BibDesk AppleScripts by Andreas Fischlin

• Selected To Clipboard (Cite Key List)
  Run this script to generate a cite key list in the clipboard from the currently selected publications. The cite key list is a comma separated list. See also the companion script 'Select From Clipboard (Cite Key List)' that can be used with such a list in the clipboard to find and select publications in the top document.
• Select From Clipboard (Cite Key List)
  Run this script to select in the top document the publications as listed by their cite key in the clipboard. The script exptects a comma separated cite key list exactly as produced by the companion script 'Selected To Clipboard (Cite Key List)'.
• Fix PDF and URL Links
  Script finds pdf's in the pdf repository folder that conform to the naming convention '< cite key>.pdf', '<cite key>_S.pdf' (for supplementary material), '<cite key>_S1.pdf' (for more supplementary material) etc., fixes web of science URLs, and cleans up DOIs.
• Fix DOI and Case In Title, Author
  Script fixes DOI data, e.g. by removing redundancies, and tries to fix the case of all upper case titles and authors.
• Fix-Paste Abstract
  Script converts the abstracts of selected publications from 'UTF-8' to 'Western (Mac OS Roman)' encoding. In case a single publication is selected and the clipboard contains some text, the clipboard is pasted into the field 'Abstract' of the selected publication before encoding conversion. Feel free to change the encoding conversion to anything you like, since only a simple, straighforward modification of the AppleScript is needed for other conversions. The conversion done by this script as realeased is the one needed to save BibDesk files when the Files preference of BibDesk for 'Open and export BibTeX files using encoding' is set to 'Western (Mac OS Roman)'.
• Inspect Linked Files
  Script inspects the status of file links of currently selected records
• Link PDF from Adobe Reader
  Script links frontmost document currently open in Adobe Reader to the currently selected BibDesk record
• S-F-X Linking
  Script that uses information from the record currently selected in BibDesk such as ISSN and page numbers to jump to the article on the internet via S•F•X service. You or your institution need a sucbscription to S•F•X services to succeed.
• Extract For e-Reading
  Script useful for iPad (or iPhone, iPod Touch) owners to extract a bibliography from all records currently selected in BibDesk. Important is that pdf's are copied to a particular folder, your e-Reading folder, that typically resides on an iDisk (Apple's MobileMe service) or a designated folder within a DropBox folder. On the iPad, use an App such as GoodReader to access that folder to read and possibly annotate pdf's. GoodReader has an excellent syncing capability and is therefore recommended. The generated index.html file can also be viewed in GoodReader and gives an overview of what files are available. This script duplicates pdf's only incrementally, i.e. it copies only files missing in the target folder or overwrites in the target folder only those files, which have an older modification date than their counterpart in the source folder. Once you have annotated pdf's, sync them back to your Mac, i.e. BibDesk's repository folder, by using companion script 'Sync Back From e-Reading'. As script 'Extract Bibliography' this script requires templates. (*) (+)
• Select e-Reading Publications
  Script useful to select in BibDesk all publications for which you currently have some pdf's in the e-Reading folder (cf. script 'Extract For e-Reading'). This script is typically executed just before running script 'Sync Back From e-Reading'. Note, to succeed this script requires that the cite key is contained in and can be extracted from the pdf's file names. I use following pdf naming convention: '.pdf' and for any supporting material pdf's '_S.pdf', '_S2.pdf', '_S3.pdf' etc. This script works out of the box for such a naming convention. If you use another naming convention, you may have to adapt the script by modifying the filtering. (+)
• Sync Back From e-Reading
  Script useful for iPad (or iPhone, iPod Touch) owners to sync back pdf's that you have annotated on your e-Reading device. It is a companion script to the script 'Extract For e-Reading' and works with the same e-Reading folder. This script duplicates pdf's only incrementally, i.e. it copies only files missing in the target folder or overwrites in the target folder only those files, which have an older modification date than their counterpart in the source folder. IMPORTANT: Avoid annotating pdf's simultaneously on your Mac and your e-Reading device, or you risk loosing some annotations. This script requires to first select the publications within BibDesk that you wish to sync back before executing this script. The result is that your annotated pdf's are synced back to the BibDesk's repository folder on your Mac. To make sure all pdf's are synced back, use first script 'Select e-Reading Publications' or a similar mechanism (e.g. a BibDesk smart group that responds to a custom field marking publications that you have exported for e-Reading. In such a case, you may have to adapt of course script 'Extract For e-Reading' accordingly). (*) (+)
• Extract Bibliography
  Script extracts a bibliography from all records currently selected in BibDesk. An index.html file is generated listing all records together with abstracts, active links to the internet, e.g. doi links, and notably to pdf's if the records had linked files. Sorting order is by cite key. Typically the pdf's are also copied from the pdf repository to the loaction where the generated index is stored. This technique allows to selectively extract a bibliography from BibDesk as a browser readable collection of pdf's. See an example here >>. (*) (+)
• Extract Index-Abstracts
  Script similar to 'Extract Bibliography'. The only difference is that abstracts are not listed in the index, but are made available via a separate html page and there is an option to list the references either by cite key or by year. See an example here >>. (*) (+)
• Export to EndNote
  Script exports to EndNote all records currently selected in BibDesk.
• Cleanup Duplicates
  Script cleanups a BibDesk bibliography by searching for duplicates (by cite key) and deletes all records with the same cite key up to the very youngest record added latest. This script is typically called after having reimported the same records, e.g. after an update, that was made outside of BibDesk. The script preserves membership to static groups, but should nevertheless be used with caution. If using the first time make sure you have a backup of your bib-file and test whether you obtain exactly the desired result under all circumstances.
• Import by DOI
  Run this script if you wish to import an article from which you know the doi into the currently open BibDesk bibliography.

All scripts contain detailed documentation that is best consulted by opening the scripts in the AppleScript editor. The scripts are best executed from within BibDesk.

(*) The script requires templates and post processing shell scripts to be installed into BibDesk's template preference. Download these auxiliary files from here:

• Extract_Bibliography-(SEHtmlExportAuxFiles).zip (also needed by AppleScript 'Extract For e-Reading')
• Extract_Index-Abstracts-(sePubsExportAuxFiles).zip

  If installed, BibDesk's Preference tab 'Templates' should look similar to this:

(+) The script may look for a small text file 'LITMYPath.txt' in ~/bin, in case the property specifications you have edited in the AppleScript itself are not successful in identifying involved folders such as your e-Reading folder. Download a sample 'LITMYPath.txt' file from here:

• LITMYPath.txt.zip
  To install, edit 'LITMYPath.txt' according to your system configuration and move it to the bin directory in your home directory.

Bottom Preview Templates (enhanced variants from the templates described here and provided from here):

• Two_Columns_Bottom_Preview_Templates.zip
  If installed, BibDesk's Preference tab 'Templates' should look similar to this:

  To activate, choose in BibDesk menu command "View -> Bottom Preview -> <template>" (Ex.: "View -> Bottom Preview -> Two Columns HTML Template")

Further links:

BibDesk
GoodReader
DropBox
SugarSync
Andreas' BibDesk Tutorial
Using our literature management system - LiteratureMY
Wissenschaftliche Arbeiten schreiben mit LaTeX, BibTeX, JabRef (Kurs ETH Bibliothek)

Contact: Webmaster ( Last modified 6/8/18 )