A citation marker management


It is already possible to use Scrivener with BibDesk/BibLatex via MMD to get a Latex file with a bibliography. And it is possible to use Scrivener with Endnote via MMD to get a Word Document with a bilbilography. But it is not possible to get both with the same Scrivener document, because the needed citation markers are too different and too complex to be changed by Scrivener’s Replacement tool.

So I wish to have Scriveners own citation marker management which could export to BibDesk AND Endnote styled markers. This would be very helpful for academic writing, because of all these journals and supervisors with different needs and expectation regarding your output file.

Kind regards!

Could you please give an example of the citation formats used for each? I’m wondering if there’s any way Scrivener’s Compile Replacements could be adjusted to accommodate this.

All the best,

for BibDesk/Latex export I use [p. 55][#Bieri2007]

for EndNote/MS Word I use {Bieri, 2007, Bieri2007@55}

Any advice?

All the best,

As an academic, I’m uncertain why you would want to use two bibliography systems simultaneously. Given that EndNote (the system I am most familiar with, I’m sure the same applies to BibDesk) can format into almost any academic style you can imagine, why would you want to go to the effort of double entering every citation? I shudder at the thought! :open_mouth:

When dealing with other academics, I have always simply compiled draft documents with EndNote citations as-is (i.e. still with the curly brackets). There is enough information in those for people familiar with the material to know if relevant citations are missed. If it is a near-complete article requiring proof editing, then I compile to Word, process the bibliography with EndNote, then send the appropriately formatted file (for me, this is usually APA style). In this latter case, the document then appears submission-ready with an appropriately formatted reference list at the end. Doesn’t matter whether I use APA-style, Harvard or something else, EndNote will take care of it.

I have yet to find a colleague (or supervisor) with whom this system does not work. My thesis was done this way (I lost count of the number of times it went back and forth to different supervisors) and am using the same system for articles I am preparing with colleagues.

Can you clarify why you even need to use two bibliography applications?

i like this topic its good i like it…

that is no problem, because BibDesk has got a very good export option to EndNote, so I do not need to double entering any citation.

The point is just this: I - and a few colleagues are Latex users (because it has sveral huge advantages over word). But Latex has only a pdf or ps output. So there are supervisors or reviewers who do not want pdf, because they like to comment a doc document. So I want to use Scrivener and Word during the review process and Scrivener-Latex for the final formatting. But then I need two different bibliography managment systems because there is no MMD/BibDesk integration to MS Word.

Yes, this could be done like this for exchange with my colleagues. For me I would give them the MMD formatted citation from the Scrivener file and a bibliography via Latex Export. But what if a journal wants everything as a nicely formatted word document? And what if another editor wants a Latex file? Or think of cooperating: you are working on the same document with colleagues but you are each using different bibliography systems and different word-processors for final editing. Here Scrivener could be the missing link.

Furthermore I think one of the great advantages of Scrivener is to produce very different output documents. But for academic writing you need to have a solution for reference management. Because there are already so many different bibliography programs out there - maybe it is a good idea to have the ability to transform citation markers flexibel for the needed bibliography program.

Isn’t that enough then? If BibDesk can export to EndNote, then… :question:
Excuse all the questions, I’m simply trying to understand because I’m genuinely curious (and a little concerned that my questions could come across as rude - please know that is not my intention).

But BibDesk exports EndNote? I’m definitely missing something crucial here.*
Note: I don’t use Latex - tried it once or twice and couldn’t see any gain (for the type of writing I do) that would outweigh the pain of learning it. I mention this to help explain my ignorance.

Once I’ve submitted to an article to a journal, that article has (for me) left Scrivener. It has been written and is now in the formatting stage. I use Scrivener for the writing, other apps for the formatting. For me, that’s usually Word because that’s what my collaborators use (or at least, all have access to) and usually the journals I submit to require Word format.

But haven’t you already submitted it?

Pretty much explains my writing existence - but we all use Word (or apps that can use Word file format).

For myself, I compile to Word whenever I need to share with collaborators (or supervisors, or editors, or… etc). Often this means I subsequently re-import an edited version back into Scrivener, but this is a blessing as much as a curse. Note that, to date at least, I have never needed to share my EndNote library. Collaborators see the EndNote citations and, as noted earlier, these are human-readbale enough that they can interpret the references cited. Occasionally they will recommend additional citations that I then add to my EndNote library. I don’t even know whether some of them use EndNote or not, it’s just not relevant (for us) at the writing stage. Since only one of us is going to compile the thing, then as long the references are formatted for their bibliography app then all is well. We’ll each review the formatted penultimate draft (because there’s always more changes) in Word anyway.

But, having said all that, I’d like to understand your process. Maybe I can learn a thing or two and adopt some new strategies used (several planned articles due this year) or at least tweak the ones we use already.

*UPDATE: I think I just identified the missing part of my comprehension.

coupled with

It seems I was unknowingly equating Word with EndNote when I read those lines the first time. :blush:

Yes, this is the crucial point! :slight_smile: Sure, for final formatting I could search for the MMD citation tags in my Word Document and transform them to EndNote readable format manually - but I wish to have an automatic solution for this for the time when I will face about 300 pages… .

No problem - maybe I am wrong or do not see an easy solution. And you are right, the MMD tags are human readable, too - and not so distracting like the BibTex commands - so may be this will do it for a start. My problem arises because I am trying to use Latex and Word and have set my hopes into Scrivener to cross these worlds… - maybe that is to much.

I would have thought that it ought to be possible to write some sort of macro to change one kind of temporary citation into the other. After all, the bibliographic software can parse the file and change all the temporary citations to permanent ones in the right format. In fact, if I were you I would see if it is possible to either get EndNote to read the BibDesk type of temporary citation, or get BibDesk to read the EndNote style. It’s a long time since I’ve used EndNote, so I can’t remember how flexible it is when it comes to the format of the temporary citation. I know Bookends is very customisable in this sense. Indeed, I’d be tempted to download the demo of Bookends, and see what could be achieved with it. If not, then I know that Word used to be able to achieve some fairly sophisticated Find / Exchange operations, but again, I haven’t used it for a long time. I would think it ought to be possible in Nisus, and there are very helpful people on their forums who would probably write a regex macro for you if you asked them nicely. It looks like it is just a question of changing the position of certain elements in the temporary citation, and inserting (or removing) some brackets. I wouldn’t give up hope yet.


Edit: OK – even I with my extremely limited knowledge of Nisus Writer Pro have managed to come up with a Find / Exchange that seems to convert one temporary citation to the other – but experiment first and use with caution – I don’t know what I’m doing :smiley:

Find box: {[^\n\f]+, [[:digit:]][[:digit:]][[:digit:]][[:digit:]], ([^\n\f]+)@([^\n\f]+)}

Replace box: [p. \2][#\1]

I agree with Martin. If you visit the Nisus Forum there are some very helpful guys over there who are capable of writing macros that will do pretty much anything.

One of them has in the past, written me a macro that converted:- {MHRA formatted footnote text} - which was in the main body of the text, into perfectly placed and numbered footnotes.

I’ve been talking to Ioa about this, and he pointed out that the best way of approaching this would be for Scrivener’s replacements to support RegEx. RegEx through the search features in Scrivener is on the list for the future anyway, but I’ve moved it up for the Compile “Replacements” feature, so that as of the next update, the “Replacements” feature has an extra column:

The expressions in the “Replace” and “With” fields in the image above would turn BibDesk citations into EndNote citations during Compile.

(Note, however, that RegEx replacements will only be available on OS X 10.7 and 10.8, since Apple added support for RegEx searches only to Lion.)

Amazing! There could be all sorts of uses for that.


It seems that this will do it.
Great - thanx for caring! :smiley: - so when is the next update released? :wink:

( I do not understand the code inside the “Replace” and “With” field - Could anyone explain it to me, please? )

I’ll have a beta up in the Beta Testing thread in the next few days, and the official release should be February, March at the latest.

Pfft, don’t ask me - Ioa gave me these RegEx expressions. :slight_smile: It’s RegEx (“regular expressions”), though, which is a powerful search and replace syntax used in all sorts of places:


All the best,

There is a tutorial on regular expressions (regex) here:


A search on Google will bring up plenty of information about the system. It can get quite complicated, but it’s nothing to be afraid of, and some knowledge of it can be quite useful.


I see Keith beat me to it, but the more the merrier!

O’Reilly and Associates has an excellent book on Regular Expressions. I read the first two chapters, and can do just about anything I’ve ever needed to do with them. Regex is HARD CORE geek-fu, and not for the faint of heart, but if you have the gumption and the stomach, you can do some amazing textual gymnastics with it.

Well part of that looks more messy than it is because most of the punctuation marks on the keyboard are used as regular expression syntax. Hence, if part of your search requires punctuation marks to be found, like square brackets, they often need to be escaped with the ‘’ character.

At any rate that example would probably not be super robust, I just meant it as a quick demonstration of multiple capture points and then shuffling the captured data into a new format in the replacement. That pattern will match the example you provided earlier, and any others that are typed like that, but would fail if for instance you didn’t specify a page number.

Here is a good online tutorial which covers a flavour of syntax that is very similar to the one 10.7+ uses. So yes, super geek-fu, and nearly everyone hates them, but there is nothing else out there that comes close, short of a full programming language and dozens or hundreds of lines of code.


It’s hard, but I think it is finally time to admit that my best geek days are behind me. To quote the fictional Roger Murtaugh from Lethal Weapon, “I’m getting too old for this ****.” <insert 80’s saxophone solo here>

MSWord supports regex with search and replace.

See the following:

office.microsoft.com/en-us/suppo … 87305.aspx

If it is a full regex implementation, you should be able to use the strings Keith supplied in his example to transform the citations within Word using Replace All.