I still don't have a reference manager, help me

I have managed to get by so far without a reference manager, but soon I will be writing chunky academic papers, so I need one. What should I use, and how?

Here is info on how I"ve been working:

• I do all my writing in The Archive, and I put the full reference at the bottom of each zettel.

• I started using pandoc recently to get eg. .docx files to submit.

Is there a way I can go straight from that to full papers, without bringing in some other program? Or do I always need an extra place to 'store' the full reference, which I then make reference to with a cite key? If so, what is going to be best for me to learn?
I gather my problem is I don't know how to use cite keys.

I am more or less prepared to learn LaTex, and Overleaf, I guess, which my institution has a subscription to.

But is something in there redundant and I could do it through pandoc directly from the Archive?

Does anyone know?

Thankyou xxx

• edited December 2020

There is no perfect solution, so it would probably be best to test a range of them and see what suits you. There are plenty of options. In no particular order you could try applications like Bookends, Bibdesk, Zotero, Endnote, Papers, Mendeley, and probably a few others I have forgotten. If you need LaTeX then you should probably look around on some forums dedicated to that. I've never needed it for my work. Oh, and have a look at CiteProc.

• I've only used extensively Bibdesk (free, macOS). This was using LaTeX but I guess you can use it with out any additional knowledge.
I tried Mendelev a long ago and it seems like it could also work really well.

Best advice: Try the trial versions a decide for yourself. If possible use software you can export your data and use it in other packages.

• The process is more important than the exact tools. While I'm not advocating that you follow my exact workflow (find a process that meets your needs), here's what I do:

1. Zettels are for ideas. I consider them drafts when they enter a paper. Sometimes this longer work is in the Archive, sometimes it is in Overleaf (I, for one, have not settled on a text editor, though I would like to work in the cloud less). Pandoc could certainly help convert Markdown to other things.
2. I use Zotero as my reference manager. It has the nice feature of being able to use BibTeX when I'm writing papers, but export bibliographies to my clipboard if I need to paste references into forum posts (which my university uses a lot).1 It also means that I can create a .bib file containing the references I originally cited in my Zettels.
3. Then I upload the .bib file to Overleaf in the appropriate project. When needed, zettels are uploaded into a project folder, too. I can then compile everything in LaTeX.

To answer your question directly, I learned to use cite keys in the process of learning TeX. I'm still hoping to do all of this without relying on a cloud service like Overleaf, but I'm not quite comfortable enough in TeX yet (Overleaf's error notes are a comfort to me). Nevertheless, a reference manager helps me keep my ZK focused more on my own responses to articles and books and allowed me to understand how a reference manager interacts with a LaTeX editor. Once I get more comfortable with pandoc, I could see myself doing everything on my own machine, but I don't see myself skipping over having a reference manager. In the same way, because my academic work benefits from precise formatting, LaTeX plays its designated role as my typesetting tool.

Again, I'm not saying that you do what I do. I'm only using my process as an example. For the level of academic work I'm doing, a reference manager and LaTeX are part of that toolbox, playing a distinct role from my ZK.

1. If pandoc can properly convert my Markdown footnotes to a list of references at the end of a text, with the right parenthetical references instead of footnotes, I could skip this feature in a reference manager. Since I haven't figured out the proper way to configure that, I let my reference manager do it for me. ↩︎

Observations logged here: write.as/via-poetica

• @Steph said:
Here is info on how I"ve been working:

• I do all my writing in The Archive, and I put the full reference at the bottom of each zettel.
• I started using pandoc recently to get eg. .docx files to submit.

>

I use a reference manager (BibDesk) to have a structured list of all the information per reference.

But you could get by with the tools you mention. Not that I recommend this.

The downside is that when you want to insert a reference/full citation, you have too either write it from scratch or copy & paste it from old notes. A reference manager helps speed this up. I can open BibDesk, hit the search, then ⌘C using my Markdown template, and insert the reference in my note.

I'm using MultiMarkdown citation syntax for this, roughly like so:

Text that needs to be cited.[page 1234][#authorYEARbook]

[#authorYEARbook]: Author, The (2001): "My Best Book!", City : Publisher


If you already stick to that and spent the time to get the reference right, you can work with that. It's not as convenient, but it'll do, since it contains all the information necessary. When you assemble a paper from your notes, you have to clean up the references a bit: in your final output, you'll get what you put in into these MultiMarkdown references, and if one prof requires MIT and the other APA and the other something different, you'll have to rewrite these reference defininion lines again and again.

With pandoc, you can convert MultiMarkdown (mmd) with this reference syntax to other formats. Or you can dump the MultiMarkdown reference stuff and rely on pandoc's own citation header data. I think that's too unwieldy to be practical, though, and it comes with similar downsides. You can specify the citation format (APA etc) with the structures pandoc data, but it's in the header at the top of your notes, so meh.

BibDesk stores its database as a LaTeX/BibTeX .bib file, and pandoc can read the info from these files just fine, too, so I really only see benefits in using a simple tool to maintain your main bibliography .bib file for you. The data is structured, and you can combine the .bib file with style like APA and then automatically get the correct output. The separation of data presentation (the styles) and storage (the .bib file) can be a real benefit, especially if you want to work with your notes for ages and need to cater to different citation styles over the years.

Author at Zettelkasten.de • https://christiantietze.de/

• Thankyou all. I just don't wanna learn a fancy GUI that works best with Word, if I'm gonna abandon it for the more command line approach anyway down the line. I'd probably rather bite the bullet and get comfortable with the barer bones, although I'm a bit scared of it. So I think bibdesk and .bib files seem good, I will go and look them up and start using.

• edited December 2020

I think the fancy GUI is the same with all of them tbh. Bibdesk looks like Mendeley and the old nicer version of Papers as well. It is more about which manager works best for your workflow.

For this referencing you don't really need a command line, at least I never used one for academic papers. All LaTeX written within Text Mate and a keyboard shortcut for typesetting the pdf

• Steph, I use Joplin which is an opensource alternative to Evernote. As I read a research paper which I store in folder called "Scientific papers" with the format [Year-Author] Title, I open a new note on Joplin where I keep what I find interesting, along with figures and math equations. Then in my Zettelkasten, I refer only to notes in Joplin since these are the papers that I have examined, by using something like

"This bla bla text written by (AuthorYear) shows bla bla"

So Joplin for a reference manager along with a simple folder.
And a software for Zettelkasten. I use Zkn3 at the moment.

Now if you want to easily add references on Word documents, you can use Zotero. It's pretty good for easy referencing when you write a publication, but terrible for keeping notes.

• Hey,

There is a nice reference management app called Snowyowl. Its mac native, intuitive and has some nice features (cite to pages). Also very responsive developers. Recommended.

https://snowyowl.app

• edited February 20

The topic is three months old, but if you are still reading or someone else is interested in a workflow without the need of a reference manager, I would point you to this article:

http://wcm1.web.rice.edu/plain-text-citations.html#fn4

If you want to handle pdfs as well, I would suggest giving them a UID and paste it in the literature note. This way you only have to fire up a search in your filebrowser and you are directly pointed to the source material.