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Lyx Bibliography Generation Options

Categories: BibTeX, Bibliography, Lead2Amazon, BibTeX

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Tools for working with BibTeX-files

Editors with BibTeX modes

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.

BibTeXBibliography

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

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.

Lead2Amazon

Lead2Amazon

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 entries. The entire document is scanned for entries, ending when 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:

http://www.unc.edu/~nghoffma/resources/useEndnote.pdf

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. will produce Freds�e 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).

http://dret.net/bibconvert/

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.

http://tazman.princeton.edu/osx

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 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:

http://fundamentalthinking.blogspot.com/2009/03/exporting-references-from-endnote-to.html

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

Categories: Bibliography, Branch, Jurabib, Natbib, Humanities

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Using LyX for Humanities Papers

by Anders Dahnielson, Bennett Helm, Charles de Miramon, J�rgen Spitzm�ller, and Arne Kjell Vikhagen

Choosing a Document Class

The standard classes are not very feature-rich and often not suited for humanities work. Especially the following two enhanced document classes are recommended for working with LyX in the humanities. Both are very powerful, configurable and well documented. Your choice depends on the specific features you need and on your personal taste.

KOMA-Script

KOMA-Script (German homepage) is a very powerful package that is highly recommended for working with LyX and humanities. There is an English manual online that explains everything you need to know in a relatively simple way. Click here to download the KOMA-Script manual as PDF

Memoir

Memoir is an alternative to KOMA-Script. It's as powerful and configurable in general, in detail and approach, however, the two classes differ. Memoir ships with a very detailed documentation. Click here to download the Memoir manual as PDF. If you want to use Memoir, see also the Using Memoir in LyX page in this wiki.

Tricks with Branches

Branches are chunks of text that can be "activated" or "deactivated" – turned on or off – within document settings. Why would you want to do this? The official suggestion is to create problem sets: you might put the answers to problems in a branch that can be turned off when you print out problem sets for students, but turned on when you print out an answer key for yourself. How can this feature be used in the humanities? Below are some suggestions (followed by a sample file illustrating these tricks), but first instructions on creating branches.

To create a branch, go to Document→Settings→Branches. Type the name of a new branch into the "New" field, and click the button. (If you like, you can select a branch in the list of Available Branches and click on to turn it on or off, or to change the background color for text in that branch as it appears in the LyX window.

Once a new branch is created, you can designate text as belonging to that branch by selecting that text and choosing Insert→Branch→[name of branch]. Alternatively, you can insert the branch first and then type your text.

Notes and Outlines

As you write a paper, you might phrase something poorly but not want to stop writing to go back and fix it, or you might promise to do something later and not want to forget to do it. In each case, you might want to flag the text with a note that is a clearly visible reminder, but which you can turn off if you wanted to give the paper to someone else. Simply create a note branch for this purpose. If your note is very short, you might want to insert a marginal note (Insert→Marginal Note) within the branch, and put your note inside that. If your note is long, you might want to put it in a box (Insert→Box) (and you can right-click on the box label to modify its appearance – by drawing a rectangle around it, for example). If your note is very long, you might want to insert a line (Insert→Special Formatting→Horizontal Line) before and after it – within the branch.

Perhaps you like to have an outline to work from as you write a paper. Create that outline in the document itself, break it into manageable chunks, and put each chunk in an "outline" branch.

Preparing Papers for Blind Review

Using the branch feature, it is possible to switch easily between versions prepared for blind review and versions with full bibliographical citations. Follow these steps.

  1. Prepare your bibliographical database (.bib file). You will need three separate files here. (a) One for your own published work, fully cited. (Call this "".) (b) One for your own published work, prepared for blind review. (Call this "".) Thus, you might specify the author field as "Author's book", the title field as "[Reference deleted]", and after that only specify the year. (c) One for everything else, fully cited. (Call this "".) The only trick here is that the cite keys for Mine-not-blind.bib and Mine-blind.bib must be the same.
  2. Within your LyX document, create two branches (Document→Settings→Branches). Call them "" and "".
  3. At the end of your document where you want the bibliography to appear, insert a "blind" branch (Insert→Branch→blind). Inside this branch, insert a bibliography, and select and . Do the same for the "not blind" branch, selecting and .
  4. You might also want to put other things in a "not blind" branch: the author environment, acknowledgements, etc.

When you're ready to typeset, first go to Document→Settings→Branches, and activate/deactivate the appropriate branches. So if you are ready to send the paper off for blind review, activate the "blind" branch and deactivate the "not blind" branch. After the paper is accepted, do the reverse.

Example

Here's a file illustrating the use of branches: sample-article.lyx.

Bibliographies

Preliminaries

LyX has native BibTeX support for bibliographies. By default, LyX is configured to use the bibliography style , which is used in other sciences and which cites references in text by number rather than by name and date. If you need to use a bibliography style for author-year references (a.k.a. Harvard style), you should use the or the package (see this page for information on the differences of those two packages). To find out more about using BibTeX in LyX, see the BibTeX Group on this wiki, read the documentation that comes with the described packages (, , ), or get yourself a copy of the excellent book The LaTeX Companion. Second Edition by Frank Mittelbach et al. (Addison Wesley 2004), which describes the bibliography generation, amongst many other things, in all details and very clearly. Note that you might have to add stuff to your preamble in order for LyX to format your bibliography correctly.

The most recent and mightiest bibliography package (with many additional features particularly for the Humanities) is biblatex. Since this is a pretty complex package, LyX still does not have native support for it, but it is possible to use it with some workarounds that are documented here. If you are not yet tied to one of the other approaches mentioned here, it is highly recommended that you consider biblatex, notwithstanding the imperfect support in LyX.

Non-BibTeX-proficient users of LyX might find it useful to use a graphical interface program to manage their BibTeX bibliographies. There are many such programs for all platforms. A selection is listed on this page. Most of them can communicate directly with LyX, e.g. in order to insert citations. So they work together with LyX similarly to how Microsoft Word and Endnote work together.

Establishing and maintaining a bibliographic database

In order to use BibTeX, you have to get or make a bibliography database () first, which contains your bibliography entries coded to BibTeX conventions. If you are migrating from Endnote, convert your .enl bibliography. If you are starting from scratch and know nothing about BibTeX, you might want to start making your own bibliography database with a GUI (see BibTeX Programs).

Using Jurabib

To set up LyX to use , go to Document→Settings→Bibliography and check .

Add the following to your LaTeX preamble:

\jurabibsetup{%
titleformat=italic,%
titleformat=commasep,%
commabeforerest,%
ibidem=strict,%
citefull=first,%
lookat,%
oxford,%
pages=format,%
idem%
}

It will set up with an oxford citation style, see the documentation for more information about available options.

To add a bibliography to your LyX document, go to Insert→List/TOC→BibTeX bibliography, and hit "Add" to add a database. Select the .bib file from the list* or browse to find it on your computer. Then select the citation style .

*Hint: If you save your bib file in a place where LaTeX can find it (usually ending in ), then it will appear in the list in the "Add" dialog, after you have hit "Rescan" in Tools→TeX Information. The same holds true for style files.

After you have closed the BibTeX dialog, LyX will have access to your bibliography and you can add citations from inside LyX using Insert→Citation. To cite using footnotes: insert a footnote the normal way using Insert→Footnote, then insert the citation in the new footnote (don't forget to follow your citation by a period inside the footnote). Or, add "super" to your preamble, which will convert ordinary citations into footnoted ones.

If you don't want a reference/bibliography list printed you can use the option of \nobibliography. Add the following in ERT (shortcut ) at the end of your document:

\bibliographystyle{jox}
\nobibliography{Bibdatabase}

Doing this alone won't allow you to insert citations from within LyX. So trick LyX by inserting the regular BibTeX bibliography in a Note (and always leave it in the note). A bit messy, but once it's set up you won't need to fuss with it.

Using Jurabib for Oxford style footcite with the normal cite command

If you have problems with the above settings, and/or would like to have footnotes, but using the normal command, you can use these settings when you import jurabib:

\usepackage[%
titleformat=italic,% Titles in italic\\

titleformat=commasep,% A comma between athors and title
titleformat=all,% Always show a title (or a short title)
commabeforerest,% A comma after title\\ ibidem=strict,%
citefull=first,% The first citing in full form
oxford,% The oxford style
super,% Footnotes
dotafter=true,%
see,% An extra optional argument as a prenote
idem
]{jurabib}

Using Jurabib for Harvard Style In-Text-Citations

If you want to achieve in-text-citations with author names in small capitals (which Natbib does not really offer) or want easier tweaking and configuration possibilities for the bibliography and therefore use Jurabib, you can put this little bit of code in the preamble, to get a Harvard Style citation:

\jurabibsetup{authorformat=smallcaps,authorformat=year,round}
\renewcommand{\jbcitationyearformat}[1]{\unskip,\space#1:}

Beware to choose the first citation style when citing with the LyX citation dialogue (Author/<before>). You do not need to use brackets, Jurabib will add them automatically.

Using Natbib

To set up LyX to use , go to Document→Settings→Bibliography and check .

Add the following line to your LaTeX preamble:

\bibpunct{(}{)}{,}{a}{,}{,}

This specifies in-text punctuation options for citations, i.e., Author (Year), commas between citations, and so on. See the documentation for details.

To add a bibliography to your LyX document, go to Insert→List/TOC→BibTeX bibliography, and hit "Add" to add a database. Select the .bib file from the list* or browse to find it on your computer.

*Hint: If you save your bib file in a place where LaTeX can find it (usually ending in ), then it will appear in the list in the "Add" dialog, after you have hit "Rescan" in Tools→TeX Information. The same holds true for style files.

Then select a citation style. Note that it has to be one that has been designed for natbib. Use either one of those shipped with natbib (, , ), get one from the internet, or design your own with the utility (which is an interactive command line tool by the author of natbib that asks you some questions about your formatting wishes and creates the appropriate style file for you – see this page for more information).

After you have closed the BibTeX dialog, LyX will have access to your bibliography and you can add citations from inside LyX using Insert→Citation. The dialog allows you to choose from the following options for in-text citation:

Author (Year)
(Author, Year)
Author Year
Author, Year
Author
(Year)
Year

You can cite multiple entries from the Add Citation dialog by hitting "Add" several times for various entries and then click "OK."

Sectioned bibliographies

As of v. 1.4, Lyx has enhanced support for the package, which means that to make sectioned bibliographies is much easier than before This page and section 3.1.2 in the "Extended Features" document under the help menu explain how it works. As explained there, you need multiple bibtex files (JabRef is a really good, cross-platform reference program that also can import from Endnote → see above). Then you add as many Bibliographies inside the Lyx document as you need.

Publication lists

This page explains how to use BibTeX to generate a List of Publications semi-automatically.

Wanted features in coming Lyx versions [humanities].

Options for Jurabib

In the Documents→Settings→Bibliography menu, when selecting Jurabib as your preferred Bibliography there should be a line there to enter your jurabib options instead of putting the \jurabibsetup in the preamble. Many tutorials show you how to send options to Jurabib through the preamble by using \usepackage[...]{jurabib}, but this will not work if the Jurabib options is set in the Documents→Settings menu.

Support for footcite

Jurabib offers a \footcite command which automatically places a citation in a footnote. It would be useful to provide an option to use this command. A workaround introduced in jurabib 0.6 is to use the "super" option in the preamble, which will convert all %ert\cites to \footcites.

Specific information for specific disciplines

  • The LinguistLyX page covers tips and tricks for linguists.
  • Lawyers may find these tips on indexing useful for constructing tables of cases and statutes.
  • A guide to Latex for Historians, includes jurabib information Latex for historians(approve sites)

BibliographyBranchJurabibNatbibHumanities

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