Each to their own etc. etc…
Some ramblings from a fellow PHD student.
Tying together my thoughts about what has been raised above:
1.) I too prefer to use tools that specialise in their particular field.
I also use Bookends. The support is second to none - which helps, since the Manual etc. can be rather confusing… I’m still discovering features, where a face-palm or three has me thinking “if only I realised that earlier”…
I haven’t really found a way into its annotation and notes feature. I don’t find it to be particularly intuitive, and haven’t had the time to dig in… Others appear to find it really good - so maybe its worth exploring.
Regardless, I use BE exclusively for the citation side of things. The ability to generate an instantaneous bibliography, is a real plus as well. And whereas many might not see the need for a reference/citation manager - if you’re one that intends on publishing frequently, then it’s a no-brainer IF your discipline makes use of varied citation styles. My field, sees virtually every Journal use a unique referencing style - being able to edit one Format, and having all citations transform instantly to match that style at the click of the button - priceless, imo.
Similarly, DTPO takes care of managing/accessing my research. All the PDFs are OCR’ed on my mac - as suggested, this is basically non-negotiable. To truly get the most out of your machine, it needs to be able to “read” everything. Take the time to do this - it will pay you back a-thousand-fold in the long run.
[I used PDFPen Pro and Hazel, to automagically scan and OCR several thousand PDFs on my mac, over the space of about a week. It was the reason I bought Hazel. Of course, the latter does much more - but even if only used for OCR’ing - worth every penny.]
Scrivener to write. Word to convert right at the end.
Keyboard Maestro in conjunction with ActionsApp for iPad, ties everything together - I have workflows set-up where I can type an author’s name in Scrivener, tap my iPad which invokes a KM macro, jumps into BE, and using ShortcatApp, runs a search for the author as selected - one more tap on my iPad to insert the relevant pages, and back to Scrivener to insert. That sounds far more complex than what it is - a few taps, and done.
Scrivener and DTPO play nicely together. BE and DTPO - there are basic functions that would be far more useful were my BE library to be complete - since its still a work in progress, I prefer to search inside BE, than accessing it from with DTPO. That being said, when the day comes that everything inside my BE library has been autocompleted, with will become really useful.
Annotation.
FWIW, a few suggestions that I found really help.
I use several primary highlight colours to highlight PDFs inside DTPO, using the built in annotation feature. I bought a little Bamboo Intuos Pen & Touch Small, and find it does a fine job of allowing quick highlighting.
I use 3 colours to indicate “summary variants”. Then, in addition: Red for VITAL bits; Purple for “To quote”/Also NB parts"; Electric blue for “look up later”; Green for “This is why I’ve added an Annotation RTF file” [DTPO’s built-in feature].
Those 3 summary variants, actually work really well. Initially, I always used to highlight in one colour, typically yellow. I’d maybe differentiate NB parts with Red. Then the purple etc.
Thing is - when you go back to review that article 6 months later - you are visually met with pages and pages of yellow paragraphed text… It took a while to find what you are looking for, since there was no easy visual way to distinguish the text… Then I started using the 3 colour approach.
First point worth highlighting - Colour 1. NEXT (unrelated) point worth highlighting, Colour 2. NEXT point, Colour 3. NEXT point, back to Colour 1, and repeat.
This way, when I come back to review that PDF, I start reading the 1st highlighted part. If its not valid, I can skip along to different points far quicker, by being able to distinguish between the different colours. It sounds kind of lame, but it really works a treat for me - it’s something I suggest you consider if you’re expect to do plenty of highlighting, digitally.
I ONLY use the built-in DTPO annotating service to highlight - anything else is done on the iPad, since making sticky notes, will mean they remain unsearchable - something to be avoided, if possible.
I set the same colours up in Goodreader on my iPad. That way, when annotating on my iPad, I’m using the same criteria - which provides useful consistency. I popped something up over here [[url]Need some help re my Annotation workflow-DTTG<>Goodreader], about my use of Goodreader on the iPad, with DTTG as the conduit between DTPO and Goodreader. I must probably look at things again, given the new developments in iCloud, but haven’t had the chance yet.
The above procedure is a bit clunky, but it works. Whether it’s for you, only you will know. Skim would obviously make this process much easier, as would the Highlights App [see here: [url]"Highlights" app - export annotations to DEVONthink, etc.]] - but then it would ignore using the iPad as an annotation tool - something it excels at, imo. My clunkflow at least allows me to generate annotation-sticky-notes inside my PDF on my iPad, that end up being searchable inside DTPO…
To conclude - and hopefully, this isn’t too presumptuous of me - but since this also interests me, I’ve been following many of these questions as well - here are some useful forum posts, on the different workflow-type options:
** Make annotation files for each citation plus notes+tags: [[url]Make an Annotation with Links, Notes, Tags v2]]
** PDF Annotation (made easier) - KM and ActionsApp: [[url]PDF Annotation (made easier) - Keyboard Maestro & ActionsApp]]
** Mystified by Annotation - is there a plain-language tutorial: [[url]Mystified by Annotation - is there a plain-language tutorial]]
** Linking Bookends entries and pdfs in Devonthink: [[url]Linking Bookends entries and pdfs in Devonthink]]
** Integrating Scrivener with DTPO and BE: [[url]Integrating Scrivener with Devonthink and Bookends]]
** Make an Index Document (RTF) for a selection of Documents: [[url]Make an Index Document (RTF) for a Selection of Documents]]
** Manually cross-linking & adding a RT note to items?: [[url]manually cross-linking & adding rich text notes to items?]]
TL:DR >> There are no simple workflows. 