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Academic Workflow - Any Suggestion for an Application/s?

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Posted by Matthias Steffens
Feb 24, 2020 at 03:18 PM


Paul Korm wrote:
> Keypoints looks interesting, but is it different than Highlights?

The basic idea behind Keypoints is indeed similar to Highlights app, i.e. while highlighting text in a PDF, the app extracts these highlight annotations as Markdown text.

That said, there are a some major differences between the apps:

1. Keypoints stores all of its highlight notes as *individual* (Multi)Markdown notes, and each highlight note will be mirrored as an individual plaintext file on disk.

2. All notes are self-contained, i.e., for each note, Keypoints automatically adds a link to the associated PDF file, the PDF annotation info, creation date and (if possible) the bibliographic metadata from your reference manager.

3. Keypoints is a document-based app where each document can contain notes from many different PDF files. Since the generated notes are independent from each other, they can be filtered/gathered freely. When you select a note, its associated PDF file will be automatically opened in the app’s PDF preview, and the PDF will be scrolled to the location containing the original highlight/quotation.

4. Each highlight note has its own unique ID and can thus be linked to other notes (e.g., via drag & drop).

5. Besides adding your own title & comments to a note, you can also assign (via drag & drop, autocompletion, or keyboard shortcut) any keyword(s), a named color label, and/or a rating. These elements help to organize/filter your notes.

6. The organizational note elements (like labels, keywords or links to other notes/files/publications) are hot-linked/clickable and can be used to form a browseable network of notes (which can also be visualized). The app also offers buttons (and swipe gestures) for easy back+forth navigation thru your history of searches & selections.

7. Keypoints parses all recognized elements (title, quotation, page & annotation info, label, creation date, rating, keywords, links to other notes/files/publications) from the plaintext notes, and populates its data model properties with these elements. This, for example, allows to search, filter or sort by just these elements. Plus:

8. Keypoints is heavily scriptable and exposes most of its data model properties via scripting. This means that you can form advanced queries or directly set a note’s property like its title, label or rating etc (you can also do this for many notes at once). Keypoints will then automatically update the note’s text accordingly.

9. Under the hood, Keypoints has the data model of a full-blown reference manager. While this helps with fine-grained metadata imports, this currently isn’t used much. But it may allow for further bibliographic features in the future (like auto-fetching of academic PDFs), and sound integration with reference managers like Bookends, Papers or Bibdesk.

MadaboutDana wrote:

> Dang, Keypoints looks very interesting - nice website already!
> I’ve subscribed so I can get updates. Best of luck with that!

Many thanks, it’s much appreciated!


Posted by Paul Korm
Feb 24, 2020 at 03:25 PM


Thank you for the long and thoughtful reply, @Matthias Steffans.

I’m sold!  Is there a beta?  I’d love to get started.


Posted by Matthias Steffens
Feb 24, 2020 at 04:06 PM


Paul Korm wrote:
>I’m sold!  Is there a beta?  I’d love to get started.

Thanks! Unfortunately, there isn’t a release yet, not even an alpha one. I still have some work to do, esp. on system compatibility, and there are a few bugs that I really should fix first. I’d love to offer a release today, but since this is a part-time effort for me, it still may take a bit until I get there. Sorry for that & thanks for your understanding!

That said, if you’re really advantageous, I may be able to send you a private build. Note that this wouldn’t be meant for productive use but rather as a means for initial testing and to give feedback. You can contact me via https://keypoints.app/contact/ if you’re interested.

Thank you,


Posted by Darren McDonald
Feb 25, 2020 at 03:34 PM


Hello Matthias :)

Wow! Keypoints is exactly the application I am looking for! Thank you very much for posting to me the forum. It is wonderful to have you and your talents work on development for this application. :)

I would have responded earlier with a post, but I was working on a chapter for a book.

During the writing of the chapter, I put to the test the workflow I worked out and found that my biggest problem was finding the citations and my comments I had spent many, many hours collecting. I wasted a lot of valuable searching for the citations and comments which had me often losing my train of thought. The solution you have developed in Keypoints looks like the application I need!

Your explanation about how you have managed to link documents with citations/notes has me really excited:

>Since all your highlight annotations are self-contained plaintext notes,
>you can search and filter them freely, and gather them again in
>structure/overview notes. Selecting a note will also jump to its quoted
>text in the PDF. And clicking a highlight annotation in the PDF will
>select its note.

The only thing that scares me is the use of markdown. I work with rich text because I have a hard time reading and mentally processing markup. I am trying to get over this, but at the moment I am using applications like Scrivener rather than Ulysses for writing. But don’t try and accommodate me regarding this issue in your development at the moment. I do not want to slow development down.

I will give you more feedback on the information you have posted. However, it may be difficult without being able to try the application out.

For now, I just wanted to say a big thanks for developing Keynotes! :)

Cheers! :)



Posted by Matthias Steffens
Feb 26, 2020 at 11:12 PM


Hi Darren,

many thanks for the motivating feedback, it’s much appreciated!

> The only thing that scares me is the use of markdown. I work with rich text because I have a hard time reading and mentally processing markup.

I see, and I understand that formatting markup can get distracting or make things more complex. However, in Keypoints, I choose plaintext as a base format for the notes since this is the most stable & future-proof format.

And adding some very simple Markdown markup (like # for the “title” heading, > for quoted text, or *emphasis*) may be all you need to write your note. In Keypoints, when you select some text in the PDF and create a new note from it, the note’s title and quotation get already created for you (in Markdown syntax).

Other note elements can be added by drag & drop or a menu command / keyboard shortcut. As an example, take a look at the text note displayed in this scrrenshot:

The note contains some quoted text that was highlighted (the text with the light blue background), a link to another note, links to publications (linked via their cite keys), a green label, a (one star) rating, and some keywords. While it’s true that all of these elements require some syntax, they can all be added via drag & drop and/or menu command / keyboard shortcut. And after insertion of an element, its markup is printed in light grey which helps to focus on the content instead.

This approach strives to have these elements both human readable AND machine readable (which I think is crucial). If the notes were only human readable instead, it would be very difficult for an app to add smart features on top of it (like, e.g., the visualization of note connections, or the direct manipulation of note elements via menu/scripting commands). IMO, the Markdown syntax is a good compromise which allows for notes that are both human readable and machine readable.

That said, I plan to offer rich text (RTF) as an export format. That way, one could push all notes to, say, DEVONthink or Scrivener and further work with the notes there.




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