13.5 years ago

Goldbear ▴ 130

Hi, I was wondering if there is a web service that extracts all of the PMIDs that are in the results for a BLAST search? Example: I input the sequence for enchanced FLP and get a list of all the PMIDs associated with the genbank entries.

I believe this is possible by parsing the XML, just wondering if there is already a solution out there. Thanks!

blast • 2.0k views

ADD COMMENT • link updated 13.5 years ago by Casey Bergman 18k • written 13.5 years ago by Goldbear ▴ 130

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can you please show us a sample of your XML file(Or post it on gist.github.com)

ADD REPLY • link 13.5 years ago by Pierre Lindenbaum 164k

score 3 · Answer 1 · 2011-06-07

The closest thing I am aware of that is currently working is GoGene, which takes a fasta sequence gene name as input and BLASTs against UniProt to find linked abstracts in PubMed associated with that UniProt record. If you look at the bottom of a GoGene result page, there is a link to the list of PubMedIDs that you can access programatically via wget.

Another option is to try to download the code from MedBlast and get it working, but it is probably wiser just to develop your own method using remote blast and eutils.