From: W. Trevor King <wking@drexel.edu>
Date: Sat, 16 Apr 2011 15:13:10 +0000 (-0400)
Subject: Add entrez post.
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=ad7ca46ebc68872d4cd7ea1090ac659e1ad1e793;p=mw2txt.git

Add entrez post.
---

diff --git a/posts/entrez.mdwn b/posts/entrez.mdwn
new file mode 100644
index 0000000..b174029
--- /dev/null
+++ b/posts/entrez.mdwn
@@ -0,0 +1,59 @@
+Since 2008 I've been using a script ([[entrez.py]]) to search
+[PubMqed][] 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",
+    }
+
+[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/
+
+[[!tag tags/programming]]
+[[!tag tags/python]]