Bibdesk Texshop Bibliography Generator

BibDesk is an open-sourcereference management software package for macOS, used to manage bibliographies and references when writing essays and articles.[1][2][3] It can also be used to organize and maintain a library of documents in PDF format and other formats. It is primarily a BibTeX front-end for use with LaTeX, but also offers external bibliographic database connectivity for importing, a variety of means for exporting, and capability for linking to local documents and automatically filing local documents. It takes advantage of many macOS features such as AppleScript and Spotlight.

First launched publicly in 2002, BibDesk is under continuing development by various contributors via SourceForge.[4] The original developer was Michael McCracken, and much of the code has subsequently been written by Adam Maxwell and Christiaan Hofman.[5] Also available directly from SourceForge (see § External links), it is currently bundled with the MacTeX distribution of TeX Live.[6]

Features[edit]

BibDesk offers an iTunes-like Cocoa-based graphical user interface for creating, editing, managing, and searching BibTeX databases.[7] It supports BibTeX features such as macros and crossrefs.[8]

Importing[edit]

Users can add new items to a BibTeX database, and copy items between databases, by dragging or pasting, or by using one of the included macOS services.[9] BibDesk enables one-click importing of items from several kinds of external groups:[10]

  • Search groups retrieve items from external bibliographic databases, such as PubMed, the U.S. Library of Congress, Web of Science, or any other database searchable via the Z39.50 or Entrez protocols. BibDesk enables one-click importing of references to articles and books listed in these databases and library catalogs.[10]
  • The Web group displays a built-in WebKit browser that recognizes bibliographic entries on some web pages (such as Google Scholar, arXiv, JSTOR, WorldCat, and Wikipedia) and harvests them (using COinS, hCite microformat, or BibTeX) for easy searching and single-click import.[11]
  • External file groups retrieve items from a remote URL on the Internet or from a local file.[10]
  • Shared groups contain items that other BibDesk users share on the local network, discovered using Bonjour, similar to local sharing of music in iTunes.[10]
  • Script groups generate their items using any script, either a shell script or an AppleScript, that returns valid BibTeX or any other text format that BibDesk can import.[10]

BibDesk can also import records in RIS format.[12] It can import from other formats with the help of command-line conversion tools such as BibUtils.[13]

In addition, users can combine the Firefox extensions Zotero and Zot2Bib[14] to do one-click importing of references from Firefox to BibDesk using Zotero's ability to harvest references from a wider variety of websites.[15]

Organizing[edit]

BibDesk permits articles residing on a user's computer to be linked to BibDesk database entries via drag and drop or a menu command or scripting, and BibDesk can optionally auto-file linked PDFs or other external files into a user-specifiable folder.[16] There is a graphical interface for managing custom database fields,[17] as well as a variety of ways to annotate citations.[18]

Within BibDesk, references can be organized in groups and smart groups (similar to playlists and smart playlists in iTunes),[19] and in field groups (a simple kind of smart group based on database fields).[20] Multiple groups can be selected to display a list of references in any group (union) or in all groups (intersection).

Citing[edit]

References can be cited in any document by copy and paste or drag and drop from BibDesk, or via a macOS service.[21] A custom URI scheme, x-bdsk://citekey, allows hyperlinking to BibDesk references from any other application.[22] In addition, a reference can be opened quickly in BibDesk by first selecting any cite key in a LaTeX document or other text document and then using the provided macOS service "Show Reference With Cite Key" (which, like all services, can be assigned a custom keyboard shortcut).[23] Cite key autocomplete is available in some applications (including TeXShop) via a macOS service.[24]

Searching[edit]

A quick search field permits searching any field in a database,[25] or any associated PDF annotations created in Skim (an open-source PDF reader created by BibDesk's developers), or the entire content of any linked external files.[26] A more detailed "find and replace" window allows finding and replacing text in any field, with support for regular expressions.[27]

The entries of any BibTeX database that has been opened and saved in BibDesk are made accessible to Spotlight searches anywhere in macOS, so any system-wide Spotlight searches will also search title, author, abstract, and keywords fields of BibDesk databases.[28] Individual references are listed in Spotlight and, when opened, will be selected in BibDesk.

BibDesk database entries can also be searched with some other macOS applications such as Alfred[29] and DEVONthink.[30]

Exporting[edit]

References can be exported via a menu command, cut and paste, drag and drop, or a macOS service.[31] Although it was created to import and export in BibTeX format for use in LaTeX documents, BibDesk has a built-in graphical editor for creating custom export templates using Apple's key-value coding,[32] which the user can program to export selected references in any citation style or in any structured text format.[33] Sample templates are included for plain text, RTF, HTML, RSS, and some other XML formats, and other templates are available on the BibDesk wiki.[34]

BibDesk can format entire bibliographies internally either via previews that use BibDesk's export templates or via previews of LaTeX output. In its previews of LaTeX output, BibDesk can automatically produce citations in any of the basic BibTeX styles or in any style for which the user has a BibTeX style (.bst) file.[35]

BibDesk does not itself contain citation styles (such as APA, MLA, Chicago) and does not support Citation Style Language (CSL).[36] Users who wish to use BibDesk but need to use CSL can export a BibTeX file to another application that supports CSL, such as Zotero,[37] or Pandoc,[38] which when combined with Markdown can also serve as a simpler alternative to LaTeX for producing academic writing.[39]

Scripting[edit]

BibDesk offers automation using AppleScript,[40] and using other scripting languages via AppleScript.[41] Example scripts are available on the BibDesk wiki and elsewhere.[42]

System requirements[edit]

The following table shows which version of BibDesk is compatible with each version of macOS.[4][43]

See also[edit]

References[edit]

  1. ^O'Malley, Kevin (3 February 2004). "LaTeX: it's not just for academia, part 1". macdevcenter.com. O'Reilly Media. Retrieved 9 March 2017.  
  2. ^Courtland, Rachel (1 May 2008). "Programs promise to end PDF paper-chase". Nature. 453 (7191): 12. doi:10.1038/453012b. PMID 18461713.  
  3. ^Fenton, William (3 March 2016). "5 tools that make managing, sharing citations less of a headache". pcmag.com. PC Magazine. Retrieved 9 March 2017.  
  4. ^ ab"BibDesk wiki". sourceforge.net. Retrieved 9 March 2017. 
  5. ^"BibDesk wiki: developer information". sourceforge.net. Retrieved 9 March 2017. 
  6. ^"MacTeX: more packages". tug.org. TeX Users Group. Retrieved 9 March 2017. 
  7. ^"BibDesk wiki: BibDesk 2.0 design document". sourceforge.net. Retrieved 9 March 2017. 
  8. ^"BibDesk help: 2. BibTeX intro". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  9. ^"BibDesk help: 5.2 Importing references". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  10. ^ abcde"BibDesk help: 5.10.4 External groups". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  11. ^"BibDesk help: 5.10.5 Web group". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  12. ^"BibDesk help: 3.3 Opening an RIS file". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  13. ^"BibDesk help: 3.2 Opening a file". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  14. ^"Add-ons for Firefox: Zot2Bib". addons.mozilla.org. Retrieved 9 March 2017. 
  15. ^MacKerron, George. "Zot2Bib". mackerron.com. Retrieved 9 March 2017. 
  16. ^"BibDesk help: 8. AutoFile: keeping local copies of papers organized". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  17. ^"BibDesk help: 11.8 Default fields". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  18. ^"BibDesk help: 5.3 Editing references". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  19. ^"BibDesk help: 5.10 Grouping references". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  20. ^Robertson, Will (2 November 2005). "WSPR: BibDesk trend-setting and metadata". willwont.blogspot.com. Archived from the original on 22 May 2007. Retrieved 9 March 2017.  
  21. ^"BibDesk help: 9. Inserting citations". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  22. ^"BibDesk release notes: Changes since 1.3.14". sourceforge.net. Retrieved 9 March 2017.  
  23. ^Centers, Josh (5 February 2016). "OS X hidden treasures: services". tidbits.com. TidBITS. Retrieved 9 March 2017. 
  24. ^"BibDesk help: 9.2 Autocompletion". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  25. ^"BibDesk help: 4.1 Quick search". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  26. ^"BibDesk help: 4.4 Searching file contents". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  27. ^"BibDesk help: 4.3 Find and replace". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  28. ^"BibDesk help: 4.5 Searching With Spotlight". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  29. ^"Search BibDesk library". alfredforum.com. Retrieved 9 March 2017. 
  30. ^"How to index individual BibDesk entries in DEVONthink". devontechnologies.com. Retrieved 9 March 2017. 
  31. ^"BibDesk help: 9.4 Inserting formatted bibliographies". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  32. ^"BibDesk help: G. Template tags". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  33. ^"BibDesk help: 10. Templates". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  34. ^"BibDesk wiki: templates". sourceforge.net. Retrieved 9 March 2017. 
  35. ^"BibDesk help: 5.8 Previewing typeset output". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  36. ^"BibDesk feature requests: #501 Support for CSL". bibdesk.sourceforge.net. 7 April 2008. Retrieved 9 March 2017. 
  37. ^"Zotero wiki: citation styles". zotero.org. Retrieved 9 March 2017. 
  38. ^Endsley, K. Arthur (28 January 2015). "Custom citation styles in LaTeX with CSL and Pandoc". karthur.org. Retrieved 9 March 2017. 
  39. ^Tenen, Dennis; Wythoff, Grant (19 March 2014). "Sustainable authorship in plain text using Pandoc and Markdown". programminghistorian.org. The Programming Historian. Retrieved 9 March 2017. 
  40. ^"BibDesk help: 12. AppleScript". bibdesk.sourceforge.net. Retrieved 9 March 2017. 
  41. ^Sanderson, Hamish; Rosenthal, Hanaan (2009). "Interacting with the Unix command line". Learn AppleScript: the comprehensive guide to scripting and automation on Mac OS X (3rd ed.). Berkeley: Apress. doi:10.1007/978-1-4302-2362-7_27. ISBN 9781430223610. OCLC 308193726. 
  42. ^"BibDesk wiki: BibDesk AppleScripts". sourceforge.net. Retrieved 9 March 2017. 
  43. ^"BibDesk release notes". bibdesk.sourceforge.net. Retrieved 9 March 2017. 

Further reading[edit]

  • "BibDesk mailing lists: bibdesk-users". sourceforge.net. Retrieved 9 March 2017.  The BibDesk manual says: "If your questions aren't answered in this help file, the bibdesk-users mailing list may have an answer. Your question may have been answered already, so you can check the list archives to get instant gratification."
  • Brandes, Tim (28 February 2012). "How to write your thesis in LaTeX with Scrivener 2, MultiMarkdown 3 and BibDesk". timbrandes.com. Archived from the original on 4 November 2016. Retrieved 9 March 2017. 
  • Brandes, Tim (9 April 2014). "Optimize BibDesk, Multimarkdown and Scrivener for a nice scientific bibliography and citation workflow". timbrandes.com. Archived from the original on 1 April 2016. Retrieved 9 March 2017. 
  • Burt, John (11 March 2015). "BibTeX and BibDesk for beginners"(PDF). brandeis.edu. Brandeis University. Archived from the original(PDF) on 4 December 2015. Retrieved 9 March 2017. 
  • Cruz, Kelle (29 October 2009). "Why I use BibDesk instead of Papers". astrobetter.com. Archived from the original on 9 March 2017. Retrieved 9 March 2017. 
  • Davenport, James R. A. (4 September 2015). "How I cite [with BibDesk]". ifweassume.com. Archived from the original on 3 August 2016. Retrieved 9 March 2017. 
  • Koga-Browes, Scott (5 March 2012). "Scrivener–LaTeX integration 1: Setting up BibDesk". orthostat.wordpress.com. Archived from the original on 13 August 2013. Retrieved 9 March 2017. 
  • Krycho, Chris (26 February 2015). "Academic Markdown and citations: a workflow with Pandoc, BibTeX, and the editor of your choice". chriskrycho.com. Archived from the original on 11 May 2016. Retrieved 9 March 2017. 
  • Nieuwenhuis, Rense (29 June 2008). "Academic reading without paper: the BibDesk & Skim duo". rensenieuwenhuis.nl. Archived from the original on 8 October 2011. Retrieved 9 March 2017. 
  • Sheffler, Dan (9 July 2014). "BibDesk and LaTeX citations [with Pandoc]". dansheffler.com. Archived from the original on 2 January 2017. Retrieved 9 March 2017. 
  • Watson, Matthew (26 August 2008). "How to generate MLA, APA, Chicago, or any other style bibliography from BibTeX/BibDesk files". wordminer.us. Archived from the original on 21 February 2011. Retrieved 9 March 2017. 

External links[edit]

Bibliography in LaTeX with Bibtex/Biblatex

Learn how to create a bibliography with Bibtex and Biblatex in a few simple steps. Create references / citations and autogenerate footnotes.

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[View example on Overleaf]

  1. Creating a .bib file
  2. Using BibTeX
  3. Autogenerate footnotes with BibLaTeX
  4. BibTeX Format
  5. BibTeX Styles

We have looked at many features of LaTeX so far and learned that many things are automated by LaTeX. There are functions to add a table of contents, lists of tables and figures and also several packages that allow us to generate a bibliography. I will describe how to use bibtex and biblatex (both external programs) to create the bibliography. At first we have to create a .bib file, which contains our bibliographic information.

Creating a .bib file

A .bib file will contain the bibliographic information of our document. I will only give a simple example, since there are many tools to generate the entries automatically. I will not explain the structure of the file itself at this point, since i suggest using a bibtex generator (choose one from google). Our example will contain a single book and look like this:

@BOOK{DUMMY:1, AUTHOR="John Doe", TITLE="The Book without Title", PUBLISHER="Dummy Publisher", YEAR="2100", }

If you don't want to use a BibTeX generator or a reference management tool like Citavi (which generates BibTeX files automatically for you), you can find more examples of BibTeX formats here.

Using BibTeX

After creating the bibtex file, we have to tell LaTeX where to find our bibliographic database. For BibTeX this is not much different from printing the table of contents. We just need the commands \bibliography which tells LaTeX the location of our .bib file and \bibliographystyle which selects one of various bibliographic styles.

\documentclass{article} \begin{document} Random citation \cite{DUMMY:1} embeddeed in text. \newpage \bibliography{lesson7a1} \bibliographystyle{ieeetr} \end{document}

By using this code, we will obtain something like this:

I named my .bib file lesson7a1.bib, note that I did not enter the .bib extension. For the style, I've choosen the ieeetr style, which is very common for my subject, but there are many more styles available. Which will change the way our references look like. The ieeetr style will mark citations with successive numbers such as [1] in this example. If I choose the style to apalike instead, i will get the following result:

Most editors will let you select, to run bibtex automatically on compilation. In TeXworks (MiKTeX) for example, this should be selected by default.

If you use a different editor, it can be necessary to execute the bibtex command manually. In a command prompt/shell simply run:

pdflatex lesson7a1.tex bibtex lesson7a1 pdflatex lesson7a1.tex pdflatex lesson7a1.tex

It is necessary to execute the pdflatex command, before the bibtex command, to tell bibtex what literature we cited in our paper. Afterwards the .bib file will be translated into the proper output for out references section. The next two steps merge the reference section with our LaTeX document and then assign successive numbers in the last step.

Autogenerate footnotes in $\LaTeX$ using BibLaTeX

The abilities of BibTeX are limited to basic styles as depicted in the examples shown above. Sometimes it is necessary to cite all literature in footnotes and maintaining all of them by hand can be a frustrating task. At this point BibLaTeX kicks in and does the work for us. The syntax varies a bit from the first document. We now have to include the biblatex package and use the \autocite and \printbibliography command. It is crucial to move the \bibliography{lesson7a1} statement to the preamble of our document:

\documentclass{article} \usepackage[backend=bibtex,style=verbose-trad2]{biblatex} \bibliography{lesson7a1} \begin{document} Random citation \autocite[1]{DUMMY:1} embeddeed in text. \newpage \printbibliography \end{document}

The \autocite command generates the footnotes and we can enter a page number in the brackets \autocite[1]{DUMMY:1} will generate a footnote like this:

For BibLaTeX we have to choose the citation style on package inclusion with:

\usepackage[backend=bibtex,style=verbose-trad2]{biblatex}

The backend=bibtex part makes sure to use BibTeX instead of Biber as our backend, since Biber fails to work in some editors like TeXworks. It took me a while to figure out how to generate footnotes automatically, because the sources I found on the internet, didn't mention this at all.

BibTeX Formats

This is not meant to be a comprehensive list of BibTeX formats, but rather give you an idea of how to cite various sources properly. If you're interested in an extensive overview of all BibTeX formats, I suggest you to check out the resources on Wikibooks.

Article

@ARTICLE{ARTICLE:1, AUTHOR="John Doe", TITLE="Title", JOURNAL="Journal", YEAR="2017", }

Book

@BOOK{BOOK:1, AUTHOR="John Doe", TITLE="The Book without Title", PUBLISHER="Dummy Publisher", YEAR="2100", }

Inbook (specific pages)

@INBOOK{BOOK:2, AUTHOR="John Doe", TITLE="The Book without Title", PUBLISHER="Dummy Publisher", YEAR="2100", PAGES="100-200", }

Website

@MISC{WEBSITE:1, HOWPUBLISHED = "\url{http://example.com}", AUTHOR = "Intel", TITLE = "Example Website", MONTH = "Dec", YEAR = "1988", NOTE = "Accessed on 2012-11-11" }

This is a list of the formats that I have most commonly used. If you think some important format is missing here, please let me know.

BibTeX Styles

Here's a quick overview of some popular styles to use with BibTeX.

Abbrv

Alpha

Apalike

IEEEtr

Plain

I'm trying to keep this list updated with other commonly used styles. If you're missing something here, please let me know.

Summary

  • Generate a bibliography with BibTeX and BibLaTeX
  • First define a .bib file using: \bibliography{BIB_FILE_NAME} (do not add .bib)
  • For BibTeX put the \bibliography statement in your document, for BibLaTeX in the preamble
  • BibTeX uses the \bibliographystyle command to set the citation style
  • BibLaTeX chooses the style as an option like: \usepackage[backend=bibtex, style=verbose-trad2]{biblatex}
  • BibTeX uses the \cite command, while BibLaTeX uses the \autocite command
  • The \autocite command takes the page number as an option: \autocite[NUM]{}

Next Lesson: Lesson 8

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