I've made a comment on another discussion (http://forums.zotero.org/discussion/1262/pdf-highlighting-and-sticky-notes/#Comment_105462), but saw this one and thought that I'd expand on it here.
Highlighting and comments can be made in pdfs stored by Zotero:
Select a pdf document. To the left of the sync button is the 'Locate' drop down list. Select 'Open in external viewer', make changes, save, and close (no need to Save-As...).
Changes are then saved in Zotero, and visible when just double-clicking on the pdf, or when opening in an external viewer again. (I use Foxit Reader, but I expect that the same would apply to Adobe Reader etc too.)
While comments are saved, they cannot be indexed by Zotero. However, text added using the Typewriter tool can be indexed and searched by Zotero (if reindexed by clicking on the circular arrows beside 'Indexed' in the Zotero entry for the pdf).
The typewriter tool cannot be minimised in the same way as comments can, and doesn't look as elegant (text size cannot be changed). But once an entry is added with minimal text, it can be later edited with lots more text without increasing the size of the displayed box (at least this is how it works in Foxit). The full text is visible on hover, though.
This does what I need at present. Does it work for anyone else?
well but it still would be nice to be able to highlight and make annotations directly in pdf. I'm just looking for a sowtware that meets my needs and I really like Zotero, but with Mendeley you can make notes in pdfs directly...
There are long-term plans to use LiberTexto for annotation (http://www.libertexto.org/), if the project proves sufficiently powerful and stable. Mendeley took the easy route, open only to for-profit firms: they licensed the commercial PDF manipulation library PDFTron (http://www.mendeley.com/release-notes/).
Moreover, if I'm not mistaken, Mendeley doesn't support native PDF annotations, which can be read by Acrobat, Preview.app, etc without recourse to "exporting" the PDF. I think iAnnotate might suffer the same problem. Anything Zotero implements is going to be the real deal and fully cross-platform.
I think the "annotating pdfs" feature is really a red herring - as noted above, there is plenty of software that can do that on the two main operating systems, and us linuxers can do OK with pdfXchange and wine. I don't see why Zotero should bother with replicating functionality that exists already.
What Zotero can't do (and where I'm not sure where the other programs stand, though I think they can do some of that, Citavi looks pretty impressive in that regard: http://www.citavi.com/en/features.html#documents - but they're also Windows only) is to integrate PDF annotations into the client - e.g. being able to click on an annotation or a quote in a note and have the pdf open at the respective passage and vice versa.
The Zotfile annotation export is a first step on that. Libertexto seems to be able to do a lot of that, but unfortunately the project doesn't appear very active and the current plugin is super-buggy.
What Zotero can't do [...] is to integrate PDF annotations into the client - e.g. being able to click on an annotation or a quote in a note and have the pdf open at the respective passage and vice versa.
Yeah, I agree that this is far more important than replicating perfectly good annotation support.
I think the zotero database structure already has a lot of advantages over other databases that would be very useful for additional annotations support. I am particularly thinking about the fact that child notes are independent items. They can be tages, related...
The zotfile annotation and highlight extractor could be used for much more. Currently, my extraction is a simple 'get all in one note or nothing' mechanism. In theory, zotero could keep track of the annotations so that I can add an additional annotation to a pdf document and only this new annotation is added to zotero... the click on an annotation to open the pdf at the respective position is another idea.
I am just saying, the zotfile extractor is all you need outside of the FF/zotero/javascript framework. Everything else could be done within zotero. I won't do it but if someone jumps at it, I am willing to make the required changes to the extractor (e.g. extract more information about the annotations that is currently not extracted such as the date added, date modified...)
Just a note that https://www.mozdev.org/bugs/show_bug.cgi?id=19196 also affects zotero. This is a real bummer, because otherwise zotero+okular works perfectly as an annotation tool (the annotations are stored in okular's database, which is potentially a problem, since I imagine they'll probably be lost if I move the zotero database).
To follow up on adamsmith's and Dan's comments: zotfile now extracts pdf annotations on all platforms and I like the idea of adding a link to open the pdf at the respective passage. But right now, I am not even able to open links from zotero notes. Did that ever work? What is the problem and is there a work around?
Upgrade Storage
Highlighting and comments can be made in pdfs stored by Zotero:
Select a pdf document. To the left of the sync button is the 'Locate' drop down list. Select 'Open in external viewer', make changes, save, and close (no need to Save-As...).
Changes are then saved in Zotero, and visible when just double-clicking on the pdf, or when opening in an external viewer again. (I use Foxit Reader, but I expect that the same would apply to Adobe Reader etc too.)
While comments are saved, they cannot be indexed by Zotero. However, text added using the Typewriter tool can be indexed and searched by Zotero (if reindexed by clicking on the circular arrows beside 'Indexed' in the Zotero entry for the pdf).
The typewriter tool cannot be minimised in the same way as comments can, and doesn't look as elegant (text size cannot be changed). But once an entry is added with minimal text, it can be later edited with lots more text without increasing the size of the displayed box (at least this is how it works in Foxit). The full text is visible on hover, though.
This does what I need at present. Does it work for anyone else?
But annotation is important, and this is nonetheless an area where Zotero is somewhat behind the other programs.
What Zotero can't do (and where I'm not sure where the other programs stand, though I think they can do some of that, Citavi looks pretty impressive in that regard: http://www.citavi.com/en/features.html#documents - but they're also Windows only) is to integrate PDF annotations into the client - e.g. being able to click on an annotation or a quote in a note and have the pdf open at the respective passage and vice versa.
The Zotfile annotation export is a first step on that. Libertexto seems to be able to do a lot of that, but unfortunately the project doesn't appear very active and the current plugin is super-buggy.
The zotfile annotation and highlight extractor could be used for much more. Currently, my extraction is a simple 'get all in one note or nothing' mechanism. In theory, zotero could keep track of the annotations so that I can add an additional annotation to a pdf document and only this new annotation is added to zotero... the click on an annotation to open the pdf at the respective position is another idea.
I am just saying, the zotfile extractor is all you need outside of the FF/zotero/javascript framework. Everything else could be done within zotero. I won't do it but if someone jumps at it, I am willing to make the required changes to the extractor (e.g. extract more information about the annotations that is currently not extracted such as the date added, date modified...)
Here is some info about opening pdfs at specific locations (but I really just started to take a look at this):
http://kb2.adobe.com/cps/317/317300.html