Notes as attachements versus as annotations

Zotero has two ways of taking notes. One can create notes in the database attachments (or standalone) notes, available through the Attachments tab (or New Standalone Note button). One can also create notes as "annotations" on snapshots of pages.

The attachment notes have the benefit of being full-fledged database objects, capable of their own properties such as related items and tags. The annotation notes do not seem to have this capability, as they are not represented as full objects in the database. On the other hand, annotations have the benefit of being placed adjacent to relevant text, just as if one were to jot down ideas next to a paragraph relevant to one's research. The attachment notes lack any sense of position with regards to the document they are attached to.

Given these differences, how are you making use of Zotero's two methods for note-taking? Do you prefer one over the other? Do you use one exclusively? Do you make use of both, and if so, do you use each for different tasks?

I'm also interested in hearing the developers thoughts on these two options for taking notes. Will annotations become full-fledged database objects in a future release of Zotero? How did you intend for people to use each method?

I appreciate any thoughts, comments, and opinions.
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  • At the moment I don't have the option of taking annotations. I have been using the notes tab, but may want to transfer them into annotations later. I want to be able to use that option since the bibliography I am working on is going to be an annotated bibliography. I don't have the icons come up when I am on a web page or at any other time. Do annotations only work on web pages and not for books ? I'm guessing that with books people would mostly use the notes tab. Is this something that show up in the Zotero toolbar in Word?
  • Annotations work on any HTML document. The type of item is irrelevant. (For example you could get a whole book, or a article, or a court transcript in HTML and then annotate it in Zotero.

    To clarify, the annotations we are talking about are not synonymous with annotations in a annotated bibliography. In zotero annotations are the sticky notes you stick on HTML documents. (See )

    We do not have a direct way to send flag notes as annotations in the annotated bibliography sense of the term. In this case your best bet is to use the generate report function to see all the notes you have attached to a set of items and paste them over to Word.
  • I'm a relative newcomer to Zotero. The discussions about highlighted text annotations, "sticky note" annotations and Zotero Notes touch on some important aspects of Zotero that must be addressed, I believe.

    I've posted ( a short discussion and example of how annotations, highlighted text and sticky notes are managed in Skim, a PDF reader for Mac OS. Skim clearly differentiates text that's been taken from an existing manuscript (highlighted annotations) and text that's been generated by the end user (sticky notes). All the while these remain searchable, indexed, and cross-referenced back to their locations in the original manuscript.

    Zotero's suggestion to select text from an online source to create a Note ( effectively puts the researcher at risk of confusing another's words as their own. It doesn't help that Zotero's sticky note annotations aren't indexed, searchable or otherwise available in the Zotero collections.

    All the plans for Zotero collaboration/server and so on are nice, but for many of us the research and authorship process is a solitary one. Until the limitations of Zotero's annotations/highlights features are addressed, we'll find it hard to be the Zotero cheerleaders that we really, really wish we could be.
  • This has been discussed before, but just to underline the point, yes, it's critical to be able to clearly distinguish who authors content (annotations/notes vs. excerpts/quotes, etc.).
  • edited May 3, 2008
    Ideally, Zotero should eventually consolidate all forms of annotation and notetaking into one (easily searchable and printed in reports), with some way to generate/enter a locator, be that location in an html/pdf document, GPs locator for maps, timecode for audio/video (as in Vertov), or plain page numbers for physical printed works.
    Annotations work on any HTML document. The type of item is irrelevant. (For example you could get a whole book, or a article, or a court transcript in HTML and then annotate it in Zotero.
    I know I sound as a broken record since this has been discussed before, but there are still scholars (historians, for example) who usually work with physical books, old newspapers, etc. For these analog documents, there should be an easy way to enter and cite page numbers for notes (and quotes). Zotero shows somewhat of a bias toward digital sources when interface for entering page numbers is not planned, while analogous interface for digital documents--annotations and highlights--is continuously improved. I believe Zotero is intended as research software for all scholars, not just for those who work with digital sources.

    Adding interface for page numbers doesn't seem any different than adding x & y coordinates for annotations in html docs or any other locator--in Vertov, for example, the in/out timecode data looks to the user as if it exists in two separate fields, when it's really stored in the note itself as XML. It would be great if an interface like that for entering page numbers was added in the future.
  • I have not yet made up my mind on this. I used the standalone notes for short citations, but then I had to type a short title for annotations. Moreover they cannot be related to each other. When working on 19th century documents I now create a 'book' for each document and attach all my notes to it. In theory, these notes can be moved to other files, but you risk to lose the original source and that is a historian's nightmare. So, I leave them under the title of the book. The disadvantage then is that individual notes cannot be related to each other.
  • edited July 11, 2008
    The disadvantage then is that individual notes cannot be related to each other.
    Yes they can--use the "Related" link at the bottom. Why wouldn't that work?
  • Yes indeed, they can be related thanks!
    Then there is there is another problem. When working on the 3x5 cards I used to shuffle them on my table, mostly to find some order especially just before writing a paper. Now this seems to be a bit more complicated with zotero. When you take notes from a book, or from a document, you make a list of annotations sorted under the book, or document. So when it comes to shuffling you have to detach them from the book i.e. make standalones of them. But being detached from the book, you risk to end up with dozens of standalones without knowing where they come from originally. So the question is: what comes nearest to the original shuffling process (which I regard as necessary to creative, yet systematic writing).

  • edited July 14, 2008
    For now, you should use reports. There are several open tickets for more notes support--those will allow users to display and organize notes independently of sources in the middle column and in saved searches.
  • In order to imitate the shuffling of cards on a table, it is recommendable to insert a freeze/unfreeze function of notes, that is a possibility to arrange notes in a certain order which can be saved. All this should work without laborious decimal codes, but by a more convenient drag and drop function so that a dozen of cards can be shuffled on the screen (comparable f.e. to windows powerpoint, but preferably with more trees).

  • @erazlogo: Using reports to organize notes is at best completely off-putting. Manually entering numbers for custom sorting is laborious and inflexible to the point of being prohibitively time-costly. In the page you link to, which describes the reports workaround, the instructions read:

    "First tag each note with a description, such as “chapter one”. "

    Note-tagging hasn't been implemented yet; I'm sure the instructions (and the person who wrote them) mean to tag the parent item to which the child item (=note) is related. But the slip of the tongue in the instructions underscores the significance of tagging notes. I've read a number of threads regarding extending the functionality of notes - both child and standalone notes - and I'm puzzled as to why *at least* tagging capability for notes has not been added.

    I do understand development priorities and milestones, and it seems like extending note-taking capability is not a high-priority at this point. I also understand the sentiments of those who are hesitant to integrate more complex note-taking / organization functionality with Zotero. The program is presently excellent at managing references. But without the extension of note-taking / organization functionality, I'm left thinking 3x5 notecards still (in this digital age) have appeal, especially when the alternative is the (very awkward/laborious) reports workaround.

    I would love to see Zotero become a true replacement for 3x5 index card systems that many of us (I'm 30, in grad school) learned to use "back in the day". I take all my notes on the computer, and manage my references with Zotero. But continuity in WORKFLOW just isn't there, and could be if notes were bestowed with not-so-magic, but appropriate to their status in the research process, power.

    Adding tagging functionality to notes (especially standalone notes) would be a great start. It would be equally useful if child notes could be "independently sorted" (ticket #672), i.e., for one to drag several child notes from a particular collection into a "notes" collection, maybe for a book chapter or article section (=a collection titled "Ch1" or "Sec1").

    I know there are tickets for these things, but my point is that they are related in terms of workflow. As a research tool, I would love to see Zotero evolve in ways that improve not only the organization of references, but also the way we organize and construct our understanding of these references.

    (Apologies for the verbose post; I've been saving this up for awhile.)
  • @ all the devs: Plz read my comment as constructive. My colleagues and I all use Zotero and appreciate having an open source, free program that does so much.
  • Note-tagging hasn't been implemented yet
    Note tagging has been possible since Zotero was created. Click "Tags" below the note editor.
  • ::unimaginable blush::

    Thx Dan for the speedy response! This helps. I'll keep following the threads related to custom ordering of items (including/specicially notes) for news on that part of my post.
  • Tagging sticky note annotations would be incredibly useful for qualitative researchers because it would allow one to use Zotero for grounded theory type studies
  • It seems that many other people in the forums are dealing with the problem of sorting notes. See for example the discussion 'Which is better for an historian'. I have been working with Zotero for more than a year now. It is unsurpassed as a search, storage, retrieval and reference assistent, but it fails to assist researchers in the final phase of a project: the writing out of a paper. What we need here, is a method to sort the notes in the order of a paper (in development). Tags, relations don't do this job, nor does a numbering system (too complicated). To print all the notes as 'reports' comes closer to it, but demands too discipline while taking notes; if the report becomes too long, the sorting becomes too difficult and you risk to loose the original source.

    Lacking a sorting function in Zotero, I still work with index cards (referring to zotero) while writing, but this is far from ideal. I am also experimenting with writing papers on google docs together with zotero; search in zotero, sorting on google docs, but this is not the same as the old shuffling and sorting of cards. Moreover, google docs and zotero are not yet connected to each other (like word and zotero).

  • Being able to sort notes manually would be crucial. It would help a lot when writing a paper.

    It would also be great if we could attach one note to another and so on: not just to items, but notes to notes, in different levels.

    Many thanks!

  • Just came across this in the forums. It looks like there's some demand for more flexible report output from zotero. With basic web programming skills and a bit of javascript you could implement the notes shuffling tool with the code that I've written at as a basis. NB it only works with Firefox 3.5 right at the moment until the developer of the webserver-inside-firefox fixes some bugs with his code and firefox 3.6, but hopefully that will be fixed soon.
  • Kieren, could you explain this in a little more detail?
  • TheCyberProf: I don't think my tool will support the tagged notes stuff that you mentioned. I've investigated using Zotero for qualitative analysis but I couldn't see how to get an efficient workflow going, and the kind of reporting I wanted. However, given the awful state of the commercial tools in the area, I ended up writing some prototype tools in perl for retrieving tagged text in about the same amount of time it would have taken me to learn to use Nvivo properly.

    As far as the Zotero tool I've put together goes, the README file at explains the basics of what I've done to get web application style development with the zotero API, which simplifies the development process quite a lot. The shuffle notes idea is quite interesting, and I suspect that I may get around to implementing it next time I feel a dose of writers block coming on.
  • Thank you, Kieren. I will check it out during my current bout of writer's block.
  • "Lacking a sorting function in Zotero, I still work with index cards (referring to zotero) while writing, but this is far from ideal. I am also experimenting with writing papers on google docs together with zotero; search in zotero, sorting on google docs, but this is not the same as the old shuffling and sorting of cards."

    Amen! I spent 200 hours configuring Procite a long time ago to have an electronic bib AND note taking for my discipline. But Procite hasn't been updated since 2000 and Endnote would require the same laborious work around. What I did with Procite is format each source type so that it looked like an index card (header in bold, reference citation, my notes, then tags/keywords). Great for sorting (like Zotero) but I can also export to actual cardstock and cut them up as 4X6 index cards.

    I wish Zotero could export to something other than reports (not useful). My last project had the electronic equivalent of 6,000 note cards and to shuffle them in the end I actually exported to Word and had them all (2 per sheet) printed and cut on card stock! Obviously I can have 6,000 "note cards" on Zotero but how do I shuffle them as with note cards.

    It's funny: I'm always teaching new electronic research tools, I've turned my students on to Zotero but beyond a very short paper, they (and I) still return to index cards!! This would be a killer app.

    (Yes, I know I brought this up years ago and got slammed but it seems that now returning years later to this forum that many other people think Zotero has developed so that this might be a next step?).

    Thanks for listening.
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