Academic referencing

I’ll be honest, I don’t get it. Scrivener is a writing product so why is it not standard to have a direct connection with at least one referencing tool?

I’ve read various help topics that give work arounds but they still seem unnecessarily complex. What’s peoples experiences of either zotero or mendelay with scrivener?

It makes me wonder why use scrivener. I love it but if it’s making referencing difficult, and I hate to say this, going back to word may have to be an option.

Any feedback or options welcome

Handling of scientific literature is so much more than just writing. And writing science is so much more than just handling scientific literature. Sometimes the two meet, but most of the time not.

Scrivener is a complex piece of software. Good literature handling software are also complex. Combining the two is not at all easy. And a majority of Scrivener users would be irritated if L&L decided integrate just one of the many alternatives.

What’s wrong with the current situation? You can use any reference software that uses cite keys that can be handled afterwards.

Tried to use Zotero with Scrivener but that didn’t end well. Fortunately some kind academic users on this forum pointed me to BookEnds and it worked right out of the box as advertised. It was money well spent and only costs US$59, $10 more than Scrivener.

For more discussion on this topic see:


Scrivener works fine (and has direct links, use ⌘Y and see Prefs) with several reference manager tools.

When i tested a couple of months ago, Mendeley was a disaster as it has created a new online/offline system that removed many options like the ability to generate citekeys for compatibility with other writing apps. Writing to their support and all I got was marketing speak answer that they value my input blah blah blah. Zotero at least has a workflow for anyone that doesn’t use Word. Neither option is particularly great, offering poor management of references. Mendeley in particular is a step backwards functionality-wise and basically a ploy to lock you in to that publisher’s ecosystems as far as I can tell.

I’ve been wondering how to best insert temporary citations if you ultimately want to compile via MMD/pandoc to LaTeX.(I’m only getting started learning how to do this using Bookends, but I’m already realizing that all of my temporary in-text citations probably need to be changed) Pressing ⌘Y for me that just opens Bookends – which is basically like I’m just switching between applications, which I could also do with ⌘⇥. I’d then have to manually click into the search field, type in a search key to find the relevant reference and then drag & drop it into my Scrivener project (which has vanished into the background). The much better alternative seems to double-clicking ctrl: A small floating window will appear in which you can search for the reference without leaving the Scrivener window or having to click anywhere.

However, both ways will insert temporary citations of the type that Bookends itself can read and convert in a scan, usually {Author, Date, #uniqueID}. Now from my preliminary working knowledge I gather that for exporting via MMD/Pandoc to LaTeX they should be in the format {@citekey} where cite key is the unique BibTeX citekey. So I have two questions here:

  1. How do I tell BE to insert @citekeys via the floating citations window ?
  2. Are there different variants of the @citekey format I can use, like the BE qualifiers or LaTeX command, to prompt different in-text citation formats like “Author (YY)” or “(Author YY)” across a range of different formats (Word, Mac, etc) ?

Yes, [⌃ctrl][⌃ctrl] is also a very neat way to quickly insert refs, but just to mention that ⌘Y works both↔ways, in Scrivener it changes focus to Bookends, but in Bookends it inserts the selected ref back into Scrivener. The main advantage is Bookends window has more control for searching and more context/details than the floating citation window. There is nothing stopping you from mixing and matching these two. Another alternative if you use Alfred is to use my bookends workflow which also has a floating citation interface to search and insert, its mostly what I use (out of habit).

  1. See … nd-pandoc/ for instructions on how to set up Bookends to output the [@pandoc2021] temporary citations format.

  2. You do not have access to the same modifiers as Bookends, and Bookends doesn’t understand or translate the modifiers to Pandoc format. Therefore you need to manually edit the citation as you require. The formatting details can be seen here:

Thanks a lot ! Of course setting up a BE format in Pandoc syntax makes so much sense.

Thanks, I hadn’t known this to be the case. Although it only works if Scrivener is set as preferred word processor in BE. So far I’d kept that blank, as I also want to output to Word (and probably scan bibliographical entries there) but perhaps that still remains possibly.

Oh that seems pretty tedious… Do you edit the whole text document manually before compiling via LaTeX to PDF or do you simply stick to the available Pandoc syntax for citations? From what I gather there are however three kinds of modifiers, right?
[@smith04] → creates regular in-text citation in parentheses
[-@smith04] → ommitts name /prints only year within parentheses I am assuming
@smith04 [p. 33] → ommitts brackets /prints year together with pages in brackets I am assuming

I always stick to Pandoc modifiers in Scrivener as they support every output and in general I output more to DOCX than LaTeX anyway. They do everything I need for my research field. CSL (the system Pandoc and many others uses), does have some limitations for more complex citations used in e.g. legal work, but for most fields I think it handles 98% of most referencing formatting. The other advantage is Pandoc can handle the switch between author-date and footnote styles relatively well.

Yes those modifers are the main ones, although note that you can add prefixes and suffixes inside the brackets, e.g. [please see @ref2001; also @ref2002 for more details]. I don’t find this tedious at all, indeed I prefer it to the UI that i.e. Endnote enforces in Word. I mostly either exclude author (simply add -) or add prefix/suffix which I prefer to write in Scrivener than a tiny text entry field in a floating UI…

Thanks a lot for your message - this is really good news and hence I think I’ll stick to that.

Btw I learned a great deal from your scrivomatic documentation that I’ve been trying to wrap my head around for the last 2 days. (Thanks a lot!) There are still quite a few things I don’t yet understand but I think I’m getting there… Where would be the best place for asking questions about it?!

If they re general questions about a pandoc/multimarkdown workflow you can ask here so others can learn from it, but if they questions that may be specific to your setup or a bug, then possibly better to use Github. The only problem with Github is I don’t get emails when a new issue is posted, so it takes me time to respond. You can PM me here if you want more timely feedback.

Thanks so much for your kind offer! The log file already helped me fix all the preliminary problems so I could finally replicate your workflow (it’s marvelous - thanks a lot!)

This is probably more of a question for the BE forum, but thought you might know: is there an easy way to replace temporary citations using their current specified format (without having to write a script for it ) ? I previously used the standard {Author, Year #unique ID} but now switched to Pandoc citations. I’ll still have to edit them manually because of the modifiers but it would be very tedious to have to replace everything manually…

Try to use BE’s scan to fix the references, but that only applies to the final output document. If you want to edit the refs in Scrivener, then only thing I can think of is a slight shortcut, my Bookends tools has a script to copy selected text, clean it up and use Bookends quick search. So for example you can select the temporary citation {Bickford, 2021, #2024}, and my script will clean it up to give “bickford 2021” and switch to Bookends and paste that in the quick search field. This means it is immediately selected. You could then press ⌘Y and the Pandoc formatted equivalent would be pasted back over the selected text. This saves quite a bit of time but still requires manual selection of each reference.