I’ve been increasingly using an app (iOS and OS X versions) that you might be interested in: MarginNote. It is for document annotation – but is sui generis when it comes to that. An annotation can combine highlighted text from the document + personal notes + Wikipedia or other web clips + images + sketches (made in-app). The app displays notes and text side by side, and the notes can be displayed in a mind map format or hierarchical outline (or both). With the mind map the notes can be moved around in whatever hierarchy you want. (Somewhat like FluidText but much more flexible.)
Any number of documents (“books” in the app’s terminology) can be combined together in a single “notebook” – providing a set of notes that covers multiple sources. Notes can be exported in MindJet MindManager format (.mmap) for use in that app or others like iThoughts. They can also be exported in OmniOutliner 3 format (.oo3) from which they can be changed to OPML, etc. Notes can be “studied” as flash cards – which is nice for review. There is an extensive manual for MarginNote, and I would caution that it takes time to figure things out and get synchronization working between platforms (OS X / iOS): the effort is well worth it.
MarginNote does not play well with DEVONthink, so don’t expect it to be a good companion for your databases. PDFs can be opened in MarginNote from DEVONthink but that’s about it. PDFs opened in MarginNote are stored in MarginNote – they are not indexed. MarginNote is a standalone app, and has several limitations (no bibliographic citations, e.g.) – but IMO is definitely worth consideration by researchers.
I’ve not seen anything like MarginNote. It is a great example of so-called artisanal software: an independent developer who has very different and creative ideas about what software should do, and the skills to make it happen.
Thanks for the reference to MarginNote, however I’ve discovered that my existing highlights made in PFD Expert and viewable in other PDF viewers are not viewable in MarginNote. Now, I have just started testing the app and I’m sure I’m missing the proper way of using it, but not having existing highlights displayed is discouraging. If MarginNote is fully proprietary, then that’s a deal breaker.
To be fair, I’ll have to play around with it more. There does seem to be a bit of a learning curve.
This app is on my to-do list of one’s I’d like to explore. Glad to hear about the comprehensive manual - the 20 second promo clips flash by in seconds, and makes using the app seem like it requires mastery of some dark arts… Which probably just means in starting to get old!
Regardless, looks very powerful. Thanks for the heads up on the integration with DTPO - will be something to keep in mind.
Well, that’s not good. I managed to get into marginnote.com – though it’s so slow, the site must be hosted on a Z800 somewhere in Antartica. Anyway, after 10 minutes or so the site finally was rendered and I grabbed the manual. Only thing, it’s v2.0.3 but the current version of the app is 2.3.2.
MarginNote keeps improving. Now it has added export to DEVONthink to its features. Unfortunately, the exported rtfs do not have their names numbered acccording to their pdf page. But they do include hyperlinks to the highlights in the pdf.