Roam / Obsidian Academic Workflows

Just wondering if any fellow Paperpile users have some established workflows you are using with either Roam Research (or Obsidian)?

I see some posts from last year about Obsidian and or Roam, but was curious if anyone had an effective workflow with perhaps some useful automated processes.

I see lots of discussions about Roam and Zotero, Obsidian and Zotero - but for me, I have really enjoyed using Zotero with the same gusto I love using Paperpile, so was keen to stick with Paperpile and see what I can achieve. Likewise, despite their slowness with a mobile app, I prefer Roam Research.

Thanks in advance

PhD Student - Newcastle, Australia


I don’t know which kind of workflow you have in mind, but if you keep a bib file updated with paper pile, there should be options to cite in obsidian. if you are thinking about exporting annotations or something else i don’t know.

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Don’t know if you have seen this thread which suggests a couple of ideas. Identify all annotated papers? - #6 by heumed

I’ve modified my workflow to give each paper its own page in Roam now. I usually have a line about it on the Daily Notes Page (something like 'Found #@Author2021 and a 1 sentence summary /relevant tags) and then create a new page for the paper itself with the metadata, the annotations from PaperPile, and any of my notes or thoughts.

I’d be interested to hear how anybody else is doing this.


I will share my current workflow using Workflowy. I have tried both (Roam and Obsidian) but somehow wasn’t able to connect with these applications.

Here are my steps:

  1. In Workflowy, I make a new node with the title of the paper.

  2. Transfer the annotations from Paperpile (PP) to Workflowy. I prefer the OPML format as it fits perfectly with outliner applications.

  3. For every key point, I add the page number manually.

  4. I simply drag the relevant point to my thesis node. There I either paraphrase or leave it as a quotation.


Thanks for your thoughts :pray:t2:


I just saw the other day that notes in paperpile can be exported as JSON, this suggests someone could add a plugin that lets you pull those lit notes into obsidian the way you can with Zotero. Or, use a JSON to markdown converter. I haven’t played with this yet but I was going to give it a try over the weekend.

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Over the past year, I have migrated my academic workflow to When it comes to reading and highlighting papers in PP, exporting the highlights to Obsidian, the workflow works well enough- if a little clicky and could use some QOL- but I’m not complaining. Writing in Obsidian is also a pleasure, with the ability to link, open multiple panes, etc…

However, when it is time to get it into Word for polishing, etc… I have to re-input all the citations again using the word plug in. I know markdown based workflows is on the roadmap (still planned :slightly_frowning_face:) but till then, any folks here who have figured a work around? In particular, can you get text with citations from Obsidian to MS Word intact? If so, how?

When using Obsidian & Paperpile for my Master’s, I found the best approach was to insert the cite key for the paper in my writing, where the full in-line citation would usually go. I put these into square brackets, as I’d use that linked note for my general dumping of highlights, thoughts, and such after reading and annotating.

That way, the annotation locations were easy enough to spot once I was ready for pasting over to Word. It was then a matter of double-clicking the in-line cite key, Ctrl+C to copy it, hitting the keyboard shortcut for the Paperpile Word plugin, and pasting the cite key into the paper search box to bring up the correct paper to reference in that location.

Not the slickest method, and it would be lovely if the plugin scanned through the text for all of the cite keys and did an automatic replacement, but that process just became part of my final read-through and auditing.

In the end, I sucked it up and learned to use LaTeX, partly because Word’s implementation of equations was making me very angry… The Bibtex reference worked from the citekey, and it became second nature to type /autocite{citekey} while in the writing flow.

As an aside, that workflow was similar to mine except I downloaded the .md export of highlights and imported it into Obsidian. There seems to be some difference between the Markdown generated in the browser, and for the download. The latter kept more useful formatting, for me personally.


Thanks Kyle. I just started using cite keys as well, along with the citation plugin in Obsidian and the bibtex export workflow in paperpile. From your workflow, it doesn’t seem there is an automated way to scan the cite keys in word and turn them into a bibliography.

Perhaps it can be done with something like Overleaf, but LaTex raw text still is hard to wrap my brain around; not to mention that Academia in my neck of the woods literally runs on MS Word, so I would be adding yet another layer in the workflow.

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Maybe not entirely relevant, but… I built a CLI tool (but it can use GitHub Workflows) to sync Paperpile’s BibTeX exports to Notion databases (one for articles and an optional one for authors).

Recently, though, I’ve been playing around with Obsidian to see if there’s a way to do similarly (since I’d rather use Obsidian over Notion). However, before putting time into engineering this, I’d like to see if there’s anyone else that would make use of this adapted CLI. (I’m thinking the Obsidian-oriented one would name files their citation key.)

Depending on the amount of work involved in making a plugin, something like @Kyle_Marriott’s /autocite{citekey} could be modified to mask themselves as Obsidian backlinks and nicely exported to LaTeX (I imagine this could be “easily” setup to use whatever citation commands your preferred BibTeX bibliography engine supports).

If you wanna check out the Notion-centric CLI – it’s available on GitHub. I’m currently working on expanding the docs/setup procedure, prioritizing diff syncs, and some weird Notion API response errors, but otherwise it’s ready to be used. If you’re okay with running it locally, it works without issue, but using GitHub Workflows allows it to be automatically run.


I certainly would!

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Someone is working on a plugin that can read Paperpile’s BibTeX export and pull citations into Logseq. The plugin is still in early stages and needs work.

In other news, this amazing Zotero plugin can scan your Obsidian or Logseq database for BibTeX data and link it to your Zotero database. That is, if it sees a markdown note with the ID it will tag the item and also allow you to open that note directly in the target app. I don’t know if we can even dream of Paperpile having something like this?


Has the been created yet? I looked on Obsidian, and I did not find it. How can I find it if it had been created?

It is available here. Note that this is a Logseq plugin.

It is inspired by this one for Obsidian:

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Hi April, there is a community plugin for Obsidian that will integrate your Zotero library quite nicely, and allows you to pull metadata across from your exported bib file, e.g. to create literature notes - just search for ‘Citations’. There’s also Reference Map, which adds a reference sidebar listing full refs for all work cited in the note, and Zotero Integration for creating citations and importing annotations.

I did try this workflow with a .bib. file exported from PaperPile, but it didn’t like the downloaded bib file for some reason.

I use the citations plug in on Obsidian and simply use the path to the paperpile bibtex file in google drive (on my computer). It works like a charm, very little delay if any between adding a new citation in the browser extension and it being available in the bibtex file. I also use the same process for Zettlr for my writing.

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