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My workflow (with Zotero and Zettlr)

Following recent discussions on here, here's a shortened text version - original with images is here. In the spirit of "working with the garage door open" I'm using a task that I'm working on right now.

The task

I'm writing a book review for a magazine from one of my professional bodies.

Create a new note for the book

This is not the note that will become the review but will instead come to contain either a summary or an index of more detailed notes about the book. I want to make a link here between the note about the book, and the book itself, but this needs a little more work elsewhere first.

Create a new note for the book review

I know that I'm going to need another new note, so may as well make it now. This is what will become the book review.
In this case, the title is the name of the book, and keywords 'book_review' because it's a book review, 'xyz' for my eventual personal publication site, and 'BACP' for the professional publication.

Add some links

I link the general note about the book and the review to each other. I also link (or index if you prefer) the note for the review from (or in) [[§ Now]], as it is something that I am currently working on.

I still need to make some connection to the book itself, which comes next.

Organising notes

[[§ Now]] is an index of current work. These are things that I am actually working on, not everything that I want to do at some future time. That bigger list of things that I'd like to do or think about is kept in [[§ In My Mind]] so that I don't have to actually keep it all in my mind. I think of this as a hierarchy, with [[§ In My Mind]] being the top level and [[§ Now]] as a current to-do type of list. The § at the front of the filename ensures that I can sort alphabetically and have these top-level notes at the top of my directory listing.

I am currently going with the default YYYYMMDDhhmmss.md file format within Zettlr for all note filenames. Please be aware, I have changed my mind about this several times already, and no, I have not studiously gone back and updated all of my previous notes to reflect the latest format every time (gasp!). If you are new to this way of working, then just start, and don't worry about everything being done 'right' straight away.
I then use a standard format for the text (body) of the note which includes a YAML title and keywords. I could type this in every time, but life is too short for that so I have a TextExpander snippet that puts this in. Again, this is an evolving concept, and updating the TextExpander snippet as my preference emerges is trivial work. TextExpander is not open-source, but I have not found a better option so far.

Deal with the book

It arrived in the post, and after a quick flick through I'm looking forwards to reading and reviewing it. I want to be able to reference it, so I need to add it to my reference manager.

Add the book to Zotero

Zotero is an excellent reference manager, and it allows you to cite from your collection in Word, LibreOffice, and (with some very minor work) Zettlr. I usually add books by their ISBN or DOI, and then check that the auto-filled details are correct. I use the Better Bibtex plugin which keeps a JSON version of my Zotero library always up to date. I have already told Zettlr about this (see the Zettlr documentation for how to do this, it's very easy) which means I can now cite the book within Zettlr.

Link the book to the notes

Now I can add the citation to the book note and the book review note. A simple @ and I can search for and then cite the book. Following the link will open the book entry in Zotero, and if I had a PDF version also in Zotero, I could open that.

Notes we have so far

  1. [[§ In My Mind]] - The top level note of my life, which has a link to...
  2. [[§ Now]] - What I am currently working on. This has a link to…
  3. [[20200628161052]] Out Of The Shadows Book Review - This is linked to the Book Note, is currently indexed in [[§ Now]] and cites the book's entry in Zotero. When it eventually comes out of [[§ Now]] (because the review is completed) then this note will not be indexed anywhere else. If I write several reviews, then I might create a Book Reviews index note.
  4. [[20200622165143]] Out Of The Shadows - This is the note about the book, and is linked to the Book Review Note. It also cites the book from Zotero, but is not currently indexed anywhere. If I end up with a lot of these then I might create a Books Index note, but for now the full-text search and the book_review tag (aka keyword) is enough for me to find it whenever I need to.

Read the book and make notes

This might sound obvious. But there are things to consider at this stage too.

For physical books

As in this example, I will be making notes as I go in a separate paper notebook. I tend to ensure that I have at least a chapter summary for every chapter, and then any specific ideas I want to capture get their own note. This format works well for academic books, but for fiction, it makes less sense so I stick to themes and specific points of interest for those.

For PDFs

I highlight and annotate as I read, using standard MacOS Preview and iOS PDF handlers, making sure that every highlight has an associated note. As with the paper version of this process, I end up with chapter summaries as well as notes for specific ideas.

Zotero and iOS

One of my few frustrations with Zotero is the lack of a native iOS app for Zotero. Some people still have success syncing their Zotero library with the Papership app, and this still works for me, although there are numerous reports that Papership is no longer actively developed, and of this process being unreliable. Alternatively, you can use the Zotfile plugin to manage moving documents between devices. There is a web interface for Zotero, which works well for viewing and searching your collection, but I have not been able to use it to update highlights or notes in PDF files.

Extract the highlights and notes from the PDF

I use the excellent Zotfile plugin for Zotero, which automates this process, creating a note in Zotero linked to the book entry in Zotero, with all of my highlights and comments in it.

Put the notes into Zettlr

This is, after all, the point.

Chapter summaries

I usually leave these in the Book note I created earlier. But if they are becoming unmanageable, the book note becomes an index of the chapter summaries and whatever else I am recording.
A chapter summary may also include links to ideas or themes that appear elsewhere in my zettelkasten. This is the beginning of making sense of the wider body of knowledge ad idea that I am creating.

Notes for ideas

As is the Zettelkasten way, each idea (or theme) gets it's own Zettlr note, using the same template as before. As with the Book note, I also cite the book in the idea note (with additionally page or chapter references for specificity), which keeps things tied together.
Ideas are the building blocks of my zettelkasten, and so I am likley to make connections in this new idea across different notes that already exist. Maybe they coalesce and form a more consolidated idea or theme, maybe they spark a whole new concept (and so a whole new note).

Write the review

Now I can begin to write the review. I usually link any notes that I want to include in whichever section is relevant, and then gradually replace the links with the text of my review as the piece comes together.

Tidy up

When it's done, and therefor no-longer a current piece of work, I will remove the book review note from the [[§ Now]] note.

Comments

  • Thanks very much jadcx,

    My conversion to zettlr has been recent and your description helps. I have been using zotero for years and have a enormous collection of pdf's I use for research, and pleasure.

    Writing a difficult thesis was hampered by many things, LibreOIffice became a stumbling block in the end.

    I am now tacking my time in order not to waste time. End product is a pdf typeset in Tex through conTEXt (the template is being constructed), paragraph numbering throughout, lengthy quotes in endnotes. In a decade I am sure that will not needed at as a digital reference to the original work will give the context, and the note will merely qualify its use.

    Scholars forget that notes are a courtesy to the reader, not proof of authority that only well read academics can decipher. Plus too many academics are too narrow in their reading and too many well read of poor works --- electronics is turning this around (slowly).

    Zettlr is by far the most elegant solution for many needs. Stories of how it is being used are very impoirtant.

    Greg Schofield, Perth

  • @Greg_Schofield_Perth said:
    Thanks very much jadcx,

    My conversion to zettlr has been recent and your description helps. I have been using zotero for years and have a enormous collection of pdf's I use for research, and pleasure.

    Happy to know that it has been helpful.

  • Thank you jadcx !
    That's really helpful.
    Let me know the answers to my elementary questions:
    [Add some links

    I link the general note about the book and the review to each other. I also link (or index if you prefer) the note for the review from (or in) [[§ Now]], as it is something that I am currently working on.]

    How exactly do you do it?

    [Link the book to the notes

    Now I can add the citation to the book note and the book review note. A simple @ and I can search for and then cite the book. Following the link will open the book entry in Zotero, and if I had a PDF version also in Zotero, I could open that.]

    I've downloaded a pdf book to Zotero. I open both Zotero and and a note in Zettlr and from this point :smile: where do I put my simple @ to get the trick? Or what should I do to connect my not with a particular book or article in Zotero?

  • I’m also wondering how the @ symbol is used.

  • It's great that this has been helpful. It would have been even better if I provided the correct link! So try here for the post with images!

    @Mike
    Adding links:
    Let's assume that my book review note is called 20200628161052.md and has the YAML title: Out Of the Shadows Book Review. The full YAML block looks like this:

    ---
    title: Out Of The Shadows Book Review
    keywords:
    - book_review
    - xyz
    - bacp
    ...

    To add a link to in my [[§ Now]] note (which is just a list of links to notes that I am currently working on) I would add:

    * [[

    This opens in the in-line search, where I can search for and find the book review file. I select the correct file, and the finished entry in [[§ Now]] is:

    * [[20200628161052]] Out Of The Shadows Book Review

    @Mike And @Feuizl
    The @ citing
    First, you need to set up a JSON source. Using Zotero is easiest, and is already well documented here.

    Then, typing @ will open an in-line citation search, similar to the note search above, where you can select the entry from your exported Zotrero library to cite. This is also documented already here.

  • Ah, I see. Thank you @Mike

  • Literally integrating Zotero & Zettlr

    Warning

    I found to my cost that using Zotero's server as a backup device does not work well for this form of integration — only the recognised file types are preserved, everything else is purged from folders. The zotero storage directory needs to be separately backed-up.

    Putting Zettlr into Zotero

    Dropping Zettlr.appimage into Zotero marking it as "software" means it can be launched from there, but making a sympbolic link of it means it can be placed in the desktop environment. The zotero reference is like any other, which is useful to keep track of things:

    Erz, Hendrik. Zettlr (version 1.7.0 beta 13). Appimage. Markdown Writing Environments. Germany: Zettlr openSource, 2017. https://www.zettlr.com/.

    The app.link is dropped into a desktop directory Zettelkasten In Zotero I drop in template documents, for instance illustrations are made in Inkscape SVG, a blank SVG file is dropped in and renamed "Ricketts' chart" and identified as 'Artwork' similar to the 'Software' reference to Zettlr. I use the Zotilo add-on's "Copy attachment paths" to put it's pathway into the clipboard, and a small script that spearates the file name from the directory path and puts into the /Desktop/Zettelkasten/img/ a link to the zotero directory, renamed (-.svg) to "Ricketts' chart". After making the illustration I export a PNG version for the publication into the same directory Zettlr treating the 'links' as its own directory paths.

    This can be done with virtually anything, a MD file template a note collection, every note saved into that folder, liked into the desktop is in Zettlr and Zotero: Bibliographies, CSL, Text preambles, etc.,

    In this I get the best of both worlds, a library system for my work as archive and formal self-reference (the environment as its own bibliography), and a Zettelkasten markdown environment for doing the work. It is early days,k but it appears to be working fine (see Warning).

  • Wait … I may have missed something, but do I understand you correctly, that you launch Zettlr like a PDF? :lol:

  • That's an interesting use-case @Greg_Schofield_Perth - I'm not sure why I would want it, although I'm also not sure I fully understand it, but I'm intrigued anyway :smiley:

    Can you explain the image workflow with a little more detail, as the file renaming and linking doesn't make sense to me? For instance, how is the final png linked to anything?

  • @hendrik said:
    Wait … I may have missed something, but do I understand you correctly, that you launch Zettlr like a PDF? :lol:

    Me being unclear. It is dropped into Zotero like a PDF, but all that does is create a directory in storage if the and appimage. I can eithher view the file (open thhe directory) or make a symbolic link of the directory and double click the image to open it. I am on Linux so I made a .desktop file that appends like any other app.

    The only advantage is that it keeps the links in zotero environment.

    I put everything into Zotero, including the Bib.json and CSL files --- the main idea is that in the future if I am looking for anything I can use Zotero as a the search engine.

    I apologize for the confusion. My system suffered from a excess of files of all kinds I have been using Zotero to classify, organize and hold them. I spent far too much time trying to remember obscure filenames, now I treat everything as some kind of publication,

    Greg

  • @jadcx said:
    That's an interesting use-case @Greg_Schofield_Perth - I'm not sure why I would want it, although I'm also not sure I fully understand it, but I'm intrigued anyway :smiley:

    Can you explain the image workflow with a little more detail, as the file renaming and linking doesn't make sense to me? For instance, how is the final png linked to anything?

    Sorry jadcx part of the reply is in is in the post above.. I was working in libreoffice until now. Part of my research included nearly 1,000 maps, which I digitally downloaded and referenced. I had to find old lease borders so a subset were given coordinates for overlay maps (QGIS), each of these had to be saved in a Geotiff format, the original in jpeg, both were saved into the same zotero folder, hence they could be found easily.

    I then applied this to the ethno-mapping I was doing, and later in illustrations used to trace smallpox disease outbreaks in 1789, each step had its own collection of sources (written and graphic) the SVG file used to create the artwork in Inkscape and a PNG file for publication, using layers inkscape might be used for show various stages with the result that there would be 3 or more PNGs all related and hence belonging together --- this is working well. Plus the 22 regional maps produced in QGIS were rendered in Inkscape and produced their own sets (x3) of PNGs.

    I had tried many different systems, but this has been the most sustainable, especially when I find something new and need to incorporate into illustrations already in Libreoffice. I am an expert on what doesn't work!

    Problem I unambiguously finding the right file without opening is where Zotero excels. But Zotero is a library not a workroom. Zettlr gives me the workroom, so I can funnel what I need into its environment.

    II hope this make sense, Besides the 1,000 maps, I have piles of old newspaper articles, official documents, eyewitness reports, books and articles. The quoting is extremely important, and the number of items beyond me except for these electronic aides.

    Originally I was spending more time looking for stuff I had, than doing anything with it, that is radically turning around.

  • That makes a lot of sense @Greg_Schofield_Perth. I'm very tempted by some kind of all-encompassing asset/knowledge management solution and have looked at DevonThink many times but have not yet taken the plunge and splashed the cash. For now, Zettlr works well for me, and I can comfortably live with the built-in search (on Mac it seems pretty good anyway) to find things that are not in my Zotero library.

  • jadcx I have a chart, based on Dr Ricketts's report of a smallpox outbreak in London in 1892, it was vital because he showed how and when and at what stage of the disease the smallpox was spread I named the file "Ricketts's Chart: Smallpox 1892..svg", which is thhe name used for the 'Artwork' reference in zotero, but zotero's directory for it is "EAH9WPPR", no good for human beings or as a Zettlr directory.

    As a link file I can name the directory whatever I like, so I call it "Ricketts's Chart: Smallpox 1892", and the same name is used for the Inkscape file with .svg, but all the pngs exported will be given convenient titles for placement Rickett.01.png Rickett.02.png. whhen I need to work on or place it, I can easily navigating to it from the Zotero or Zettlr end of things.

    I am not opening files to see which one it is, or running down long lists. I get tighter control over the mechanics with little effort. It would be overkill for many projects, but I can see documents markup and filing (zotero) and note-taking, writing and publishing via zettlre , could be more collaborative, and take on large complex projects with less stress, by a library workroom combo.

    Greg

  • @jadcx I had not seen DevonThink before, not being Mac for many years. Looks interesting --- thhanks.

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