Jason
Posts: 4
Joined: 24-Jan-2018, 16:56

Workflow

24-Jan-2018, 22:26

Greetings

I'm interested to hear what apps & workflows people are currently using in order to facilitate PDF annotation and note-taking. What are the most important aspects of your (current or envisioned) workflow?
My Current workflow needs to be less complicated and cumbersome.
Currently, I use:
  • DevonThink Pro (ubiquitous file storage and PubMed queries - which are then exported to...)
  • Papers-3 (I like this reference manager but it has some shortcomings: it's no longer under development)
    • Highlights and notes are not seen in other apps
    • Highlights and notes made in other apps are not seen in Papers-3
    • Difficult to warehouse or develop a lab repository for current and future students
    • Difficult to collaborate with colleagues, especially those who aren't using Mac
    • As a LaTeX user, I am constantly exporting the entire library while working on a project
  • Skim (for reading, highlighting, annotating, and taking notes on PDFs
    • This is problematic when working with PFDs outside of Papers-3
  • Tinderbox (for trying to organize and link various notes and concepts developed during the reading and conceptualization process)
  • LaTeX
  • BibDesk
  • Text Shop
I long for some way to:
  • aggregate all the annotations I make to a PDF
  • have the application scriptable
  • automate some tasks
  • search, sort, and sift through my annotations
  • organize annotations in various ways (e.g., topic, author, findings, information in the body of a note, etc.)
  • making the information somehow visible to other applications
  • have the ability to go from a note directly to a PDF
  • the ability to link a note to multiple PDFs
I will update this as other ideas occur to me.

Cheers,
Jason

msteffens
Site Admin
Posts: 10
Joined: 17-May-2017, 14:28

Re: Workflow

25-Jan-2018, 23:26

Hi Jason,

many thanks for describing your workflow and tools!

W.r.t. annotations made in Papers 3 not being seen in other apps: I've previously written a few scripts to export note+highlight annotations from Papers 3 to, say, Finder folders of individual files, the clipboard, DEVONthink, Bookends, or Evernote A script which would export all note+highlight annotations to Skim likely would be also possible.

Having been part of the Papers Mac team until it was bought by Readcube, I also find it quite saddening that Papers 3 isn't being developed any further. And I guess that the upcoming Papers/Readcube merger likely won't be scriptable. Since Papers 3 is scriptable, Keypoints can integrate with it to automatically look up citekey & reference info when creating notes for a PDF that's stored in your Papers library.

In addition, Keypoints can be setup as a viewer for PDFs double clicked in Papers, so it's easy to quickly see all notes for a certain PDF in your Papers library.
I long for some way to:
  • aggregate all the annotations I make to a PDF
  • have the application scriptable
  • automate some tasks
  • search, sort, and sift through my annotations
  • organize annotations in various ways (e.g., topic, author, findings, information in the body of a note, etc.)
  • making the information somehow visible to other applications
  • have the ability to go from a note directly to a PDF
  • the ability to link a note to multiple PDFs

Most of these things should be possible with Keypoints, and are (partially at least) already implemented: aggregating, scripting, searching, sorting, grouping by keyword/label/publication/file, automatically jump to PDF, etc.

Other things from your list are planned, like sharing of info with other apps or users. I'd also love if my app would be able to push notes to a static site generator so that you could easily publish your notes and share them publicly on the web (or within your research group's intranet). In general, one of the goals with Keypoints is that your notes should be reusable as much as possible, and that they can be exported or shared in various ways. This is still work that needs to be done, though.

W.r.t. automation of some tasks, could you give some examples of tasks that you'd like to get automated?

The last item on your list is the only item where I'm not really sure if this can be supported in Keypoints. In Keypoints, a note is usually connected to a single PDF file (and publication). However, you can, of course, insert links to other files (or notes, publications, keywords, labels, etc) into a note. In what situation would you want to link a note to multiple PDFs?

Thanks,
Matthias

Jason
Posts: 4
Joined: 24-Jan-2018, 16:56

Re: Workflow

19-Mar-2018, 18:55

Sorry for the delay in getting back to you. Life...
W.r.t. annotations made in Papers 3 not being seen in other apps: I've previously written a few scripts to export note+highlight annotations from Papers 3 to, say, Finder folders of individual files, the clipboard, DEVONthink, Bookends, or Evernote A script which would export all note+highlight annotations to Skim likely would be also possible.
Given that Papers3 doesn’t seem to be under development any longer, I will likely migrate to something else. This is really sad for me because Papers has the features I want in a reference manager. Nothing else out there seems to have all the same features. As I use LaTeX, BibDesk would be a logical move, but it doesn’t auto-populate all the fields like Papers3, especially when dragging and dropping and PDF. Highlighting the text to specify each of the fields is just a pain...
Most of these things should be possible with Keypoints, and are (partially at least) already implemented: aggregating, scripting, searching, sorting, grouping by keyword/label/publication/file, automatically jump to PDF, etc.
Awesome 👏
Other things from your list are planned, like sharing of info with other apps or users. I'd also love if my app would be able to push notes to a static site generator so that you could easily publish your notes and share them publicly on the web (or within your research group's intranet).
Very nice! 👍
In general, one of the goals with Keypoints is that your notes should be reusable as much as possible, and that they can be exported or shared in various ways. This is still work that needs to be done, though.
Very good. Let me know if I can help in any way.
W.r.t. automation of some tasks, could you give some examples of tasks that you'd like to get automated?
Off the top of my head I was thinking of something like: Having a rule or agent type of thing that would automatically highlight predefined keywords in a pdf. Another nice feature would be to automatically group or link notes based on their content or some other specification, if that makes any sense.

The last item on your list is the only item where I'm not really sure if this can be supported in Keypoints. In Keypoints, a note is usually connected to a single PDF file (and publication).
To me, this is where Keypoints could be the best thing going! This is a shortcoming of everything out there (in my opinion)!
However, you can, of course, insert links to other files (or notes, publications, keywords, labels, etc) into a note
This would be moving toward what I am thinking about and would definitely be an improvement to most everything on the market.
In what situation would you want to link a note to multiple PDFs?
When reading, writing, or working on a manuscript or grant application, I would love to have a single source of information (i.e., a note) about a specific topic. For example, currently I have 15 notes, one for each study/pdf, where I comment that placebo analgesia reduced pain and was associated with brain regions XYZ. I would rather have a single note where the same comment is associated with all 15 PDFs. Does that make any sense? In some ways I guess my idea is somewhat similar to a smart group, but that still doesn’t fit the need I am trying to describe.

As always, thanks for the time and please let me know if I can help in any way.

Side note: If you had a 'donate' button somewhere, I'd happily contribute.

Cheers,
Jason

msteffens
Site Admin
Posts: 10
Joined: 17-May-2017, 14:28

Re: Workflow

20-Mar-2018, 01:33

Hi Jason,
Given that Papers3 doesn’t seem to be under development any longer, I will likely migrate to something else. This is really sad for me because Papers has the features I want in a reference manager. Nothing else out there seems to have all the same features.

I agree. I still plan to support Papers 3, esp. due to its high level of scriptability (which allows for a good integration). Also, I guess there's quite a few users for whom Papers still works fine, e.g., users still running macOS 10.11 (El Capitan) which still has Apple's original PDFKit framework and thus less issues.
As I use LaTeX, BibDesk would be a logical move, but it doesn’t auto-populate all the fields like Papers3, especially when dragging and dropping and PDF. Highlighting the text to specify each of the fields is just a pain...

I see. I plan to support BibDesk (esp. since it also offers good scripting support). In the future, Keypoints could even synchronize its publications with apps like BibDesk or Papers 3.

In the distant future, I'd like to extend the bibliographic capabilities in Keypoints. Under the hood, Keypoints has the data model of a full-blown reference manager, and I'd like to make good use of it. Similar to Papers, I'd like to offer automatic fetching of bibliographic metadata for publications, and (where possible) auto-download their PDFs. Sames goes for the publication's figures, cited references and related content. That's a lot of work, though, so it will take some time to get there.
W.r.t. automation of some tasks, could you give some examples of tasks that you'd like to get automated?
Off the top of my head I was thinking of something like: Having a rule or agent type of thing that would automatically highlight predefined keywords in a pdf. Another nice feature would be to automatically group or link notes based on their content or some other specification, if that makes any sense.

Thanks for the explanation and examples. Indeed these would be nice features. But I guess that it will take quite some time until I'd get there. To achieve something similar, you could probably use DEVONthink and index all your Keypoints notes in DEVONthink, then use its semantic features to auto-group or cluster the notes.

Speaking of DEVONthink, I also plan to offer direct export to DEVONthink (with support for rich text, tags, metadata, PDF indexing, clickable backlinks, etc). And notes exported to DEVONthink could be even kept in sync between the two apps.
The last item on your list is the only item where I'm not really sure if this can be supported in Keypoints. In Keypoints, a note is usually connected to a single PDF file (and publication).
To me, this is where Keypoints could be the best thing going! This is a shortcoming of everything out there (in my opinion)!
However, you can, of course, insert links to other files (or notes, publications, keywords, labels, etc) into a note
This would be moving toward what I am thinking about and would definitely be an improvement to most everything on the market.
In what situation would you want to link a note to multiple PDFs?
When reading, writing, or working on a manuscript or grant application, I would love to have a single source of information (i.e., a note) about a specific topic. For example, currently I have 15 notes, one for each study/pdf, where I comment that placebo analgesia reduced pain and was associated with brain regions XYZ. I would rather have a single note where the same comment is associated with all 15 PDFs. Does that make any sense? In some ways I guess my idea is somewhat similar to a smart group, but that still doesn’t fit the need I am trying to describe.

Ah, I understand better now! If I understand you correctly, what you're describing is actually one of the major goals/outcomes for Keypoints. I call the feature "overview notes". I'm not there yet (and, again, it may take me some time to get there), but I think that these overview notes could work nicely for this use case.

Since the "overview notes" feature is a larger topic, I've given more details about this planned feature in a separate thread.
As always, thanks for the time and please let me know if I can help in any way.

Side note: If you had a 'donate' button somewhere, I'd happily contribute.
Many thanks for the offer, it's much appreciated! I'll think about it.

Cheers,
Matthias

Jason
Posts: 4
Joined: 24-Jan-2018, 16:56

Re: Workflow

24-Jul-2018, 20:12

Hi Matthias,

I just wanted to check in and see how things are going.
Is this project still being developed?
If so, I’ve hit a work lull (end of summer) and would love to help with this project in any way possible.
I hope to hear from you soon.

Cheers,
Jason

msteffens
Site Admin
Posts: 10
Joined: 17-May-2017, 14:28

Re: Workflow

24-Jul-2018, 23:09

Jason wrote: I just wanted to check in and see how things are going.
Is this project still being developed?

Hi Jason, many thanks for your continued interest! The app is (and will remain) under continuous development. Unfortunately, I can only work on this part time, and I wish things would move faster.

I'm currently on holidays (traveling with my family) but I've given an update about the current development state here. I'll be back home beginning of August. I'll try to get back to you then.

Thanks again, Matthias

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