journal-abbrev
This is a set of small scripts for converting BibTeX files to use journal abbreviations, which are required by some scientific publishers. Additionally some unnecessary fields can be removed from the BibTeX entries, in order to reduce filesize.
My use case is that the BibTeX export from Zotero often contains the full journal name. While there is an option to "use journal abbreviations", this only has an effect if the Zotero entry contains a proper "Journal Abbr" field. But in my workflow, this field is normally not populated, and I can't be bothered to add it manually. Additionally, different publishers may require different styles of abbreviation.
There are currently two scripts:
- get-abbrev.py downloads a list of journal abbreviations, currently from the ADS service and saves it in a simple text file, which can be edited or amended.
- bibtex-abbrev.py takes a BibTeX file and the abbreviation definitions produced by get-abbrev.py, replaces (as far as possible) full journal names by their abbreviations, removes unnecessary fields from the BibTeX entries, and writes out a new BibTeX file.
Prerequisites
You need to have Python3 installed. This was tested with Python version 3.4.3.
get-abbrev.py requires the Python modules requests and lxml. On Debian/Ubuntu, you can install them with:
sudo apt-get install python3-requests python3-lxml
bibtex-abbrev.py requires the Python module bibtexparser. It can be installed with:
pip install --user bibtexparser
or whatever way you prefer to manually install Python modules.
Usage
get-abbrev.py currently only supports the abbreviation definitions from the ADS service. It attempts to parse the abbreviation definitions from their web page, and dumps them to standard output in a simple text format, which is easy to edit and to which you can add your own definitions. Run it as:
python3 get-abbrev.py > abbrev.txt
The output file format is very simple, namely it consists of lines of the form
JwvlT = The Journal with a very long Title
That is, abbreviation and full title are separated by an equals sign.
bibtex-abbrev.py takes the names of a BibTeX file and the abbreviation definition file, replaces full journal names with the corresponding abbreviation, and writes the modified file to standard output. Example:
python3 bibtex-abbrev.py orig.bib abbrev.txt > new.bib
If additionally the option -m or --minify is given, the program will also remove some fields from the BibTeX entries, i.e. fields which are specific to Zotero or which are not needed for citations in science journals. Currently the removed fields are:
- abstract
- keyword
- file
- link
TODO
The following features may be implemented when the need arises: