Can I annotate my PDF snapshots?

Hello team,

I just found out that one can now annotate snapshots. That's a great function!

I also realized that I am able to take a snapshot of a PDF file. I can't, however, annotate the PDF file the way I can annotate the webpages. Any plans to be able to annotate PDFs that are opened within the browser? That would be very useful. Thanks!
  • Not via Zotero yet (PDFs are handled by various browser plugins, so Zotero can't directly access them). You could, of course, use third-party PDF annotation software on PDFs kept within your Zotero collection.

    See also:
  • Got it, thanks.
  • I've been working on a solution for this. At the moment there is a temporary filter here:

    I will continue this work in a month once I've finished the paper I am currently writing. At least theoretically it is quite easy to extract the annotations from a pdf. The major problem right now is that you need Acrobat to annotate a pdf (or to enable annotation of a pdf in Adobe Reader).
  • Well, thanks for working on this. I will look forward to you finishing the paper!
  • PDF-XChange Viewer is a free replacement for Acrobat Reader and allows users to create annotations.
  • Foxit Reader also allows to highlight and annotate PDF files (I prefer it to others).
  • edited September 21, 2008
    On Mac OS X (at least the 10.5.x version), you can simply use
  • One more person for this feature! A PDF annotation function would be a very useful tool for Zotero. Most of my research sources come in PDF format and I wish I could highlight sentences and add sticky-notes to PDF files, just like archived web pages. Could Zotero enable Adobe Reader's Highlight Text and Sticky Note tools when you view an archived PDF file through Zotero? How about including a simple PDF viewer that will permit highlighting and annotations within Zotero itself or as a separate extension?
  • Could Zotero enable Adobe Reader's Highlight Text and Sticky Note tools when you view an archived PDF file through Zotero?
    No. Adobe's developer API prohibits this & the only applications that can legitimately do this have been created by Adobe or have paid Adobe a hefty fee for an alternative licensing model. FWIW: I know of only two apps that do this illegitimately & they are both windows-only.
    How about including a simple PDF viewer that will permit highlighting and annotations within Zotero itself or as a separate extension?
    Yuck. Plugins like this require either an external (usually commercial) website or are OS-specific. Is it really so terrible to install your PDF editor of choice?
  • Installing a PDF editor only works if you know about these programs beforehand. Now that I know, I do intend on downloading one of these programs. That said, I still think being able to annotate PDF files would be extremely useful and an obvious way of extending the capabilities of this program. Perhaps one solution to this dilemma is to provide links to several suitable PDF editors in an accessible location within the website, perhaps in the FAQ.
  • I have to say that I fully support the directions that benmeister is pushing zotero to go. There is a need for a platform from which to collect data (webpages, PDFs, documents, whatever), and to view that data, make notes on it, and then analyze those notes, do advance searches, etc. Highlighting and annotation are exactly what readers do with documents, in order to later make sense of those documents for their research. So why not have that ability in zotero? Then, when working on a research paper, one is able to open pdfs, view them, collect in one place all of the text that refers to a specific topic, etc. And, it is all cued up and ready to be cited in the document that you are currently writing.

    A last note--PDFs can be quite big--they can be entire books, for instance. Imagine you are researching a particular subject, say Martin Luther King's I Have a Dream speech. If you are analyzing a biography of MLK, you would want to make specific annotations, and notes, on specific sections of the book. It would not be much use to simply add the tag "I Have A Dream" to the entire book. You'd want to add that tag to the sections of the book that refer to the speech, and you'd want your zotero search to immediately land you at the places that you've tagged with "I Have a Dream" so that you could easily get to those sections. Once there, you'd want to see any annotations you'd made about that specific part of the book. Ie, "the author here is referring to the biblical underpinnings of King's narrative style, specifically his references to x, y, and z..." You'd want that annotation to appear when you did a search through zotero for "I have a dream" and "biblical". And you'd want to be able to make a citation in your word processor that cited the specific pages in the original text that you are referring to...

    As for technical difficulties, cross-platform challenges, etc. As users, we'd like to ignore those challenges so that we can seamlessly collect, analyze and access information. That's what we hope software will do for us!
  • "So why not have that ability in zotero?"
    because this is something that the large open source community so far hasn't been able to come up with. As soon as it does, Zotero should (and I'd suspect will) use those (or that) tool(s) and integrate them.
    It seems a much more useful approach to have Zotero do well what it does well and then "integrate" approaches from other projects - and allow users which project they pick (e.g. maybe I really want to work with Acrobat professional, whereas noksagt maybe wants to remain fully open-source and use okular or something along those line).

    So basically if you want this to go forward, push the projects that work on better pdf editors.

    Linking to pdf editors seems reasonable in the FAQs, that could certainly be done.
  • Btw, I'd like to reccomend bluebeam to people here for annotation, it's the only editor i know of with all of the features in one program:

    - full, responsive, tablet pc inking support
    - hotkeys for highlighters of various colours
    - heirarchical bookmarking
    - drawing markups (i.e. polyline)
    - pop-up notes

    For what it's worth, zotero's own markup has a long way to go before it's ideal in posessing these features, and i currently convert html to pdf for annotation (and, it's geneerally good to have only ONE annotation interface, so that you learn it seamlessly regardless of wher eyou got your document from, so I convert everything to PDF and don't have to think much about my annotation system)
  • 1) bluebeam is a commercial, windows-only, product.

    2) a larger point: I think PDF and PDF annotation is seriously overrated, I would certainly never follow the path of converting everything to PDF (but to be fair, I'm happy with using things like grep on HTML and text, and writing scripts to work with it).

    3) As noksagt points out, it's also not entirely straightforward to program the sort of support people are asking for. I think it's way entirely unrealistic to expect Zotero to add this to Zotero itself. OTOH, if Mozilla were to add PDF support to Firefox, that might change.
  • After reading, and rereading, the multiple posts on the question of pdf-markup and zotero, I think I'm resigned to using an external pdf-editor for highlighting and making notes on PDFs, at least for now, since those in the know seem to be stressing that it's not in the cards given limitations in Firefox, etc. Also not in the cards, it seems, is specific tagging of specific text.

    However, it seems possible that Zotero might able to index the text within annotations (pop-ups notes) that have been made in external editors (like Acrobat), and that zotero be able to locate that text in searches. Is this also impossible? There seems to be some hope for that function being developed, according to this thread

    We'd seem to be waiting for developments to emerge in poppler, which will become a part of zotero? I think that's the point of noksagt's comment there. So, two questions: is that more or less an accurate understanding? and is there anything that can be done on the Zotero end of things to request that indexing of PDF annotations be worked on?

  • Although veering somewhat off-topic, it's worth noting that in partnership with MITH and supported by the Mellon Foundation we are in the process of revamping our entire annotation interface, which will soon support text, image, audio, and video. We should have preliminary test code in place as soon as next month.

    In an ideal world, we would also support PDFs immediately, but the format is problematic for the licensing and platform reasons outlined above, and of course there are other tools available. Moreover, from the perspective of the research processes that Zotero seeks to enable, PDF annotation is not as high a priority as the annotation of text, image, audio, and video, all of which are more likely to be the types of "raw" research objects that we want users to be able to mark up and to expose to wider audiences. Right now there are accepted ways to point to a passage in a PDF by page number, etc., but those traditional methods are obviously inappropriate for images (X,Y?), audio(Z?), and video (X,Y, Z?).
  • You're adding all this to Zotero; as opposed to a separate extension?

    If yes, this seems like mission-creep to me.
  • Initially the code will be in a separate Firefox add-on, and it may stay that way.
  • how about converting the PDF to an HTML snapshot during import? then the regular annotation tools could be used
  • If you are happy with that, that's great, but html translations of pdf documents are - at least in my view - usually not of acceptable quality.
    And as people do point out - there are tools out there for pdf, so it's not like there is no way to annotate pdfs.
  • it would be acceptable if the conversion to html is done well. the advantage would be to have annotations integrated with zotero, so they can be searched and shared
  • Re conversion of PDF to HTML: I used to hate PDF for its size and bulkiness, but I have to admit now that there are things it does that can't be done (or can't be done well) in HTML. I work a lot with other languages, and some of the foreign scripts are very hard to render (Urdu being an extreme case).
  • @sean

    I wonder if there is any news about the development of a revamped annotation interface? This was exciting news. Along these lines, I hope that PDFs would be included in the kinds of tools you're discussing, at least so that the compatibility with zotero would be quite high. Indeed, I wonder if it would be possible to use zotero keywords in combination with annotations-- perhaps use some sort of text symbol in front of the keyword (ie., #keyword1; #keyword2; etc)? It would be great to be able to use keywords to tag within pdfs (rather than to tag whole pdf documents), and to be able to search for text across all documents that meets with various tag criteria....

  • JonEP - as for pdfs - not going to happen in any reasonable future.
    There is not a single open sourced program that can annotate pdfs in a useful way. Zotero developers used existing open source code for html annotation and the same would surely need to be done for pdfs. Don't blame Zotero, though. Blame Adobe.

    The annotation thing seems to be going forward
    but that sounds like a relatively long term project to me.
  • With regards to "There is not a single open sourced program that can annotate pdfs in a useful way"...

    I may be missing something obvious here, but I'm using okular in Linux to annotate stuff and though the application itself is somewhat buggy at times, is there an overwhelming reason why it is impossible to use poppler for annotation in zotero? I noted another comment about poppler above but didn't see any response to it?

    As far as I'm aware it's open source, the annotations are stored separately from the PDFs, etc.
  • the problem with okular is a) exactly that: it stores the annotations apart from the pdf, which will be really annoying to people who expect their annotations to come along if they send their document to a friend or so. If you look around the internets okular's annotation feature creates at least as much confusion as benefits - and note that if it were to actually become part of Zotero, people would vent their problems here... b) that it just runs on Linux.
  • Well, another simple way to handle this would be for Zotero to expose a URL for a note. When you want to annotate the PDF, you'd first create the note and its text in Zotero. Then to make the highlighting, etc. appear in the PDF, you could use your favorite PDF annotation software and simply paste in the link to the Zotero note (e.g. using and Add Note or Add Link). That way Zotero could index and store the note as normal, and you'd have a visual indication in the PDF that the note is there. I didn't see such a URL for a note visible, but I'm pretty new to Zotero. Is it already possible to grab a direct URL to a note? If not, can that be exposed?

  • I use Onfolio and I was able to change the PDF document because I bought the PDF program. When I wanted to change the document I double click on the document Icone and it launched Adobe. If I cliked on the document name, it open the document in IE for viewing only.
  • (From one of the developers of

    If you sign up for a free account and add the "shapshot" bookmarklet ("help" main menu item once you're logged in) , then clicking the bookmarklet will activate any links to PDFs within the page. Clicking those will fetch them to where you can add sticky notes to the text, highlight regions, draw arrows etc. Its pretty easy to do a neater integration if you run your own server, but, as people have pointed out, its not open source.

    However, we do do other open source development, and we're not intrinsically against the idea for a.nnotate if we can be sure the developers still get paid somehow.
  • Alternative to okular under linux is xournal (, although I must confess I still use okular... heh heh
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