Workflow help: Collecting annotations together with DT

Hi, I found myself in the search for the perfect workflow (who doesn’t?) for storing, indexing and linking annotations.

Right now I tend to annotate PDF, EPUB and HTML files, and then put somehow everything together. It is quite a mess and the annotations are not really indexed.

Now I wanted to ditch Evernote for a while and I substitute it with DEVONThink (normal version for mac - but I can update it in case- + the iOS app) for syncing and storing personal information, and I am asking myself if, and mostly how, it can be useful for managing my workflow.

I tend to annotate (highlights and notes) resources (mostly academic) on the iPad (mostly) and on the Mac. Those resource are later used for writing papers/report etc. Right now I do everything with a combination of iAnnotate 3 on the iPad and Skim + Applescript and Hazel on the mac together with Evernote. With this combination I can annotate on the iPad, export the annotations with Skim as RTF, saving the PDF ( just automatically moving it to a folder with Hazel) on Papers (as reference manager) and add everything on Scrivener, or keep them in a folder and consult things one by one.

What I would like DEVONThink to do, is to store/index every annotation and use AI to link the notes together based on some criteria, keeping the link to the original resource that are annotating (PDF, HTML. EPUB). I would like this annotation to be standard, in such way that can be exported and added on Scrivener via Skim (or directly as RTF via DEVONThink would be also good)

  1. Is this possible? Do you have link to some documents or similar workflow that I can use to tune mine?
  2. Seems that a lot of people are using external application such as Highlights or MarginNote, and then exporting the link to DT. What’s these approaches would add in my case? I saw margin note allow to visually create and link together the annotation, but the export to DT doesn’t seems to be the best.
  3. How do I actually save an HTML annotable web page? It seems the only way to annotate HTML pages is just using html on the saved page. or to use PDF.
  4. It would be possible to automatically tag/classify highlights based on their colour (a hex colour = important, another = disagreement) ?

Moreover, quite on the side. On Safari every time I use the DT Extension it asks me “ Do you want to allow this page to open “DEVONthink”? ” . Seems a sort of a permission problem. Any ideas here?

I am pretty new to DT, but I think it can help me on my task, I just don’t know where to start! I have to admin that for as much powerful as it seems, the learning curve appear to be a bit high at the beginning, and the use of the application quite vast (given its potential I think it is pretty normal).


That’s an issue with new security measures in Safari:

Let me give some thought to your other questions… I’ve been looking for something similar too, and if I come across anything I"ll be sure to let you know. Currently I generally use PDF Expert on my Mac or iPad to export the annotations and notes as an HTML or Markdown file (depending on whether I’m on my iPad or Mac, since iPad only exports HTML) and plunk those into DEVONthink in the same group as the annotated document and tag it with “ReadingNotes”. I have a smart group set up to display anything tagged with “ReadingNotes” so even though those notes are spread across all of various groups pertaining to my extensive library of academic articles, they’re all available together in this smart group. The smart group would also be helpful if you store things across multiple databases, though in my case, all of my academic literature is in a single database.

Normally I’ll also modify the resulting HTML or Markdown file to include a link to the DEVONthink URL of the original article I’ve annotated so that I can just click that link in the annotation file and get taken straight to that article.

Thanks! :slight_smile:

I made some researches and I come up with a workflow. It is not perfect at all but for now I couldn’t really come up with anything better.

I just store the PDF of the articles/book in a folder on Dropbox and index them in DT and in Papers. I access the PDF with iAnnotate on the iPad (or whatever reader/annotator) and add some notes. When I come back on my mac I use highlights or Margin Note (still testing both, but Margin Note cannot extract as text the older highlights I made, so I am leaning towards Highlights for now…) to extract the notes and add them to a group of DT. There I just link the notes to the PDF and the other way around in order always retrieve everything.
Would be nice to have:
An automatic way to do it, such as
if annotation title = pdf title then link them together + add tag + move to folder
but for now I am not able to do any of these thing :smiley:

Even better would be a script for extracting directly in DT the PDF’s highlights and note into an RTF/MD linked to the PDF. That would, I have to say, solve most of the problem for me.

Moreover, at the beginning I wanted to store the PDFs on DT and use the x-url scheme to retrieve them from Papers, but it is currently impossible. I contacted papers’ support and they told me

so quite a good news (if they manage :smiley: )