Annotating pdfs/extracting highlights as quotes

[michaelward]

Hi

I'm struggling to find an easy way to achieve the workflow I'd like.

I wish to be able to highlight text in pdfs and have the highlit text automatically extracted to a note (as per Skim and Sente). Ideally I'd like to do this on both iPad (?using iAnnotate) and MAcbook (using something that works like skim).

I keep coming up against incompatibilities.
The reason I'd like to be able o do this is so I can eventually leave the reference, pdf, and highlighting in Devonthink.

any suggestions?

cheers

Michael

[Jon]

In Bookends, show the note stream on the right. Highlight the text you want in the pdf and drag and drop it on the note stream -- it will automatically create a editable notecard for you containing the text. (Use WebKit to display pdfs must be checked in the Action menu). We'll see what might be done in Bookends On Tap.

Jon
Sonny Software

[taja]

Is this an appropriate place to discuss feature requests for the PDF + notecard functionality in Bookends? (I know I promised I wouldn't be doing this sort of thing Jon, but I can't resist...)

[Jon]

If it pertains to this thread, yes. But I can tell you that annotating pdfs within Bookends isn't a high priority for us, it's easily easily done by opening the pdf from Bookends in an app dedicated to this purpose (like Preview, Skim, etc.).

Jon
Sonny Software

[taja]

Then unfortunately the below amounts to an argument for reprioritising annotation, but it also contains an alternate suggestion that would help with notes. Please bear with me:

I haven't adjusted to using Bookends' notecards, because in addition to creating organised snippets of relevant text – which they are excellent for – I want visual cues in my PDFs. As you suggest, this is fine; Skim is built to annotate, Bookends is not. This means I never use notecards, because it would entail either (a) going over PDFs twice, once in Skim then again in Bookends to create notecards. I can imagine few users doing this, not least because this would result in keeping notes on the same references in two very different forms. The other option (b) is to annotate in Skim, export the annotations to a text file and copy them into the Bookends notestream.

Though more convoluted (b) seems the better choice, as it doesn't require going over the PDF twice, and puts the text AND page numbers of the annotations in Bookends, tied to the original reference. This is, I think, one of the better case scenarios for using Bookends with an external PDF app. But it is also where, I think, the main argument for adding basic annotations to Bookends arises.

(b) results in notecards that despite having page numbers, are (i) no longer anchored to their origin in the PDF, as in Skim and (ii) do not relate to visual cues in the PDF – e.g. highlights. This seems like a minor issue, but its not; second to the academic requirement for verifiability of references, the value of (i) and (ii) in linking quotes to their place in the PDF, is to allow quickly chasing down the context of the quote or note. I think this is a basic and quite fundamental dimension of academic note-taking. This wouldn't be so much of an issue if it was easy to to navigate quickly to particular pages in the Bookends PDF view, but its not (iii).

Now I gather that implementing (i) is probably impossible, but the ability to add text highlights in Bookends would help with (ii), and be enough for lots of users (for me, certainly), to not bother with an external PDF reader. This would cut out a major additional workflow step out, and in the case of Skim, would result in annotations interoperable with Bookends on Tap, which is a huge bonus. But given that annotation is a low priority, I wonder whether at least (iii) could be implemented. A 'go to page' context menu command or page field for Bookends' PDF view would allow navigating quickly to pages referred to in the notestream.

[Jon]

Building an interactive, annotatable, pdf viewer in WebKit is a large task (it's difficult to do in "little bits"), and for the most part (not everything for everyone) there are dedicated tools that do a great job with this. It's something I consider and keep an eye on, but there are no immediate plans.

Jon
Sonny Software

[taja]

Ok; point taken. Thanks for responding!

[AsafKeller]

Perhaps integration with Skim's notes stream would be relatively straightforward to implement? An AppleScript that would copy notes and annotations from an open Skim file and paste them, as separate notes, in BE. Ditto for integration with Preview? BibDesk automatically syncs notes in Skim with the attached BibDesk reference; can this be implemented in BE?

An interim solution: Take notes in Skim, making sure that the preference to "Automatically save Skim notes backups" is selected. This creates a separate file of notes that can be attached to the relevant BE reference.

[Jon]

The suggestion may be do-able, but seems kind of clunky. Since you have to switch apps anyway, how is this an improvement over simply copy/paste of Skim or Preview text into Bookends (or better, drag and drop over the note stream in Bookends)? Any text you drop on a note stream will automatically be made into a notecard.

Jon
Sonny Software

[AsafKeller]

It is an improvement in cases in which you have a large number of notes in Skim that you want to import to BE, obviating the need to perform multiple, tedious copy-paste combinations. If the note streams in Skim & BE can be made to sync automatically (as in Skim & BibDesk integration), that would provide for an even more elegant solution, as all additions and deletions made in Skim would be immediately reflected in BE.

[Jon]

OK, something to think about.

Jon
Sonny Software

[taja]

Making Skim and Bookends sync automatically, as with BibDesk, would solve most of the issues mentioned above. Would be a huge boon to users with hundreds of Skim-annotated PDFs in their attachment folder. Though I guess it would also mean we'd be even less likely to see PDF annotation functions built into Bookends in the future (the unlikely dream being that notecards would eventually be linked to points in the PDF, temp citations automatically linked to notecards generated from highlights etc)

[Jon]

temp citations automatically linked to notecards generated from highlights

I don't understand what you mean by this.

Jon
Sonny Software

[taja]

Sorry, wrote that garbled sentence in a rush. I was imagining this: highlighting/underlining text or adding a text annotation to a PDF would generate a notecard consisting of the relevant text with a temporary citation and page number appended. This approximates what currently happens when Skim notes are exported or added to BE notestream, and is how I remember Sente working. On reflection, this would fall foul of varied PDF pagination, but that applies to Skim anyway. I know the thing with temporary citations can be added fairly easily in Bookends, but doing so still requires a copy/paste + add modifier step that has to be done for every quote dragged into the notestream.

the holy grail for me: selecting a Bookends reference, click something in a notecard (a hyperlinked temporary citation?) and have the PDF view scroll to the text from which the annotation originated, thus providing the context for the quote/annotation.

But an Applescript that works with Skim (or even better, Bibdesk-style integration) would still probably be better because – as I know you’ve said many times before – *some* standalone PDF viewer will usually provide a better PDF reading/annotating experience than an app designed to perform lots of other functions.

[jmm]

I moved from Sente to BibDesk. Therefore, I am interested in a good reference manager that integrates well with good apps for related tasks. In my case,

1. with DevonThink, at least through tags and links: so far, I think integration of BE with DT is behind even the one provided by some users' applescripts for BibDesk.
2. with Skim:
2.1. is Bookends capable of previewing linked PDFDs (i.e. pdf & notes) which files reside inside a DT database?
2.2. many people highlight with meaningful colors, so indicating them would be an achievable dream!
3. with Scrivener:
3.1. to enter references with autocompletion. Is this possible with BE?
3.2. to choose at a late stage if the document is scanned by the reference manager and compiled to rtf or processed in latex -I don't know if this choice is possible after the cite keys have been entered.

In short, I would like better integration with related apps, not a few more features that those apps already provide. That, and robust reference management:

a. automated collection of precise references from the web: isbn?, crossref, doi...
b. easy manual access for searches which results need to be evaluated.
I think this differentiation is important for accuracy. Papers is quite automated in general but most of the results it produced for my field were wrong, therefore I see it as an attractive toy I spent an hour with. I may be wrong.

I think this is ground where neither better looking Sente nor Papers stand. BibDesk is certainly good at what it does, but another capable but more flexible and faster app to work with would be welcomed.