Medline/Pubmed parsing...

rickkar1
Using perl, I'm trying to parse Medline/Pubmed links in order to finally pass each link to a pmid2doi conversion website < http://www.pmid2doi.org/ > ...

does one already exist? if so, could you pls point me to it...

thx in advance!
  • adamsmith
    have a look at this -
    https://github.com/zotero/translators/blob/master/NCBI%20PubMed.js
    I'm not sure exactly what you're trying to do, but the translator does extrac PMIDs from strings.
  • rickkar1
    additionally, file structure is of the form...

    --pwd
    /xxxxx/xxxxx/xxxxx/xxxxx/xxxxx/UNC00000000000042/00223468/v45i3/S0022346809003820
    --ls
    18507872 main.pdf main.raw main.xml

    where < main.pdf > has the document of interest...

    i want to parse
    additionally, file structure is of the form...

    --pwd
    /xxxxx/xxxxx/xxxxx/xxxxx/xxxxx/UNC00000000000042/00223468/v45i3/S0022346809003820

    so that i can develop the PMID and pass that to the pmid2doi conversion website...
  • adamsmith
    I'm still not sure what you're trying to do, but this doesn't strike me as the right place to ask it. If this is a Zotero relevant questions, provide some more detail about your project and ask it on zotero-dev
    http://groups.google.com/group/zotero-dev
    if you're looking for general help on parsing PMIDs in perl, stackoverflow is probably the best place to ask.
  • DWL-SDCA
    edited October 23, 2012
    As said above, I'm not sure what you are trying to do but please know that you can directly get DOIs from PubMed through their tagged Medline format or their XML. Access this by the Send To link.

    Please know also that there are many journal articles that have retroactively had DOIs assigned. These aren't being added to the PubMed records. Well, mostly they aren't. Recent examples of this are Ammons Scientific Publishers journals. All articles in all of their journals' backfiles now have DOIs.

    Using your utility, I tried a couple of Ammons journal articles' PMIDs and they don't get the DOIs. The Ammons backfiles received DOIs a little over a year ago. The "new" DOIs are recognized at CrossRef and at dx.doi.org.

This is an old discussion that has not been active in a long time. Before commenting here, you should strongly consider starting a new discussion instead. If you think the content of this discussion is still relevant, you can link to it from your new discussion.

Sign In or Register to comment.