Annotating pdfs/extracting highlights as quotes

[Jon]

I''m not sure what you're asking for, there's a lot there and some of it is vague. But here's a response.

1. Bookends works pretty well with DT -- you can insert links to Bookends references in DT, and DT can import directly from Bookends (from groups, from selections, or the entire db).

2. Bookends has no relationship with Skim, except you can open pdfs in Skim if you want (right-click or hierarchical menu option).

3. Bookends can insert temp citations in and then scan Scrivener RTF files.

3.1 Bookends has autocomplete, both for fields (if you type them in) and more importantly for references if you have the pdf. Of course, it also Update From Internet, which is another form of autocomplete, if you have the isbn, doi, or pmid.

3.2 You can change the output format and the output text style (styled text, BibTeX, HTML, plain text, etc.) at any time.

(a) Bookends will use isbn, doi, or pmid to find and import references (from a variety of sources, including CrossRef, PubMed, Google Scholar, and more).

(b) Not sure what you mean by manual access for searches, but Bookends has all sorts of searches.

If you haven't already, you can try the tutorial and take a look at the user guide (peruse the TOC for topics of interest), both available via the Help menu.

Jon
Sonny Software

[jmm]

3. I understand then that after scanning a Scrivener document and changing its references to any output format, BE is capable of reversing the process back to the original \cite{...} statements.

2. I think BE is also capable of previewing pdfs and annotations within pdfds packages.

As for previewing Skim highlights in their original colors in BookEnds, I wonder if it is something achievable. There are great AppleScripts which achieve something related from Skim:

Skim and color codes of highlights
Export Skim notes according to their highlight colors

By the way, those two blogs have several great scripts for integrating BibDesk with DevonThink and Skim. I think users could find them useful if adapted to BookEnds.

[Jon]

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.

I'm revisiting this thread to get feedback on a feature I'm planning for a future update. The right-click option "Find In PDF" will be added to the note stream contextual menu. If text from the pdf is quoted as the first line of a notecard (typically by dragging and dropping in on the note stream to create a new notecard) and the pdf is showing in the lower display pane, selecting this option will scroll to the text in the pdf and highlight it. It will be smart enough to ignore markup (headers, tags) and will allow for a trailing ellipsis so you can have visual feedback that you're quoting text in the pdf (e.g. something like: Annual statistics from...).

Jon
Sonny Software

[taja]

That sounds like an excellent feature. If the 'Find in PDF' command could be given a keyboard shortcut that applied to the selected notecard that would be even better.

[Jon]

Option-Shift-Command-N

Jon
Sonny Software

[Jon]

BTW, a "go to page" would be do-able, but would require another adjustment to the UI and wouldn't be as useful because you'd still have to scan an entire page to find the part you want. This method is transparent, requires no special characters to enter, and takes you right to the quoted text.

Jon
Sonny Software

[taja]

No, I agree: this sounds a lot more effective than a go to page command. Think I'll be using notecards again...

[Jon]

Back to this thread...

I'm working on improved pdf functionality in Bookends. One feature would be to have Bookends automatically display pdf notes as notecards (virtual notecards, if you will, which will be colored differently from real notecards). As of now these will not included comments (also called Text or Free Text), which are generally short and meant to call attention to some point in the text. It also won't included marked up text (that is, color highlighted text), which is not editable. Would heavy pdf users find this useful?

Jon
Sonny Software

[ozean]

One feature would be to have Bookends automatically display pdf notes as notecards (virtual notecards, if you will, which will be colored differently from real notecards). As of now these will not included comments (also called Text or Free Text), which are generally short and meant to call attention to some point in the text. It also won't included marked up text (that is, color highlighted text), which is not editable.

First of all: yes, this would be very nice indeed! Importing notes seems like a nice feature to begin with. Including marked up text sounds like a very nice feature, too. (I would have to take this into account when marking up though, as I would then mark less text than usual. Or use a different color?)

Do you already know if/how you will refer to different pages in the notecards?

[Jon]

That was discussed earlier in this thread. Bookends will search for the text of the first line of the notecard and scroll to it in the pdf.

Jon
Sonny Software

[AsafKeller]

I do not see this as a feature that I would incorporate in my workflow. BE records are already linked to a PDF file, and the latter contains my notes. Perhaps I am missing something, but I do not see the proposal as a major time or convenience enhancement.
I have suggested, some time ago, that a full integration between a PDF reader and BE would be ideal if it would allow for notes in each application to be synced. Skim and BibDesk integration is one example. Efforts over at https://www.docear.org is another.
Thank you for continuing efforts to improve an already outstanding application!

EDIT: I had not appreciated at first the power of this improvement that Jon is working on. I was wrong; this will allow very useful, reciprocal linking between PDFs and notes in BE. I retract my earlier skepticism.

[Jon]

This would actually provide some of the same sort of integration (although no doubt not as deep). For example, notes you made in your pdf (for those who make notes in pdfs) will appear as notecards in Bookends, and edits to those notecards in Bookends will be written back to the note in the pdf.

Jon
Sonny Software

[DeclanOB]

Sounds nice. But if there were to be any way to make the resulting notecards/virtual notecards indexable in Devonthink, it'd be even better.
We have discussed this before, and I know that this is a separate issue, but perhaps if what you are thinking of were to be linked with some way to make Devonthink communicate with the notecards (virtual or other) it'd be awesomecoolmarvellousterrificindeed.

Declan

[Jon]

Yes, that is an entirely different issue. :-)

This is about pdfs and pdf annotations. If you want to start another thread on making notecards indexable in DT, please to that. Note that you'll have to explain what that means on a practical level. And think through whether it would require collaboration between Bookends and DT. If so, AppleEvents would no doubt be necessary.

Jon
Sonny Software

[nicka]

I'm working on improved pdf functionality in Bookends. One feature would be to have Bookends automatically display pdf notes as notecards (virtual notecards, if you will, which will be colored differently from real notecards). As of now these will not included comments (also called Text or Free Text), which are generally short and meant to call attention to some point in the text. It also won't included marked up text (that is, color highlighted text), which is not editable. Would heavy pdf users find this reasonable?

I think this is exactly what I've been looking for. Just to check: here's what I do at the moment. I read in Preview, and when I find something I want to quote/agree with/disagree with I highlight it, then right-click on the highlight and choose 'Add note'. Then I type something there.
This is Ok as far as it goes, but that's not very far at present. One big problem is that those notes are not searchable from Bookends (and not from anywhere else short of opening the right pdf in Preview and using Find within it). Another is that there's no indication in Bookends of whether a pdf has been annotated in this way. (I know I could manually put all references with annotated pdfs in a group, or add a keyword to them, but life is short, and I'd forget half the time anyway.)

If I'm understanding it correctly, the proposed new feature would solve both of this problems. Is that right?