[open-bibliography] PubMed

Thomas Krichel krichel at openlib.org
Mon Nov 9 19:02:46 UTC 2015

  Daniel Mietchen writes

> Agreed- contact PubMed right away.
  You suggested it be discussed here. ;-)

  I now do have a response. There appears to be nothing but the
  API but there is a query that would get to the records 

| Hi Thomas,
| There are probably multiple ways to accomplish what you want. It sounds like you want to know
| +how to search for records that aren't available on the FTP site. Here's the search:
| publisher [sb]
| http://www.ncbi.nlm.nih.gov/pubmed/?term=publisher+%5Bsb%5D
| If you want all of those records in one go (there are around 482,286 of them), you can just
| export them directly from PubMed. (click Send-to:, then File, then select XML and Create File).
| If you want to do a recurring query for these, you can set one up
| using the API (E-Utilities). ESearch
| (http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch) will
| get you a list of PMIDs. EFetch
| (http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch) will go
| and fetch the XML for you. If you want to generate a sample PERL
| script to do this for you, you can use Ebot:
| http://www.ncbi.nlm.nih.gov/Class/PowerTools/eutils/ebot/ebot.cgi.
| In an ideal world, these things would be better-documented and synced
| up, and you wouldn't have to think so much about this. We're working
| on it.
| If you have any additional questions, please don't hesitate to
| ask. Thanks,
| David

  I will set to work with this guidance at hand. If anybody
  wants a copy get in touch. I'd love for others not to
  have to deal with this. 



  Thomas Krichel                  http://openlib.org/home/krichel

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