https://github.com/ntamas/pm2bib

PubMed to BibTeX converter script
https://github.com/ntamas/pm2bib

Last synced: about 1 month ago
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PubMed to BibTeX converter script

• Host: GitHub
• URL: https://github.com/ntamas/pm2bib
• Owner: ntamas
• Created: 2010-05-17T15:36:18.000Z (over 14 years ago)
• Default Branch: master
• Last Pushed: 2011-01-10T20:18:12.000Z (almost 14 years ago)
• Last Synced: 2023-03-10T23:12:54.615Z (over 1 year ago)
• Homepage:
• Size: 85.9 KB
• Stars: 2
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst

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README

        
============================================

pm2bib: import PubMed references into BibTeX

============================================

:Author: Tamás Nepusz

:Email: [email protected]

This is a simple Python module that can import references into a BibTeX

bibliography based on PubMed IDs. It is based on pyP2B_, the excellent work

of Jean-Etienne Poirrier (see his contact info on his webpage). I did

some refactoring, implemented the escaping of capital letters in the

**Title** field, removed the GUI parts and added support for non-numeric

values in the **Number** field.

.. _pyP2B: http://www.poirrier.be/~jean-etienne/software/pyp2b/

Usage

-----

Command-line usage is dead simple. Assuming that you have put the script

somewhere in your path (and you are not using Windows), you can run the

script as follows::

  $ pm2bib 20214776

This will output a nicely formatted BibTeX snippet for the paper with

PubMed ID 20214776. If you have your bibliography in a file called

``biblio.bib``, you can simply append the output of ``pm2bib``

directly::

  $ pm2bib 20214776 >>biblio.bib

Alternatively, if you are using ``vim`` (like I do) and you quickly

want to import a paper into your bibliography, open up ``biblio.bib``

in ``vim`` and type ``:r! pm2bib 20214776`` to insert the output of

``pm2bib`` directly into the current buffer.

Command line options

--------------------

The following command line options are supported:

-j FORMAT, --journal-title FORMAT

    specifies the format of the journal title. Currently the following

    formats are supported:

    - ``full``: the full journal title (e.g., *Biochemical Society

      Transactions*)

    - ``abbrev``: the abbreviated journal title (e.g., *BIochem Soc

      Trans*)

    - ``iso``: the ISO journal title (e.g., *Biochem. Soc. Trans.*)

Bugs

----

Nothing is perfect. If you happen to find a bug in ``pm2bib``, send

me a message to the email address above.