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Package of tools for formatting publication data and accessing data from PubMed's Entrez tool

Project description


Tools available:

  • entrez - streamlines BioPython
  • citations - creates citations for 6 different types using IMS standards
  • date - formats dates into our desired format
  • sanitizer - mostly useful for forcing unicode compliance in python2


Citations are based on a standard defined by PubMed For some publication types, passing the italicize parameter with a True value will return HTML with italic tagged journals or conference names.


The journals module uses the PMC source file to construct a library of journals keyed by abbreviation or full title.


[3.0.1] - 22 Aug 2019

  • journals module reconfigured to not write to disk on startup

[3.0] - 12 Aug 2019

  • Exlusively supports python 3

[2.1] - unreleased

  • Redesign of citation with abstract behavior.
  • "italicize" option has been replaced with an "html" option and does not do any safe escape
  • add docstrings to citation functions

[2.0.2] - 25 Jan 2019

  • Revert safe_unicode use but have it be only applicable for python 2. Not an issue in python 3
  • Unescape all fields except title and abstract if using the "escape" parameter. Those two fields are treated as HTML if escape is false all other fields are plain text

[2.0] - 17 October 2018

  • Six implementation with support for python 2 and 3 [hoskins]

[1.7] - 10 May 2018

  • Refactor some entrez functions to make it more obvious what the API endpoints are
  • Convert docstring of all intended end point functions to reST
  • Add ability to find publication by PMC ID. This is done by querying the PMC database
  • Refactor generate_search_query slightly

[1.6] - 1 March 2018

  • Fixed the book REST API calls to allow for failure
  • book REST API calls now use requests module
  • the database is now a paid service only. It should work but I don't have a service to verify this


  • Citations can now be generated as plain text without tags on journals, etc. It defaults to true here but will default to false in a future release.
  • Removed some unused parameters from citation functions
  • Cleaned up unit tests
  • Fixed issue with eCollection dates in citations


  • Refactor and reformat for pep8

Project details

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