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

Project description

# Introduction 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

Citations are based on a standard defined by PubMed https://www.ncbi.nlm.nih.gov/books/NBK7256/. For some publication types, passing the italicize parameter with a True value will return HTML with italic tagged journals or conference names. # Changelog

## [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 isbndb.com database is now a paid service only. It should work but I don’t have a service to verify this

## [1.5] - Citations can now be generated as plain text without <i> 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

## [1.4] - Refactor and reformat for pep8

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