The reference manager for note-taking

Olivier_H · June 2023

Hi again !

I saw about reference manager tools (like Zotero) for the process of note-taking (not especially for Zettelkasten).

Is it as useful as it pretends to be ?
Why do you use one ?
How does it fit in your workflow ?

Thanks !

mlbrandt · June 2023

I love Zotero. It's free yet equal to other high end reference managers which cost hundreds of dollars. Since I do occasionally publish my work, Zotero insures I have references for everything I make notes on - and lets me format the papers easily. It also allows me to save a pdf with every reference which is another big plus!

ceaf · June 2023

Thank you. Can you incorporate easily into a kindle ebook?

ZettelDistraction · June 2023

Zotero user here. Very useful and will work with Pandoc.

Olivier_H · June 2023

@ZettelDistraction said:
Zotero user here. Very useful and will work with Pandoc.

How do you proceed for each zettel ?

Something like this ?

# uuid my example title

#tag1 #tag2

body of the zettel

@fake_citation

I mean, for each atomic note based on reading a book, do you mention the reference (like example above) ?

Sascha · June 2023

BibDesk. Simple and enough.

ZettelDistraction · June 2023

@Olivier_H More or less. My Zettel template is here.

Andy · June 2023

I have a somewhat philosophical answer to the question "Why do you use one?" But first, contemplate the first two paragraphs of a four-paragraph manifesto by Riccardo Ridi, "Semantic web: no to the web of data, yes to the web of documents, metadata and human beings" (2021):

[1] If "semantic web" means to increase the quantity, quality, coherence, univocity, standardization, updating and interoperability of metadata that are present in the WWW, adding them to primary documents to facilitate their research, organization, understanding, selection, evaluation and use, then it is a sensible, realistic, useful project and librarians, archivists and scholars of library, archival and documentary sciences can provide an important help to it, thanks to their skills and values.

[2] If, on the other hand, "semantic web" means to replace primary documents with granular data combinable with each other from time to time, then it is a senseless and unrealistic project, because – as librarians, archivists and scholars of library, archival and documentary sciences know well – it is impossible even to imagine an overall system of production, storage, communication, acquisition and use of knowledge that leaves completely aside that fundamental element of the organization and management of information represented by the document. Only documentary structures with sufficient size, architecture, verifiability and persistence can actually guarantee systemic, organic, historical, philological, legal and authorial instances that can not be satisfied by information atoms that are too small, destructured and volatile.

As Riccardo Ridi said, the "fundamental element of the organization and management of information" in our collective knowledge base (the set of all public documents) is the document (or publication). The reference manager is like an interface between my personal knowledge base (my set of personal notes) and the collective knowledge base. The reference manager contains my set of references, which is the subset of the collective knowledge base that I have found to be relevant to my personal knowledge base. My set of references constitute a system that is managed systematically in the reference manager, just as my set of notes constitute a system that is managed systematically in my note system. (On the importance of systematization of knowledge, see my recent comment on what Nicholas Rescher called "the Hegelian inversion".)

Will · June 2023

I use Zotero.

[@Loy:2019a 172] are inline citations; I place these in the note's body.

Below is an example full citation. Rendered by pandoc at publication. I usually place this in a "References and Resourses" section at the bottom of the atomic notes.

Loy, David. Ecodharma: Buddhist teachings for the ecological crisis, Knopf : Distributed by Random House. 2019.

Here it is all pictured together.

Here is part of the book note, which is in the form of a Structure Note that "Sawing of the Limb" is part of.

Andy · June 2023

@Will said:

Below is an example full citation. Rendered by pandoc at publication. I usually place this in a "References and Resourses" section at the bottom of the atomic notes.

Loy, David. Ecodharma: Buddhist teachings for the ecological crisis, Knopf : Distributed by Random House. 2019.

Since the original question seems to be from a beginner, it may be worth explaining more what "Rendered by pandoc at publication" means. When I use my note system to write for publication, I will take material from my note system and put it in a separate document for publication. When I run Pandoc (with a citation processor such as the built-in CiteProc, or an auxiliary LaTeX package such as BibLaTeX, combined with a citation style file), the citation keys are converted to properly styled inline citations, and a properly styled reference list is generated at the end of the document or at the end of each chapter. This ability to delegate the tedious busywork of formatting citations and reference lists to an automatic program is another primary reason for using a reference manager.

Will · June 2023

@Andy, you are right. This is a question from a beginner, and my comment, "Rendered by pandoc at publication." is overreaching. I tried to stay within the context of the question. I apologize for the confusion I caused. @Olivier_H, please ignore my reference to pandoc; it is a tool used in the publishing world and not a necessary part of a ZK.

Andy · June 2023

I would also point out that if you use citation keys in your notes, you don't need to create an index to the ideas in a book manually like @Will did in his screenshot above, which looks like a lot of busywork to me, and which I would never have enough time to do for all the material that I read. Of course, you can create such manual indices if you enjoy it or have other reasons to do so. But it's not necessary if you use citation keys in your notes, because you can automatically generate an "idea index" for a book just by searching for the book's citation key, and, if desired, constraining the search results by certain tags.

ZettelDistraction · June 2023

@Olivier_H, My workflow with Zotero and Pandoc is this. I export a library of references from Zotero in Better CSL JSON format, which Zettlr and Pandoc consume. I use Pandoc format citation keys within my markdown files. The syntax of the Pandoc citations is given at Pandoc Citation Syntax. I'm currently moving my workflow from Zettlr to VS Code, but all the configuration files are in sync, and I can move between systems when it becomes convenient to use one editor rather than another.

Olivier_H · June 2023

@Will, @Andy don't worry I know about Pandoc. I'm used to create technical doc/slides with this last.

I tried Zotero and I admit that it is very very useful software (even if I must rework some entry in my collection).

@Andy, your point is very interesting about citation key. Actually, I'm familiar with collecting notes from my reading (mainly technical blog and not the ZK way).

That's why I asked for your workflow because at the start I was just taking a piece of note and put the source under a section "References".
I'm not using citation key at all.

Actually, my thought is the following :

"permanent note" with a copy/paste of the source
a document built from many permanent notes with citation key from a CSL file built on top of all corresponding references

May be it is bad because it make me do double work.

It could sound weird by I am also annoyed by the "software dependency" produced by using Zettlr + Zotero. An old school plain text in git makes me more confident .

Andy · June 2023

@Olivier_H said:

a document built from many permanent notes with citation key from a CSL file built on top of all corresponding references

Perhaps I misunderstand you, but "citation key from a CSL file" is not correct; there is no direct connection between a citation key and a CSL file. The CSL file only has style description, not bibliographic data.

It could sound weird by I am also annoyed by the "software dependency" produced by using Zettlr + Zotero. An old school plain text in git makes me more confident .

If you use Better BibTeX for Zotero with citation keys, there is NO software lock-in problem. This is another reason to use citation keys: you are not locked in to one reference manager. At any time you can export your references from Zotero to any other reference manager that supports citation keys. And Better BibTeX for Zotero can maintain a parallel plain-text file that is synchronized with Zotero, so you always have access to a plain-text version of your bibliographic database.

EDIT: If what annoys you is the more general idea of being dependent on any reference manager, then you probably don't need a reference manager. People who need a reference manager know that it is a solution, not a problem.

Olivier_H · June 2023

@Andy said:

Perhaps I misunderstand you, but "citation key from a CSL file" is not correct; there is no direct connection between a citation key and a CSL file. The CSL file only has style description, not bibliographic data.

Sorry, I was talking about the json file that contains references which can be used with pandoc.

so you always have access to a plain-text version of your bibliographic database

My bad, I didn't realize that I can export the entire zotero database as plain text. So, I put a bibtex and csljson file for now in my git repository. I also noticed that I can export a single collection from my "library" (eg all my references from web tech article).

dandennison84 · June 2023

@Olivier_H said:
Hi again !

I saw about reference manager tools (like Zotero) for the process of note-taking (not especially for Zettelkasten).

Is it as useful as it pretends to be ?

Yes, it is. It doesn't pretend. Any reference manager is going to better than not using one.

Why do you use one ?

If you do any kind of work where you want to cite your sources and manage your knowledge, you need one.

How does it fit in your workflow ?

At the front: Zotero can suck in web resources as well as those using various forms of universal identifiers. You can store notes, pdfs, annotations, link references to each other, tag them, organize them in different manners, etc. Since Zotero stores only one logical reference, but allows you to use that reference in different collections, it is easy to maintain project-based repositories.

At the publishing end: Zotero can write (and keep updated) an external file of your references in various formats. bib, for example, for latex workflows. It also manages and exports style sheets for references in CSL files. You can export both and run them through pandoc for output.

Thanks !

ZettelDistraction · June 2023

@dandennison84 said:

@Olivier_H said:
Hi again !

I agree with everything @dandennison84 says. When utilizing a reference manager, it's best to incorporate your references as you go. Procrastination will lead to an unmanageable backlog. Not to mention, we all understand the issues that arise from using uncredited sources with overlooked origins.

ZettelDistraction · June 2023

@Andy said:
@Olivier_H said:

a document built from many permanent notes with citation key from a CSL file built on top of all corresponding references

Perhaps I misunderstand you, but "citation key from a CSL file" is not correct; there is no direct connection between a citation key and a CSL file. The CSL file only has style description, not bibliographic data.

I beg to differ. I use Zotero with the BetterBibTeX plugin, which helps to generate citation keys. The exported Better CSL JSON format file does indeed contain citation keys as well as bibliographic data--behold:

Here is one of the entries.

{"id":"brownTopologyGroupoids2006","author":[{"family":"Brown","given":"Ronald"}],"call-number":"QA611.A3 B76 2006","citation-key":"brownTopologyGroupoids2006","contributor":[{"family":"Kolomatski","given":"Taras"}],"edition":"Rev., updated, and expanded version","event-place":"Deganwy","ISBN":"978-1-4196-2722-4","issued":{"date-parts":[[2006]]},"number-of-pages":"512","publisher":"https://www.groupoids.org.uk","publisher-place":"Deganwy","source":"Library of Congress ISBN","title":"Topology and groupoids","type":"book","URL":"https://groupoids.org.uk/pdffiles/topgrpds-e.pdf"},

Andy · June 2023

@ZettelDistraction said:

a document built from many permanent notes with citation key from a CSL file built on top of all corresponding references

Perhaps I misunderstand you, but "citation key from a CSL file" is not correct; there is no direct connection between a citation key and a CSL file. The CSL file only has style description, not bibliographic data.

I beg to differ. I use Zotero with the BetterBibTeX plugin, which helps to generate citation keys. The exported Better CSL JSON format file does indeed contain citation keys as well as bibliographic data--behold:

Your file is (1) a JSON file containing citation data, which has file extension .json. Olivier spoke of (2) a CSL file, which has file extension .csl and which contains the style definition written in Citation Style Language (CSL), an XML-based language to describe the formatting of citations and bibliographies. The confusion here is due to the fact that the JSON file containing citation data is written in the CSL-JSON citation schema, which also contains the letters "CSL" since it was developed by the CSL project, but it's a JSON file, not a CSL file.

ZettelDistraction · June 2023

@Andy, I stand corrected; thank you!

Olivier_H · June 2023

@Andy said:

The confusion here is due to the fact that the JSON file containing citation data is written in the CSL-JSON citation schema, which also contains the letters "CSL" since it was developed by the CSL project, but it's a JSON file, not a CSL file.

Yes, I was talking about json file which is displayed "Better CSL JSON" in the "Export assistant".

@ZettelDistraction , what is your pattern for generating the citation key please ?

ZettelDistraction · June 2023

@Olivier_H

I let the Zotero plugin Better BibTeX generate the citation key. Thanks to my inability to find citation styles the least bit interesting (I swear there was neither confusion nor misplaced certainty--I guessed the function of the CSL JSON file without checking), I am making amends for my previous error by citing chapter and verse on citation key generation in Better BibTeX: https://retorque.re/zotero-better-bibtex/citing/^†

By default, BBT generates the citation key from the item information, and this key may change when you edit the item. Such keys are called dynamic keys, which are marked with a pushpin the item list view and in the item details to distinguish them from dynamic keys.

You can fix the citation key (called pinning in BBT) for an item by adding the text Citation Key: anywhere in the extra field of the item on a line of its own. You can generate a pinned citation key by selecting one or more items, right-clicking, and selecting Generate BibTeX key, which will add the current citation key to the extra field, thereby pinning it.

† I learned this game-theoretic strategy from my father: if you aren't sure of something and are too lazy to look it up, guess the answer or ask as if you don't know. If make a guess, you are right, and no one corrects you, fine, though you won't know why you are right. If you are wrong and someone corrects you, you have learned something without making an effort. None of this was communicated explicitly--I picked it up. Sometimes it backfires and leads to tremendous reputational penalties. Against that, the embarrassment has the effect of solidifying long-term memory.

Andy · June 2023

@ZettelDistraction said:

Thanks to my inability to find citation styles the least bit interesting

I'm the opposite: I often have to switch CSL files but rarely use CSL-JSON, since I keep my bibliographic data in BibTeX format. So I didn't even think of CSL-JSON when Olivier said "a CSL file"; if I had thought of it, I would have passed over it in silence or responded with my last comment instead, which would have forestalled the response from @ZettelDistraction. But it's all good since we got to peek at some of @ZettelDistraction's data in the course of the discussion.

ZettelDistraction · June 2023

@Andy, your response to me was helpful; thank you. Now I'm more interested in CSL files, etc.

dandennison84 · July 2023

The point of CSL files, for me at least, is I can use what I would consider a more portable, easy-to-use format for reference info. Pandoc is the key here. CSL provides the styling. This is important if you want to create your own styles. I’ve done that for example with an Evidence Explained genealogy reference style based on CMOS. I can then use for any output format.

The equivalent for latex is to use an ancient postfix language to generate your own .bst files for latex. The experience is rather like using sandpaper for toilet paper

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The reference manager for note-taking

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