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Joplin for research

I'm thinking of using Joplin as a knowledge bank for my research work. Ideally I'd be able to save papers, annotate/summarize them in an easily searchable way. I'm wondering if anyone in the awesome community here has a workflow for this!

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You can find useful workflow examples spread throughout different forum topics, which admittedly isn't a particularly time-saving hint. But I often find new ideas for workflow in discussions that start with someone unhappy with Joplin as compared with some other application. Sometimes the new ideas stem from users explaining why they came back. Forum searches aside, I'll start things out here with some lessons I learned in porting over thousands of notes from Evernote. I'm not as experienced other users however and only use three plugins. You can look through the available plugins for other examples of adapting Joplin to particular needs/workflows.

First, a caveat: Joplin is design for quickly recording and retrieving notes. It's not designed for annotating or searching within documents you might attach to your notes. You can attach a PDF, for example, and so have an archive copy so to speak in the database. You can then view the contents of that PDF within Joplin or click on a link within your note to view the PDF in an external viewer or PDF editor. So far as I know you'll have to rely on an external program for searching within a PDF or annotating it. Ditto for documents generated by Microsoft Office programs, or generating OCR information from images. I don't often have the need to search within such documents, YMMV. On important PDFs such as court decisions or equipment manuals, I've created notes comprised solely of the PDF and its link, with unique terms/topics in text underneath to aid later searches. And of course you also have the basic search tool refinements of tags and notebooks.

When it comes to organizing information, I use the Favorites plugin so I have a lower-left pane with a short list of project note titles. The project notes serve as virtual desktops and make it easy to pick up where I left off when I need to shift contexts. Those notes contain not just text but also links to various other notes so I don't have to resort to searching for resources I often use. You can also save notebook and tag names to your Favorites, which will narrow the note list results accordingly.

For more specific search queries I use the Embedded Search plugin. As an example, when converting Evernote notebooks I was annoyed to discover internal links between notes were stored as URLs generated by Evernote's server. Not particularly useful. So I created a Shards note on my favorite list. The contents of that note included ```search "www.evernote.com/shard/" which automatically generated a list of notes lacking Joplin note title links. You can have multiple searches within a note so the top of a note could for example have "notebook:Resources tag:verified" and the bottom "notebook:Resources -tag:verified".

For long notes, use the various levels of markdown headings. You can then enable quick navigation by putting "[TOC]" at the top, which will create a set of navigation links based on those headings. I also find topic headings useful for the Folding in Code Mirror Editor plugin, which enhances the markdown editor pane with collapsing/expanding headings. It functions like a folder/directory navigation tree in other applications. I find it useful for removing information clutter when focused on writing/editing a particular section of a note's text.

That's all that springs to mind from my rudimentary Joplin workflow. Have fun exploring Joplin's many possibilities.

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I saw the other day that logseq supports now embedding PDFs and copying highlighted annotations into the notes: Initial pdf support on Logseq desktop app

I'm not sure if a plugin could do something similar?

Joplin supports embedded pdfs and you can copy text from a pdf and insert into a note. Am I missing anything?

In my ideal Joplin world, I would create a note on Joplin desktop, insert a PDF into a note, have the note synced to my tablet, annotate and/or draw on the PDF and have the changes synced back to Joplin desktop

Is there a lot of info to store in the notes themselves?
Because if its just some remarks can they be in the annotation of the pdf?

If thats the case I wouldnt use Joplin notes as a sync vehicle but use native pdf editing in combination with cloud storage.

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Hi,

From my point of view, for PDF annotations, a good solution is to make Joplin and Zotero work together. The new annotation system of Zotero is very efficient and allows to export annotations of a document in markdown format. I export it in a folder which is automatically imported in Joplin thanks to the hotfolder plugin.

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Is there a lot of info to store in the notes themselves?
Because if its just some remarks can they be in the annotation of the pdf?

Yes, the PDF would just be a small part of it. I took PDFs as an example for its versatility, but it could just as well be a Powerpoint presentation or just a picture to scribble on instead. At the moment both the IOS and Android version of Joplin support read-only resources only. I would have to save a copy of the file on my tablet, edit it and somehow import it back into Joplin. This would add way too much friction.

From my point of view, for PDF annotations, a good solution is to make Joplin and Zotero work together. The new annotation system of Zotero is very efficient and allows to export annotations of a document in markdown format.

That would be nice indeed! Are you referring to the Zotfile plugin for markdown export? I read an interesting post on how to use Zotfile on Hendrik's (Zettlr) blog, which would be applicable to Joplin as well.

I've been playing around with another Zotero plugin called Zutilo. Zutilo can generate URI's using the "Copy Select Item Links" which can be pasted directly as a link into Joplin. Clicking on them will open Zotero with the referenced item pre-selected.

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With Zotero beta you can access to annotation feature. Their goal is :

Annotations are stored in the Zotero database, not in the PDF file, which allows for much more advanced functionality as well as fast syncing. The File menu contains a new option to export PDFs, which will convert any Zotero annotations into standard annotations in the exported file. (An upcoming version will let you omit annotations, but in the meantime you can drag files to your filesystem to copy just the file.) Similarly, when exporting metadata from your library, there's a new “Include Annotations” option under “Export Files”. We plan to support other ways to export annotations in future updates. Your annotations will never be locked in Zotero.

For export to markdown, i use the excellent zotero-mdnotes.

That's a very interesting subject !

As a PhD student, I use Joplin very extensively for all notes related to my experiments and research : that way, I get to keep all of the tiny details that can often become important when you have to justify this or that result, or improve your methodology in some way.

As to processing scientific literature, I'm currently trying a new approach to it. It might not be the right one, but for now, it seems to suit me. For that, I try to move more and more away from a one article = one note format, which I find not very practical. Instead, I'm trying to extract what I find interesting in an article into notes related to different subjects. I do so because in my own mind, I often find myself not searching information related to a particular article, but to a particular topic.

For example, let's say that I'm reading an article that is about estimating forest biodiversity with remote sensing data (e.g. satellite imagery). Instead of making one note for this article, or highlighting things in it, I keep Joplin on the side and extract what's interesting:

  • They use a new methodology that is interesting. I add some details about it in a note named Remote sensing methodology for biodiversity.
  • Their introduction contains interesting references that I might read later. I add these to a note named Articles to read.
  • Their figures are beautiful. I can add some screenshots in a note named Examples of pretty figures for inspiration when I'll have to do some.
  • Their discussion are interesting, and concern several topic that are of interest. I'll write some things about it, along with some citations and comments about the limits of their study, in different notes related to what they say : Biodiversity decline, Forest responses to climate change, and Biases in remote sensing methods.

Once this is done, if everything goes well, I will not have to read this article anymore. This avoid the work of thinking about or finding the articles related to a topic I'm thinking about, since the article I read are encapsulated into specific "topical" notes. This also avoids the work of having to re-read parts of the article to find the juicy bit about what I wanted to find or remember, since the important part is clearly cited in the notes. I also hope that this will make it much more easier to synthesize information related to different topics, as this allows for some easy comparison between the content of different articles.

To finish, all of these notes that I'm doing are in the Zettelkasten format, to make their retrieval and connection between them easier. If you want to read more about it, I wrote an online workshop to implement this method in Joplin !

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Sorry if I repeat myself; but after discussing the same subject with some friends today, I came up with a small visual. I just find this topic so interesting !

The visual represent the difference (to me) between finding interesting information based on the source (as with the one note = one article format); or finding information based on the topic (one note = one topic format, like with the Zettelkasten method).

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Yes, I agree with that. That's why I use Zotero because the annotations are separated from the document and I can reuse them for other projects or parts of them. By the themes I explore I also make a kind of Zettelkasten which includes well cards that present structures or concepts. When I mention this note in writing documents or more ephemeral notes I have a backlink.

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Maybe you can contribute to this topic ?

The main obstacles at this point for direct use in Joplin are:

  • It is impossible to select text in a PDF and drag and drop it into the note.
  • If you select a piece of text in a PDF and copy/paste it into the note, the PDF viewer returns to the beginning of the document. Because the focus was given to the note the PDF preview is updated. To work on a big document it's really very annoying.

Without this, I would dream of being able to read and take my notes directly from Joplin

Yes, I can certainly see how this can be annoying.
Maybe switching from the built-in pdf renderer to something like pdf.js could help here.

That would mean I have to get out of Joplin...:scream: I'm not used to it anymore :wink:

No, I meant if Joplin could use pdf.js instead of electron's built-in renderer

Oh yes! In that case it would be perfect :+1: