From permanent notes to a manuscript: Pandoc

As permanent notes start to emerge from processing my reading, I have the basis to create (parts of) manuscripts from the bottom up—i.e. where I used to start a manuscript with a blank page, now I write manuscripts by looking at stuff that I already have a lot of notes on. At present, my workflow to convert permanent notes into a manuscript is still very preliminary, seeing as I have only created two 10-page manuscripts with this method. To create these short documents, I used Pandoc in combination with a Keyboard Maestro automation that I can reuse for manuscripts with similar characteristics. (See Nicholas Cifuentes-Goodbody very basic but excellent video on Pandoc)

For this automation, I created a folder in my vault where I store a style sheet (a Word template with my preferred formatting), a bibliography file (.bibtex), a reference document (.csl) in my preferred citation style, and a Markdown document titled “”. Whenever I want to convert a simple (i.e. one Markdown file) manuscript, I copy-paste the text into the “” file and run the following automation in Keyboard Maestro:


# Go to the correct directory
cd "/path/to/manuscript"

# Generate the Word file
pandoc -s -o Output.docx --reference-doc "./Style Sheet.docx" --filter pandoc-citeproc --bibliography "./MyLibrary.bib" --csl "./MLA.csl" 

# Open the Word file
open Output.docx
Screenshot of the document conversion macro in Keyboard Maestro

You can find the style of choice (.csl) in the Zotero Style Repository, and you can generate a bibliography (.bib) by exporting your Zotero library. You can make a reference template (.docx) pretty easily by formatting the styles in Word and adding them to the document’s “template”, but just in case you want something quick, you can use mine:

You can download my Keyboard Maestro macro here.

Please make sure to add variable paths to the folder that contains all your documents (i.e. the, the .bib, the .csl, and the .docx):

This Keyboard Maestro automation generates a .docx document that I can tweak before submission by adding things that would be too cumbersome to do with Pandoc for simple manuscript, such as adding logos or headings. In those cases where I have to use a different style sheet or citation style, I can use this automation as a basis.

Writing the manuscript—as opposed to writing literature permanent notes—is a whole other beast and I cannot give much advice there. All that I can say is that much of the behind-the-scenes work happens outside Obsidian: the information I record in my permanent notes gets transferred onto mind maps, post-its, and spreadsheets so I can have more visual outlines in addition to tentative chapter-outlines within Obsidian. As I am writing my manuscript, I look at (and copy paste from) my permanent notes and these visual aides constantly, adding and changing bits to create a linear narrative that connects everything together. This video by James Heyton, as well as other videos by him, is currently helping me to structure the content of doctoral dissertation manuscript. These are some old pictures of visual aides:

Mindmap of Death and the King’s Horseman I made for a paper
Picture of my very messy office when I had to write the first draft of my dissertation’s literature review

What I can say, however, is that the Zettelkasten method has fundamentally changed my view on notes vs. manuscripts. Before, I made no clear distinctions between my manuscript and my notes. This inevitably led to much wasted effort and stubbornness: I did not want to delete parts of my manuscript because I was afraid I would waste the hours of effort that had gone into writing down and developing those ideas, and I would then end up with manuscripts that had a lot of tangents that did not contribute to developing central ideas. Now, I can more clearly separate the separates permanent notes (i.e. objective information, observations, and general ideas) and the manuscript (i.e. those pieces of information, observations, and general ideas in context) from each other: a manuscript is nothing more than a (highly polished) linear representation of a web of information, ideas, insights, and connections that exist between permanent notes at one given time. Permanent notes, in other words, will never be manuscript-ready, and, therefore, it is okay that they sometimes only consist of one or two lines and a long “scholarship” section, or that some only contain bullet points. Permanent notes should contain the building blocks which you can transform into an end product—they are not the end product itself.

That’s it! If you want, you can circle back to the first post of this guide to read my conclusions.

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