Bibliography
In scientific writing, we need to cite information obtained from sources such as books, articles, reports etc. Bibliography Managers are software packages that not only allow us to do this in a simple way but also provide a very useful way to organize and read the papers that we have collected over time.
Bibliography Management using JabRef
JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. JabRef is a desktop application and runs on the Java VM (version 8), and works equally well on Windows, Linux, and Mac OS X.
BibTeX is an application and a bibliography file format written by Oren Patashnik and Leslie Lamport for the LaTeX document preparation system. General information can be found on the CTAN BibTeX package information page. JabRef also supports BibLaTeX.
Bibliographies generated by LaTeX and BibTeX from a BibTeX file can be formatted to suit any reference list specifications through the use of different BibTeX and BibLaTeX style files.
JabRef Installation
Download the JabRef installation file (according to your operating system) from the following link
https://www.fosshub.com/JabRef.html
Run the installation file to install JabRef.
JabRef Configuration
After installation, we need to modify JabRef preferences in accordance with the STEAM-I group bibliography protocols. First, download this JabRef Preferences File and save it somewhere.
To import the preferences:
- Start JabRef.
- From the menu bar select "Options --> Preferences"
- At the left bottom of the pop-up window that comes up, click "Import Preferences".
- Select the JabRef Preferences File you had downloaded above, and click "Open".
- Click OK if required, quit and then restart JabRef.
These preferences ensure that the imported bibliography entries are assigned the correct BibTeX keys. Further, the linked PDF files will be renamed correctly and stored in a "Files" folder in the same directory where the .bib file exists.
Adding a citation
The procedure for importing a new Entry to an open database is as follows:
- Find the Entry (e.g. a Journal article) that you want to add by following one or more of the approaches outlined in the Literature Search page.
- Download the citation as a BibTeX file (.bib extension). Also, download the PDF for the Entry.
- Open the BibTeX file in JabRef. It will open in a new database containing the single Entry.
- Select the Entry. Copy the entry using Edit-->Copy.
- Go to the database where you want to import the entry. Paste the entry using Edit-->Paste.
- Select the newly imported Entry. Generate the proper BibTeX key for the Entry using Quality-->Autogenerate BibTeX keys. (If you want to set a custom cite key, just change it manually after double clicking the Entry)
- To link the downloaded PDF file to the Entry, drag the drop the PDF file onto the Entry. Make the following selections in the pop-up window that comes up:
- Update Existing Entry-->Only Attach PDF
- Move file to file directory
Rename file to: <automatically generated>
- The PDF file will be appropriately renamed and moved to the correct folder (as specified in the JabRef Preferences)
Pushing citations directly from JabRef to LyX (for Mac OS)
In Lyx, go to "LyX --> Preferences --> Paths" and in "LyXServer pipe" enter
~/.lyx/lyxpipe
In JabRef, go to "Preferences > External Programs" and in "Path to LyX pipe" enter
~/.lyx/lyxpipe
Make sure the following folder exists in your file directory
~/.lyx