FAQ Log in to Edit
- BibDesk FAQs
- Installing BibDesk
- Importing Data
- Interacting with Other Programs
- General
- Editing
- How can I edit several items in batch?
- I have lots of items in my .bib file from the time before BibDesk. They don't have a Date-Added field and don't get sorted correctly. How can I change that?
- I don't get what the Crossref field does / I don't think the way BibDesk handles Crossrefs is very smart. Couldn't that be changed?
- Exporting
- Templates and Macros
- BibTeX / LaTeX Questions
BibDesk FAQs
Feel free to add answers here to commonly asked questions on the BibDesk users' list!
Installing BibDesk
BibDesk will not launch!
After (re)installing an older version of BibDesk or a nightly build, sometimes the system refuses to open BibDesk, instead showing the message "“BibDesk” can’t be opened because Apple cannot check it for malicious software." When this happens, go to the Security & Privacy pane in your System Preferences, and in the General tab make sure you "Allow apps downloaded from:" "App store and identified developers". Then, navigate in Finder to BibDesk.app, probably in your Applications folder, and Open BibDesk from the contextual menu in the Finder (found by control-clicking, not by double-clicking, on BibDesk), and Accept the opening of BibDesk. After this, you should be able to launch BibDesk normally.
Importing Data
How can I import a database from Endnote to BibDesk?
Select the BibTeX style (in Endnote 9, the current style is in the toolbar; click on it, select "Select Another Style", and choose "BibTeX Export")
Then select File → Export. Save file as type Text Only, make sure "Export Selected References" is unchecked if you want to save all the references in your file, then save the file.
Rename the file with a .bib extension in the Finder.
Then open BibDesk and select File → Open Using Temporary Cite Keys. After it opens, it is recommended to generate cite keys to replace the temporary ones. Then select File → Save As (cmd-shift-S) and save the file under a new file name.
NB: Open Using Temporary Cite Keys creates a temporary file, so if you cannot just use File → Save (cmd-S) to save the file.
Alternatively you can use a custom output style. Once that output style has been made available to EndNote make it active and either export selected references to a text file that you name as a .bib file and open in BibDesk or use the clipboard (choose menu command "Edit → Copy Formatted" and then paste into a BibDesk window).
How can I import existing bibliographies into BibDesk?
There are many ways to add existing reference items to a BibDesk database.
- Drag & drop or copy & paste formatted text on the database window.
- Drag & drop or copy & paste formatted text files on the database window.
- Drag & drop or copy & paste files or URLs to link on the database window.
- Drag & drop or copy & paste on a detail editor window.
- Drag & drop, copy & paste, or Merge In items from external groups.
- Copy text to clipboard and choose New Publications from Clipboard.
- Choose New Publications from File to import from a file.
- Choose New Publications from Web to import from a web source.
- Select formatted text and choose Add to Bibliography from System Services.
- Open other file and Drag & drop or copy & paste between database windows.
- Choose Open Using Temporary Cite Keys to fix bibtex with missing cite keys.
- Choose Open Using Filter to preprocess data.
Formatted text can be BibTeX, RIS, Medline (PubMed), MARC, JSTOR, ISI Web of Science, and Refer/EndNote.
See the User Manual for more details.
Interacting with Other Programs
How do I use BibDesk with Microsoft Word, Apple Pages, or TextEdit?
There are various ways to cite from BibDesk in writing applications such as Microsoft Word, Apple Pages, or TextEdit. See Using BibDesk Citations in Editors and Word Processors for more information.
General
Why can't I create a new record by dragging a PDF file into the reference window?
Q: When I try dragging a PDF into the reference window., I do not get a new record. Instead, the PDF is added to whichever record I put it on top of. Am I missing something?
A: The table allows dragging onto records to update them with the file you drop as well as dragging into empty space on the table to create a new record. If there is no empty space to drag to, you need to drop it between two rows or at the very top or bottom; you should be able to tell that the whole table is highlighted when you move the dragged PDF up and down across row boundaries. Drop it while the whole table is highlighted and you'll create a new entry.
Linked files/URLs don't show up anymore in the Local-Url/Url column
The local file and remote URL fields, such as Local-Url and Url, have been deprecated in favor of the linked files and URLs displayed in the side panes. As a result, newly added linked files and URLs are not added to the Local-Url and Url fields anymore. If you want to display new-style linked files and URLs in the main table, you should add a Local File or Remote URL column to the table as follows:
- Choose the View → Columns → Add Other... menu item
- In the sheet that appears, click the downward triangle to display a drop-down menu
- From the drop-down menu, choose "Local File" (you can't type it in directly)
- Click the "Add" button
- Repeat steps 1-4, adding "Remote URL" in step 3 (if desired)
What are all these Bdsk-File-* and Bdsk-Url-* fields that appear in my bibtex file?
BibDesk uses the Bdsk-File-* and Bdsk-Url-* fields to save location information for linked files and linked URLs, respectively. These are the linked files and URLs that appear as icons on the right-hand side pane of the main window and the detail window. Files are now stored using Mac OS aliases, so you can move them in the Finder without breaking BibDesk's links.
If you need to translate those fields from their Base64-encoded format into a plain-text format that is readable by another application such as JabRef, you can use an export template such as this one that puts the first linked file into the the Local-Url field. Ed Summers wrote a Python script, bibdesk2zotero, that will also do something like this. Since January 2023, the Better BibTeX for Zotero plugin can read Bdsk-File-* fields and convert them to the corresponding Zotero fields when importing a BibDesk file to Zotero.
Can I create folders containing static and/or smart groups?
No. At one time this was planned for BibDesk 2, but the plan was abandoned. An alternative is to carefully plan a naming scheme for your static and/or smart groups so that some groups (the groups that you want to group) appear adjacent to each other in the list.
Editing
How can I edit several items in batch?
BibDesk does not have a dedicated batch editor like for example iTunes. This is not feasible, because the possible fields are not fixed.
However, BibDesk knows several ways to edit a single field for a batch of items.
To set a field in a batch of items to a fixed value, do the following:
- Open the "Database Find and Replace" panel from the Edit → Find menu
- Select or enter the name of the field you want to change
- Select "Overwrite or Add this field"
- Optionally, select "Only replace in selected items"
- Enter the value you want to set for this field in the "Replace with" field
- Hit "Replace All"
To Find & Replace text of a field in a batch of items, do the following:
- Open the "Database Find and Replace" panel from the Edit → Find menu
- Select or enter the name of the field you want to change
- Optionally, select "Only replace in selected items"
- Enter the text you want to replace for this field in the "Find string" field
- Enter the text you want to replace this text with in the "Replace with" field
- Hit "Replace All"
To change a fixed (sub)text in a field in a batch of items, do the following:
- Choose the field as the current group field in the popup at the top of the table on the left. Add this field if necessary.
- Double-click the group with the text you want to change
- Change the text to the text you want to replace this with
- Note that the text match is case insensitive, and authors are matched in a fuzzy way.
You can also write interactive AppleScripts to make batch changes to fields; put the scripts in BibDesk's Scripts folder, and then run them from the Scripts menu.
Finally, remember that BibDesk files are plain-text files. When they are not open in BibDesk, they can be batch edited with any plain-text editor or with Unix tools such as Gerd Neugebauer's BibTool. However, unlike using an AppleScript within BibDesk or BibDesk's Database Find and Replace, batch editing the file outside of BibDesk will not increment BibDesk's Date-Modified field for the affected publications.
I have lots of items in my .bib file from the time before BibDesk. They don't have a Date-Added field and don't get sorted correctly. How can I change that?
Currently you can't change BibDesk's sorting behavior, so empty fields will always get sorted after the newest items. But a good workaround for this problem is to change the "Date-Added" field of the old items to some date in the past.
To do so, do the following:
- Be sure to have a backup of your file in case something unintended happens, though you can undo :-)
- Sort your items using the Date-Added (Added) column
- Select all items which have an unset Date-Added
- Open the "Database Find and Replace" panel from the Edit → Find menu
- Select "Overwrite or Add this field" as well as "Only replace in selected items" in the find panel
- Enter some old date into the "Replace with" field (in a "YYYY-MM-DD" format, like "2006-01-01" for January 1st 2006)
- Hit "Replace All"
I don't get what the Crossref field does / I don't think the way BibDesk handles Crossrefs is very smart. Couldn't that be changed?
Crossrefs are not really a BibDesk feature, but a BibTeX feature. BibDesk does nothing but simulating what BibTeX does when a crossref is detected, so there is no point in changing the behaviour.
Crossrefs are very handy when you have a "parent" item (like a proceedings volume or a book that contains several articles) which should be linked to one or more "child" items (the several inproceedings or incollection items).
BibTeX's crossref mechanism is very simple, but very powerful. When a Crossref: field is detected in a "child" item, BibTeX takes all fields that are not present in the child from the parent. So, you just have to set up the child's Author, Title, Pages etc., and all the information for the parent (like Booktitle, Editor, Publisher etc.) are gained from the parent automatically.
The Title field may be a problem, since it is used in both child and parent. Therefore the parent's Title should be copied to the Booktitle field. Don't worry: BibDesk can do that automatically for you (if the "Duplicate Title to Booktitle" preference is selected). It also sorts the items correctly if the "Auto Sort for Crossrefs" preference is selected.
Exporting
How can I export items in the order they appear in the table?
To export items to the order in which they appear in the table, rather than the order in which they appear in the file, select all items in the table, choose the Export... menu item in the File menu, and select "Only export selected items" in the save panel.
Templates and Macros
How do I write a template that expands all macros except for the Month?
This comes up if you want to share data with someone who may not have the same macro expansion for the month (maybe they'll use a different style file, for instance).
Christiaan provided an example on the mailing list: He noted that in Templates there is a template to export unexpanded bibtex strings. If you want to expand all fields except for the Month, you can use the following template:
<$publications>
@<$pubType/>{<$citeKey/><$allFields.@...>,
<$name/> = <$name=Month?><$bibTeXString/><?$name?>{<$value/>}</$name?>
</$allFields.@...>}
</$publications>
BibTeX / LaTeX Questions
Underscores in URLs are not showing up correctly in my bibliography
(Answer from Daniel Becker on the bibdesk-users list, edited a bit by Michael McCracken)
You need to use the hyperref package, and the url environment to get properly encoded URLs in LaTeX.
The underscore is a special symbol for math in LaTeX, hence it wants to enclose it in dollar signs, as in $x_A^2$. For bibtex, just loading the hyperref package is not enough. If you put the url in a command like \url{www.test.de/bla_58} then hyperref kicks in and does its work.
In order to have the URL actually appear in the reference, you can either put it in the "Note" field of your item or you can to use an entry type like webpage, url, online, etc.
The bibtex style (the .bst file, specified in the \bibliographystyle{} command) that you are using must be aware of the BibTeX-type "webpage" and know what to do with "Lastchecked" or "Url". This is done by urlbst. It seems that the natbib styles also support by default URL and DOI.
You may also be interested in biblatex: Before you invest time in traditional bibtex and how to add support for URLs, consider biblatex.
Related
Wiki: BibDesk_Applescripts
Wiki: Format_Citations_for_Editors
Wiki: Main_Page
Wiki: Templates
