Bibliographies, Glossaries and Indexes

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This page covers the production and inclusion of bibliographies, glossaries and indexes in TeX documents, the management of associated databases and strategies for integrating the available tools into work flows which include non-TeX applications.


Contents

BibTeX

by Oren Patashnik

Open source (other)

Wikipedia page

Bibliography generation program. BibTeX enables the use of bibliographical databases with TeX. The user assigns a key to each entry in the database. When preparing a document, the author uses these keys to refer to the relevant entries. The document must also specify the names of the database files containing the keys and a BibTeX style file. After typesetting the document, the user calls BibTeX which generates citation and reference information by comparing the keys used in the document with the keys in the specified database files, and formatting them in accordance with the instructions in the BibTeX style file. The document must then be reprocessed at least twice in order to incorporate BibTeX's additions into the output. In some cases, another BibTeX run and subsequent reprocessing is required before all of the references are typeset correctly.

Unlike LaTeX's own citation facilities, BibTeX allows users to build up databases of bibliographical entries which can be used in multiple projects and documents.

Many BibTeX style files are available for download from CTAN or elsewhere, especially in the case of formats required for submission to journals in mathematics, logic and the natural sciences. Although humanities subjects are less well served, an increasing number of styles are becoming available and it is not too difficult to generate custom styles with the help of the custom-bib package. These customised styles work especially well in conjunction with the natbib LaTeX package which provides extensive support for the author-year systems popular in many humanities subjects, as well as the numbered references more common in the sciences.

BibTeX is part of TeX Live.

bibexport

by Nicolas Markey

Open source (LPPL)

Shell script to extract referenced entries from BibTeX database files, resolving abbreviations, cross-references etc. and producing a "clean" self-contained BibTeX database file containing all and only the entries required by a specific document. This might be useful if, for example, you need to send the document source to somebody else and do not want to include your BibTeX database files in their entirety.

biblatex

by Philipp Lehman

Open source (LPPL)

An experimental but increasingly popular alternative to BibTeX style files. biblatex uses BibTeX to sort the entries and generate labels, but relies entirely on LaTeX macros to control the style of citations and bibliographies.

bibtex8bit

by Niel Kempson

Open source (GPL)

Although BibTeX itself supports only ASCII, this 8-bit adaption supports a wider range of character sets and customised sorting of entries.

bibtex8bit is part of TeX Live.

BibTool

by Gerd Neugebauer

Open source (GPL)

A tool to manage BibTeX files.

Available from the homepage, though the version on CTAN seems to be more recent.

bibtools

by Daniel Gildea and David Kotz

Open source (LPPL)

Scripts to perform various BibTeX-related tasks:

  • aux2bib - create a portable .bib file from an .aux file
  • bib2html - create an html version of a bibliography
  • bibify - may reduce number of typesetting cycles required
  • bibkey - find entries by keyword
  • citekeys - list citation keys for a .bib file
  • cleantex - post-processing clean-up
  • looktex - find entries by regular expression
  • makebib - create a portable .bib file from existing .bib file(s) and an optional set of citation keys
  • printbib - create a DVI from a .bib file

Bibutils

by Chris Putnam

Open source (GPL)

Tools to convert between various bibliographical database formats using the Library of Congress's Metadata Object Description Schema (MODS) as a common intermediary. For example, you can use it as an import filter to BibDesk:

  1. Choose File->Open Using Filter
  2. Enter:
    /usr/local/bin/isi2xml | /usr/local/bin/xml2bib
    in the "Filter Shell Command" field of the open panel. (Note: BibDesk now supports ISI format directly.) This can be any Unix command to preprocess the input, but it needs to send BibTeX to standard output as the result.
  3. Select the ISI file and open it.

Mac OS X binaries available.


GUI Tools for Bibliographies

AquaTkbibtex

Open source (GPL)

AquaTkbibtex is an "Aquafied" version of tkbibtex, developed by Peter Corke. tkbibtex is a portable editor and browser for BibTeX files (LaTeX bibliographies). AquaTkbibtex adds additional functionality by providing a double-clickable application bundle to launch the program, as well as allowing drag-and-drop opening of bibtex (.bib) files. This allows better integration between tkbibtex and the Aqua environment.

Here are some key features of "AquaTkbibtex":

  • A fully Aquafied, standalone application.
  • Drag-and-drop opening of .bib files without AppleScript.
  • A streamlined interface for printing documents.
  • Tight integration with the LyX-Aqua LaTeX editor.

AquaTkbibtex is included in MacTeXtras.

BibCompanion

by Hitoshi Nakahara

Restricted freeware (not available to those involved in any sort of weapons development or those who are in anyway actively anti-peace; may also exclude those related to anybody involved in developing any sort of weapons - the English is unclear and the Japanese takes legal precedence but I cannot read Japanese)

Bibliography management software and BibTeX database editor. According to the author's description, features include a search function, the ability to attach files to bibliography entries and "smart/manual" libraries.

BibDesk

Open source (BSD)

Bibliographic database program designed for use with BibTeX which also keeps track of your local copies of papers. Integrates with TeX editors. See the BibDesk Wiki for details.

Some highlights:

  • Focused on smooth workflow for searching for papers online, adding them quickly, and finding them to cite later.
  • Attach files of any type to a reference and track them by file alias
  • Search the contents of attached files
  • Search online databases including PubMed, many public libraries, Google Scholar, and more.
  • Organize your papers in Groups, or by keywords.
  • Numerous import types supported
  • BibDesk uses the standard BibTeX .bib file format so you can use existing tools and share with non-BibDesk-users without too much hassle.

Application versions currently available for Panther (10.3), new features available in the newer branches for Tiger and Leopard (10.4 and 10.5).

BibDesk is included in both MacTeX and MacTeXtras.

Bookends

Cripple-Ware (limit of 50 references without fee.)
Bookends is a full-featured and cost-effective bibliography/reference and information management system for students and professionals. Bookends runs natively in Mac OS X as well as Mac OS 9.x. With Bookends you can easily import references (information about journal articles, books, etc.) from hundreds of online sources (even import references directly from PubMed ,Medline on BioMedNet, and some OVID databases without intermediary files). Import references from BibTeX, EndNote, Papyrus, and Reference Manager databases. "Scan" your manuscripts to generate finished versions ready for submission or publication, with full in-text citations and bibliographies that meet the most exacting requirements. Plug-ins let you access the power of Bookends from within Microsoft Word and Nisus Writer/Nisus Writer Express to directly format manuscripts for publication. Bookends can also scan manuscripts saved from any word processor in RTF format. Attach any file to a reference and with a single click open it in Bookends or in the application that created it. This means you can, for example, search Bookends for an article and, if present on the hard disk or server, instantly open its PDF file. Pictures and graphics (figures, graphs, diagrams, etc.) are just as easily accessed.

iPapers

by Toshihiro Aoyama

Open source (details)

Manages PDF files from PubMed. Features include searching and importing from PubMed, reference management and search, and management of supplementary files.

JabRef

Open source (GPL)

Platform independent Java based bibliography manager.

JabRef is included in MacTeXtras.

Papers

Commercial

Paper management software. According to the home page, features include online searching, downloading, archiving and organisation, facilities to add notes and share papers, and a selection of plug-ins for use with various online repositories.


Glossaries

Indices

makeindex

by Nelson H. F. Beebe and Pehong Chen

Open source (other)

Wikipedia page

Tool for generating indices.

makeindex is part of TeX Live.

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