Do I Really Need a Reference Management System?
Not an entirely rhetorical question. 
So, I have been catching up as much as possible on the threads in this forum after joining this week. My impression is that most of the contributors are in academia and publish scholarly work a lot. I am coming at this Zettelkasten concept from a different angle, I think ... more of a short-story writer, short-article journalist, science blogger.
Nonetheless, my workflow should be basically the same as the workflows that I have been reading about in this forum. Not sure.
In any case my workflow could be expressed as: select a story angle (non-fiction or fiction), do the necessary research, capture ideas that could contribute to the work, summarize in my own words how these contribute (the zettels), build the narrative (planned or seat of the pants) using a "cards on the wall" approach, by way of, for example, Scrivener ...
then, iterate if the story angle diverges along a more interesting track.
When I bring citations into my notes, I suspect it will be for me to remember where to find the source, page, and context for any particular idea that manifested along the workflow. I do think that would be useful, as any story or article may be derived or motivated from multiple sources, pages, paragraphs, sentences. But the final product--the published story--would not necessarily need the citations or bibliography. For a science piece, however, they might.
The Zettelkasten itself would, after reaching some kind of a "critical mass," likely become a source for finding new story angles ... at least that's what I hope. 
Assuming that my Zettelkasten implementation really would benefit from a reference management system, I spent the day comparing dozens that are available, some free, some contingently free, and other not so free.
My requirements for any reference | bibliography management system are as follows:
- must be able to work on both Windows and Mac
- must be able to sync between both platforms
- must be able to support import and export BibTex formats
- must support plain text
There were two out-of-the-box solutions that met these requirements and that were both contingently free ... as long as you didn't get over 600--800 or so references.
Otherwise, I would lean toward a roll-your-own web-server solution that are actually free to download and use in perpituity. Of course, because you need a web server, this kind of solution is not entirely free, though reasonable. And, the size of your reference library would not be contingently constrained.
To be sure, I do like the minimalism often expressed by @sfast. And I appreciate the kindly talking me down from the Folders|Project ledge by @ctietze. 
And I want to be able to best utilize the bibliography hooks that @Rene expertly installed in sublime-zk and sublimeless-zk (sweet!) to keep track of what I am reading in my research, which will include both articles and books. But, is a robust reference management system necessary for my expressed situation? Trial and error?
If you have any more thoughts on this to help keep the question less rhetorical ... 
Howdy, Stranger!
Comments
Hi Robert, I'm frequently lurking around in this forum, and also happen to be one of the refbase developers. :-)
Personally, I'd consider a reference database as crucial for your use case, esp. in the long run. The three "roll-your-own web-server solutions" that you've mentioned are all fine, but would probably require more setup & maintenance effort than the other two. Also, currently, their development progress is comparatively slow.
For your use case, I'd go with Zotero. Its basics are free, and it's fully featured and well supported. Also, it's well suited if you also want to store your own literature notes (refbase is more of a classic reference management & institutional repository software).
I am so glad that you lurked my way, @msteffens. And, what luck that you are a refbase developer!
Admittedly, my post is a bit of my thinking aloud about the role of a reference management system in my initial workflow and with the standing up a new Zettelkasten archive.
In doing so, however, I was hoping to attract some more experienced ZK archivists to share their own viewpoints about the when, the what, and the how of RMSs before I try to bolt one on to my archive(s). Your response is most helpful on all three points. Thanks!
I have come to the conclusion that: (1) an RMS is crucial to my workflow in the long run; so I need to get on with figuring out the path for integration, and (2) Zotero does seem like the best choice for my intended workflow characteristics, at least in the short run ... and maybe longer.
With respect to the storing of literature notes within the RMS, this discussion is encouraging. Note that with this practice, primarily for performance reasons, one should attach just one "large" note and not several smaller Zettel-like notes.
Cheers
W.r.t. storing literature notes in Zotero, I must say that I haven't used it for a larger real-world project yet. So I wasn't aware of this possible performance issue.
I'd consider it as very important to have your notes stored as individual items, so that you can tag them individually, filter & search for them, and freely organise them into groups, etc.
I'm currently developing a Mac app that tries to help with this. I.e., extract your PDF highlights & annotations as well as the accompanying bibliographic info to individual Markdown notes, so that you can then further tag, rate and comment on them – and export them to other tools such as your Zettelkasten app, or to apps like DEVONthink, OmniOutliner or Scrivener, etc. The app is heavily scriptable which allows to create custom workflows. Unfortunately, it's not ready yet. But at some point I hope that it can offer a viable alternative for managing & organizing your literature notes.
As I mentioned in your introduction, I would favor a simple app that uses the plain text BibTeX storage format. Jabref is the best cross-platform thing I know. Or you pick BibDesk for Mac and another app for Windows. Again, that's the beauty of plain text: the format is open and you can have many apps on different platforms. And @rene's tools will parse these BibTeX files, too.
I would not attach anything in my reference management system, except maybe a PDF of the original text. Say your source has the BibTeX cite key
#fast2018zettelkasten, you can just search for this string in your archive and get all the notes that reference that piece of art. Instead of attaching things to reference items, you use the note archive to look for notes related to the reference item. That's probably a bit counter-intuitive to hear at first. It works like a charm, though. And who wants to maintain 2 separate repository of notes, anyway?Author at Zettelkasten.de • https://christiantietze.de/
I was wondering about the wisdom of putting literature notes into my reference management system. But what's the antomy of a literature note? I was thinking of it like a note that has not been processed into a Zettel. Literature notes would be more like the notes initially extracted from a reading like highlighted passages and marginalia. Perhaps, these notes would have a much shorter shelf-life in terms of long-term usefulness to the note taker. These notes may even produce clutter to not only the Zettelkasten but also to the RMS.
Later, I want to do some more analysis of what knowlege work is in terms of a Zettelkasten archive. There have been many posts on the "boundaries" topic, which if find more than intriguing.
To be sure, though, your description of using the citation keys in a search for relevancy is spot on. But I think we want them imbedded in notes processed as Zettels, which I do not see as literature notes, per se. Does anyone see it differently?
Still, I wonder aout the wisdom of putting literature notes into the RMS. I am not sure that that is the functional purpose of an RMS and it could possibly affect performance.
And, as I responded to your reply in my Introdction (thanks!), JabRef it is. I missed JabRef in my initial pass through of dozens of RMS contenders. JabRef meets all of my decision criteria and it is free. And so, I have already downloaded it.
Thanks for the follow-up here too!
More to come ...
Keep us posted! I do doubt that having temporary literature notes in your reference manager that you then need to convert to Zettel notes is going to stick in the long term. Engagement notes while reading usually work well with pen and paper; I'd even say: they work best with pen and paper, because you don't need to switch contexts between analog and digital, the physical world and the computer. If things work for you with 2 digital places, please make sure to tell us about what you do and when you do it
P.S.: Maybe an
##inboxtag could work as a buffer of not yet fully processed notes, too, instead of notes inside the RMS?Author at Zettelkasten.de • https://christiantietze.de/
Thanks for the recommendation. And, I have long resonated with the pencil-and-paper practice because I have long known that writing forces the capture through the left side of the brain, which enhances the brain's retention of what's captured. I am not sure that that works as well from a keyboard ... awaiting the studies.
Perhaps the initial capture is the most critical phase of the note-taking process. It needs to be purpose-driven and, so, focused and consistent. Otherwise, garbage in/garbage out. It also implies that a Zettelkasten has a user-specific purpose; otherwise, it is just a note-collection bin ... kind of like a personal journal. [see my P.P.S note below as a case study.]
But, IMHO, we shouldn't conflate that consistency issue with not using a pencil-and-paper or any context switching during this phase (reading<=>writing). It can be argued that you are already context switching, regardless, while reading and note-taking at the same time. Your mind must switch from what someone else is saying and then to think and write about how you consider what's being said as somehow important to you ... given the purpose of why you are doing the reading or listening in the first place, for example.
Nonetheless, perhaps the quality of the archive content has more to do with the quality of this contemplative phase when deciding what goes in and what stays out of the archive ... and why. You certainly can be as contemplative while capturing input digitally. And, using a pencil and paper does not guarantee quality; it just slows down the process to match the bandwidth of the brain, IMHO.
With respect to "multiple digital places" and the often-read topic of "boundaries," it seems that there are both physical boundaries and logical (conceptual) ones to consider. Considering conceptual boundaries, we are talking about what goes into and what stays out of our knowledge-work-supportive content. To be sure, I am considering knowledge work to be the capture and processing of relevant information into new knowledge or art (e.g., a work of nonfiction). This logical boundary is inherently fuzzy and changing. Certainly, the boundary can evolve over time.
Considering physical boundaries, we are talking about the note-processing engines, which can include the pencil-and-paper practice as it did exclusively for Niklas Luhmann back in his productive times [the 1960s--1980s]. The criteria for the architectural boundary of a Zettelkasten are, IMHO: low-cost, simple, efficient, distraction-minimizing, cross-platform (in my case), and non-proprietary (future-proof).
The more the note-processing functionality can be accomplished within a single engine (i.e., within a single physical boundary) the better to meet these criteria, IMHO. These criteria shouldn't change but the design implementation may well change, slowly, over time.
In another thread (my Introduction), I mentioned how I was becoming enamored with the idea of using org-mode (emacs) as a possible Zettelkasten engine. This interest was piqued by @mediapathic [Steen] in a post last April. And, Christian, you say you are using org-mode in the context of diary notes at least. So I have been investigating an org-mode-augmented emacs as a possible all-in-one note-taking architecture.
Just yesterday, I implemented a journaling mode within org-mode using org-journal.
So, my journal notes may be within the physical boundary of my Zettelkasten, but not necessarily within the logical boundary that separates my knowledge-work-supportive content. This is a curious artifact that will require architectural design considerations. 
Maybe folders are back?
In this thread, we have been discussing the what, the why, and the how of RMSes, and you graciously pointed me to JabRef. Bingo! It fits all my criteria. And so, it is a top contender.
But, then I read a post by @jimsen, also posted last April, who mentions org-ref, yet another org-mode mode but for managing BibTex citations. Hmm ...
Org-ref is an RMS that is totally integrated within org-mode, and so, emacs. Therefore, it has the appeal as being able to accomplish (at least more) complete digital-systems unity (i.e., a single application) for the note-taking workflow.
In principle, any digital literature notes could also be within the archival engine's physical boundary ... somewhere ... and mixed with my knowledge-work-supportive content if and only if they meet the criteria needed to cross through that logical boundary. More architectural design considerations ...
Maybe forget storing literature notes, per se, and, as you suggest, use citation key references within the associated Zettel notes to get at my processed literature notes? This says that my notes from the initial capture are likely throwaways. It also says that the bar is set higher for any note to cross through that logical boundary when compared to notes taken, say, while reading (e.g., literature notes). Just thinking out loud.
Still checking org-mode out; the learning curve is not a trivial climb, but there are plenty of helpful tutorials online. So far, org-mode is very impressive and felt the need to write back about it, especially concerning org-ref.
Cheers ... and sorry for the too-long reply.
[P.S., please tell me what the double-hash tag does over and above the single-hash tag. I think it is a tagging convention associated with building structural aspects of Zettelkasten content ... kind of like categories or topical headings. This compares with the single-hash tag that I think carries the user-specific semantic features of the Zettelkasten content. Still, the differences seem subtle.]
[P.P.S., yes that
##inbox tagwill be the place for note triage as they enter into the initial digital space(s) of the note-processing system. I was doing this in Evernote while implementing something akin to the GTD method. I called it "grass catcher" instead of "inbox."What I found was that in the process of sorting out my inbox, there was a corresponding inflation of categories or folders that tried to keep pace with what ended up in the triage. To me, this is a further testimony for how critical careful contemplation is to that initial sorting process.
The Zettlekasten must be purpose-driven but purposes are not always single-threaded and they can wander. It also begs for the smart use of categories or structural tags from the get-go, in order to cope with any "jiggling" logical boundaries.]
I'm reading through this conversation, because I'm wondering the same thing myself:
"Do I really need a reference management system?"
Apparently, the answer is yes, but I'm at a loss as to why. Why shouldn't I just store reference information within the same system I'm using to keep Zettel notes?
I re-read this thread with interest too, and found that it touches some issues I've been trying to work out lately.
I am wondering, @GreenBeing, how you've gone about dealing with your "literature notes" (the reading notes you take during your "initial capture") in the meantime. Do you still keep them mixed in with your Zettels (ie, your "processed" notes)? Do you make a point of going back and processing a "literature note" into individual Zettels and incorporating them individually into the Zettelkasten (what you call the "knowledge-work-supporting content" on the other side of the "logical boundary")? If so, do you keep the original "literature note," either intact or as an outline note (or a structure note?)? Or does the "literature note" simply get dispersed once its elements have become Zettels and crossed over that "logical boundary" (as opposed to the "physical boundary" of the archival engine, which it already exists within)?
By the way, I appreciate the distinction you make between the "logical" and the "physical" boundaries of the system. It seems to me that this is a distinction that Luhmann didn't have to deal with exactly, given that in his system the physical and the logical were so closely entwined, if not identical. It seems that one risk of using a digital Zettelkasten (at least as they are described on this site) is that they allow notes to enter into the archival engine ("physical boundary") as "notes" before they are meaningfully incorporated into the Zettelkasten structure ("logical boundary") as well-integrated Zettels.
As a result, I am finding that my archive has lately become more like a personal wiki (what Daniel Lüdecke calls a "network of linked and tagged notes," see slides 26-27) and less like a Zettelkasten. That is, I have a lot of notes that are within the "physical boundary" (archival engine) but not incorporated into the "logical boundary" (Zettelkasten structure). What's worse is: the system allows me to produce notes with ID numbers, tags, and links, etc. that sure as hell feel like contributions to the Zettelkasten. But the links between the notes are often fairly weak, signifying only loose thematic connections, not tight causal or close relational connections.
In short, it seems that this digital Zettelkasten system allows me to be lazy without feeling lazy... I struggle to imagine Luhmann writing a note, putting it any old place that it sort of fit, and then walking away satisfied. As you nicely put it, @GreenBeing, it seems there needs to be a higher bar for a note/Zettel crossing over into the Zettelkasten structure. As it is, it seems like the bar almost couldn't be lower.
In conclusion (sorry, this went on way longer than I expected...) it seems possible to imagine that certain structural changes might be incorporated into the digital Zettelkasten system to raise the bar, so to speak, and to discourage the creation of personal wikis masquerading as a Zettelkastens (note-length limits??
), but I think it is more likely that I will simply have to be more diligent about creating good Zettels and strong links, and not letting my "literature notes" hang around so long that they start to feel like ends in themselves...
As for the RMS question, @micahredding, are you thinking of something like a bibliography note? A single-note list of all the citation information (author names, titles, dates etc.)?
@argonsnorts Yep, that's what I currently do. But I'm also just learning about the Zettelkasten system, and don't fully understand the rationale (or the vision) of everything.