Since 2008 I've been using a script ([[entrez.py]]) to search
[PubMed][] from the command line.  Yesterday I decided it was time to
clean up the script and make it publicly available.  It turned out to
be reasonably complicated, so I just reimplemented the guts using the
Python [SOAP][] library [Suds][] working with the [Entrez SOAP
interface][eSOAP].  I haven't been able to find the original that I
started with, but it seems to be related to `Pyblio/Query.py` in early
versions of [pybliographer][].

    $ ./entrez.py -L
    # available databases:
    pubmed
    protein
    nuccore
    ...
    $ ./entrez.py -X
    database: pubmed
    description: PubMed bibliographic record
    available fields:
     ALL    All Fields   All terms from all searchable fields
     UID    UID          Unique number assigned to publication
    FILT    Filter       Limits the records
    TITL    Title        Words in title of publication
    ...
    $ ./entrez.py -X -F AUTH
    field AUTH in pubmed:
    Description     Author(s) of publication
       FullName     Author
      Hierarchy     N
         IsDate     N
       IsHidden     N
    IsNumerical     N
           Name     AUTH
    SingleToken     Y
      TermCount     11526565
    $ ./entrez.py -v 'king[au]+yang[au]+2010[dp]+monte[tit]'
    entrezpy: INFO   run eEsearch on pubmed
    entrezpy: INFO   search returned 1 of 1 items
    entrezpy: INFO   run eFetch on pubmed
    entrezpy: INFO   convert medline XML to BibTeX
    @Article{King2010,
      author =       "William T. King and Meihong Su and Guoliang Yang",
      title =        "Monte Carlo simulation of mechanical unfolding of
                     proteins based on a simple two-state model.",
      journal =      "International journal of biological macromolecules",
      ...
      doi =          "10.1016/j.ijbiomac.2009.12.001",
      URL =          "http://www.ncbi.nlm.nih.gov/pubmed/20004685",
      language =     "eng",
    }

The [[BibTeX]] conversion uses [bibutils][] and [bibclean][] for the
medline-to-BibTeX conversion.

[PubMed]: http://www.ncbi.nlm.nih.gov/pubmed/
[SOAP]: http://en.wikipedia.org/wiki/SOAP
[Suds]: https://fedorahosted.org/suds/
[eSOAP]: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.html
[pybliographer]: http://pybliographer.org/
[bibutils]: http://www.scripps.edu/~cdputnam/software/bibutils
[bibclean]: http://ftp.math.utah.edu/pub/bibclean/

[[!tag tags/programming]]
[[!tag tags/python]]