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# Programs

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Tools for working with BibTeX-files

## Graphical editors

### Platform-independent

• JabRef: Mighty BibTeX editor written in JAVA. Database in native bibtex format. Can push citations to LyX via lyxpipe.
• Sixpack: Bibliography database manager written in Perl/TK. Can import/export from/to many other reference formats (medline, refer, ISI...).
• tkbibtex: BibTeX editor written in TCL/TK. Can push citations to LyX via lyxpipe.
• refbase: Web-based reference manager that can import and export BibTeX. Can also generate LaTeX for direct use in LyX.
• synapsen: Hypertextual card index or reference organizer, strong support of BibTeX and biblatex, written in JAVA, based on Niklas Luhmann's literature networking concept.
• Zotero: Firefox plugin, import/export in many formats, organization with collections and tags, remotely back up and sync your library, rich-text notes in any language, automatically captures references from many online sources, automatically retrieves bibliography information from inserted pdfs, collaboration with group libraries...
• For use with LyX, the references can be:
• Exported to BibTeX and inserted from LyX citation dialog or
• Inserted and managed from Zotero with the help of Zotero plugin LyZ.
• Mendeley: Modern multiplatform reference manager that does automatic extraction of document details, sharing with colleagues, export to BibTeX database etc.

### Unix: KDE

• KBibTeX: Graphical BibTeX editor for the KDE desktop (KDE3 and KDE4). Can be embedded in Konqueror via KParts. Supports webqueries. Can push citations to LyX via lyxpipe. Can import and export several formats besides BibTeX.
• KBib: Graphical BibTeX editor for the KDE desktop, based on gBib (KDE 3). Can push citations to LyX via lyxpipe.
• Tellico: General collection manager for KDE that can import and export from/to BibTeX. Can push citations to LyX via lyxpipe.

### Unix: GTK/Gnome/Xfce

• Pybliographer Bibliography manager for Gnome. Can import and export several formats besides BibTeX. Can push citations to LyX via lyxpipe.
• gBib: Bibliography manager for Gnome. Can push citations to LyX via lyxpipe.
• Xfbib: Lightweight BibTeX editor developed for Xfce.

### Mac OS X

• AquaTkbibtex is the "Aquafied" version of tkbibtex.
• BibDesk: Bibliography Manager for MacOS X. Can push citations to LyX via pipes.

### Windows

• WibTeX: Bibliography editor for Windows that can export BibTeX. Freeware. Also supports export of entries to MS Word.
• BibTexMng: BibTeX editor for Windows. Commercial, test version limited to 50 database entries.
• Qiqqa: Free research manager for Windows and Android. Converts PubMed XML, EndNote and RIS files to BibTeX for export to LyX/LaTeX.

## Command line tools

• BibTeX: bibliography tools, collection of awk scripts
• bibtool: powerfull and fast -- especially useful for large databases. Written in C, compiles on most OS.

## Getting bibliographic data

Google Scholar is one of the easiest methods. Just visit google scholar and set the "Scholar Preferences" to output BibTeX. Then, search for the references you need and simply cut-and-paste into your BibTeX file.

### Zotero Firefox Extension

Zotero is an extension for the Firefox Web browser. References can be imported from Websites and exported into BibTeX format. There also exists a Firefox extension (beta) allowing Zotero to be integrated with Lyx: old Lytero Plugin or newer Lyz

### Parsing arXiv.org

arXivBib, licensed under the gpl, retrieves abstract pages from http://arXiv.org and reformats them as BibTeX entries. It saves lots of typing if you have many such references to cite, but isn't worth the trouble if you only have a few.

### Generating BibTeX-entries from formatted bibliographies

cb2Bib is a tool for rapidly extracting unformatted, or unstandardized bibliographic references from email alerts, journal Web pages, and PDF files. Works on any OS that supports KDE. Supports direct insertion into LyX via lyxpipe.

http://lead.to/amazon/en/ is a website that exports BibTeX information for books enlisted on amazon.com Can be incorporated in the Firefox Web browser as an Search Extension.

### Generating BibTeX-entries from a LaTeX bibliography

Tex2bib is a Perl script that extracts bibliographic data from a document whose author wrote out the \bibitem entries. The entire document is scanned for \bibitem entries, ending when \end{thebibliography} is encountered.

Bibtools provides, amongst others, aux2bib, a Perl script which will take an .aux file and make a portable .bib file to go with it.

## Converting bibliographic databases to BibTeX

### Endnote

First of all, Endnote claims to have a built-in conversion filter, but it DID NOT WORK at version 7 (Edit: Or 8 or 9 or X). The following methods all involve multiple steps to work around the problems (such as, Endnote has more categories and fields in its database than BibTeX allows, which breaks the conversion process). If you're using Windows, you may want to try Method 5 first - it's by far the simplest.

#### Method 1

Have a look here:

You may not choose to use the Python code as Noah does however, you will need to have the Label field in Endnote filled in with your citation Key as used by BibTeX.

If you export from Endnote ensure you filter out all unnecessary Fields since there is a lot converted by default that LyX/LaTeX chokes on.

Tweak the Endnote BibTeX export filter to get rid of things like the Abstract field etc that cause the problems – To a certain extent you will have to “suck it and see” just which you need to get rid of!

Once you export change the file extension from .txt to .bib and run it through your BibTeX editor to check and correct the (unfortunately there will be some) errors in the conversion. Things like accents, retained CAPITALS etc will need entering with a touch of LaTeX code. i.e. Freds{\o}e will produce Fredsøe in the output.

#### Method 2

This webpage purports to do it for you. It looks very easy (single-step!), but it didn't work for me, so use it at own risk. Possibly the problem is that my file is a bit too big (~3900 entries).

#### Method 3

Nice, clear step-by-step instructions can be found at this website (Mac-specific). They cover something called DOI, if that's your cup of tea.

#### Method 4

I used JabRef to convert my huge Endnote file to BibTeX. The conversion process has several stages, one of which involves using Endnote. These instructions are based on Mac Os X, Endnote 7, JabRef 2.0.1, but they might work on other platforms that support Endnote. JabRef is multi-platform. Note: For Endnote X4 and Jabref 2.6, this still works, but the export/import type is Refman/RIS.

1. In Endnote, go to Edit>Output styles>Open Style Manager.
2. Scroll down through the styles and make sure there is a check next to the style called "Refer Export."
3. Go to File>Export and give the new file a name with a .txt extension.
4. Open JabRef. Go to File>Import and select "Refer/Endnote."
5. Find your .txt document from step 3. JabRef will import it and produce an intermediate viewer window. Click "OK."
6. JabRef should next display the imported file, which you can save. You don't need to append an extension in Mac, but it is a .bib file. you should be able to reopen the file without difficulty from inside JabRef or LaTeX.

Note: if you have special characters, e.g., ones with accents, in your Endnote bibliography, they might not convert correctly. I just got rid of them in Endnote after they turned into garbage in the JabRef rendition and re-did the conversion, but there may be smarter ways (though see this).

#### Method 5

Endnote have released a new BibTeX output style that has fewer problems than their previous attempts. The new style is available here: ftp://support.isiresearchsoft.com/pub/pc/styles/endnote4/BibTeX%20Export.ens

A method using only EndNote and BibDesk has been tested and described here: http://cgi.cse.unsw.edu.au/~nickm/index.php?Information:EndNote_to_BibTeX_export The method works on OSX (10.4.10), EndNote X and BibDesk 1.3.6 (v793).

#### Method 6: Endnote X2 (win/mac) to BibTex/BibDesk

Endnote X2's BibTex export style seems totally buggy (as is the case apparently with all previous versions of Endnote too!) I tried Method 5 above first, which failed with a Endnote X2-exported bibtex library. This procedure worked for me (Neville Sanjana) for BibDesk 1.3.20, Endnote X2 (worked on both win and mac), and OSX (10.5.7)/XP SP3:

Just install JabRef locally (I used win version... the web client didn't load up for me) and the conversion is simple and accurate using the procedure from the blog above. Basically, JabRef comes with its own Endnote export style (.ens files) that are found in the Tools->Unpack Endnote filter set menu item. You then place these output styles in the Endnote style folder and export the Endnote library using that style. Voila! (Make sure to use the first JabRef style... there are 2 of them and the one ending "2.ens" did not work.)

The only thing missing from the blog posting is that after you auto-generate cite keys (unique IDs for BibTex entries), make sure to edit any with punctuation in them (eg. O'Connor, O'Leary, etc.) since BibDesk will choke on these and refuse to import those entries. Pretty simple and works well. As you call tell by the bevy of methods here for importing from Endnote, this one is worth a try if you have the same situation (X2->BibDesk), but otherwise all bets are off.

### Others

bibutils, command-line tools to convert from COPAC, EndNote, EndNote XML, ISI, Pubmed XM:, MODS XML, and RIS to BibTeX

Pybliographic, a BibTeX manager for Linux, imports ISI, Medline, Ovid and Refer databases and saves them in BibTeX format.

JabRef can import BibTeXML, CSA, Refer/Endnote, ISI Web of Science, SilverPlatter, Medline/Pubmed (xml), Scifinder, OVID, INSPEC, Biblioscape, Sixpack, JStor and RIS.

refbase can import Copac, CSA, Endnote/Refer/BibIX, ISI, Medline, MODS XML, Ovid, PubMed, RIS, SciFinder.

utf2latex: preprocess Endnote-bibtex export in UTF-8 code witht the python script. Eventually add some more codes and {} to the latex.py.

Zotero can import/export in many formats. BibTeX