working with notes

Right now, Zotero does not seem to be very well suited for notetaking. Perhaps it is supposed to be mostly a tool for collecting references and full-text items, not for notetaking. But in case it isn't, here are some features that could be improved.

Take, for example, a saved search that contains only notes. It's impossible to know from a list of records where the notes come from. If I scroll through, I can see the titles of item types they linked to in the right pane, but only if there is a title--for item types such as letters or interviews I see nothing.

If I click above the note to get to the no-title item type, I'm taken out of my saved search and back to the entire library folder. Then when I go back to my saved search, I lose my place in the list of notes and I have to start all over again.

If I start clicking on tags to further narrow down my saved search, additional records start appearing--item types with this tag that were not found in my saved search originally. What i need to see instead is only the notes from my saved search that have this tag.

If I click on a tag that is attached only to notes (meaning in the entire library there are no item types with this tag, only notes), nothing happens at all. It seems that tags are only set to interact with item types and do not work with notes (or attachments?) at all.

In general, Zotero seems to be phasing out notes altogether. You can search for a phrase or regexp within an attachment but not within a note--are we now supposed to take our notes in a word document, then attach it, so we can locate a particular phrase within our own notes? And there is no field to add page number, which is still pretty important for people who work with printed texts, as opposed to online sources.

Again, perhaps Zotero is mostly a bibliographic tool "to collect, manage, and cite" sources, as it is described on the home page--in this case, feel free to ignore these comments.
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  • I don't think anyone intends Zotero to be a bibliographic tool to the exclusion of its other functions. I for one hope that note taking in particular is an area where Zotero continues to develop, including rich text notes (of some sort), good searching and manipulation (which is what you ask for), links to other notes and the web. Some of these are already on the development timeline. I'd love to see Zotero take on both the dedicated note programs (OneNote, EverNote, and the panoply for the Mac) and the personal wikis.

    My first response to your request for a 'page number' field is: "Do you really need that?" and "Can't you just throw it in as the last thing in a note? (in parens, for example). I would rather take all my notes for a given item in *one* note, so I can still see the connections between them (but I do want that note to have minimal structure). But I share an office with a fanatical one-quote-per-note man. To him a note on a book needs the classical 3 pieces of metadata: classification tags, reference to the resource it belongs with, and page number. Zotero handles the first two of these already.

    Perhaps you can add to your original post by saying why you want page numbers in a separate field?
  • edited April 13, 2007
    This an issue that I deal with. I wouldn't necessarily want a page field (I think that's too restrictive to particular ways of working), but I do think it's valuable to have excerpts/quotes as full semantic objects, to which one can attach a page number (or other such locator) directly.
  • edited April 12, 2007
    There are many cases when taking notes on a book in one note doesn't make sense--you may need a different note for the main theoretical argument from the intro vs. a detail of a strike or a riot from one of the chapters. These two notes will then require completely different tags. If you take several notes, it is important (for me) to know where they belong in a book--which one is comes earlier--and that's where page numbers come in. I'm also used to being able to automatically sort notes in the list view by page numbers.

    Page numbers are also relevant to working with notes apart from sources--what I'm used to seeing above the note (instead of current title or no-title link to source) is a short citation--last name of author, short title, and page number. that line makes it obvious where the note belongs. It would also be great if control-clicking on that cite would then allow me to copy a footnote reference, with page number, to clipboard (and that is not possible unless you have a separate field for page number).

    In general, there should be some field to indicate the location in a source where the note points--not just a for a book--other examples could include time code for a video/audio source, or GPS info for a map, etc.
  • Take, for example, a saved search that contains only notes. It's impossible to know from a list of records where the notes come from. If I scroll through, I can see the titles of item types they linked to in the right pane, but only if there is a title--for item types such as letters or interviews I see nothing.
    Well, part of the problem here is that an appropriate placeholder title isn't auto-generated for letters and interviews if none is specified. For bibliographies such titles can be handled via CSL, but that doesn't really help within Zotero itself. But I guess something like "[Letter from Henry D. Thoreau to Ralph Waldo Emerson]", with all but the names auto-filled, could work... You'd have to have proper localization and handle multiple participants somehow, though.

    The more fundamental problem of non-matching parent items not showing up in the search has been discussed quite a bit. See this thread and the three linked from it. We welcome other suggestions. Beta 4 offers a "Child Note" search condition that lets you search for content in child notes and display just the parent items, so you might want to consider using that instead of just "Note". I still don't know if we have a great solution for quicksearch. The best approach may be to display matching top-level items, matching children, and non-matching parents of matching children in gray. I'm not sure about non-matching siblings—on the one hand, if all siblings displayed in gray they could make browsing through search results quite tedious, but if they weren't shown that could be confusing/alarming and also require you to switch to the library to view them and therefore lose your place in the results.
    If I start clicking on tags to further narrow down my saved search, additional records start appearing--item types with this tag that were not found in my saved search originally. What i need to see instead is only the notes from my saved search that have this tag.
    Not clear on this, or at least can't reproduce it. Can you provide an example, including the search conditions on the saved search?
    If I click on a tag that is attached only to notes (meaning in the entire library there are no item types with this tag, only notes), nothing happens at all. It seems that tags are only set to interact with item types and do not work with notes (or attachments?) at all.
    As I mentioned on the ticket, this is due to child items not technically belonging to collections. I've been meaning to fix it for a while.
    In general, Zotero seems to be phasing out notes altogether. You can search for a phrase or regexp within an attachment but not within a note--are we now supposed to take our notes in a word document, then attach it, so we can locate a particular phrase within our own notes?
    Not sure why you'd reach the conclusion that we're phasing out notes... Search conditions, "Note" and "Child Note" included, are all phrase searches, and we added phrase searching in the quicksearch bar (by use of quotation marks) in Beta 3. We have no (remotely efficient) way of supporting regular expressions for note content until Mozilla supports user-defined SQLite functions in mozStorage—the REGEXP function in SQLite is just a placeholder for a UDF.
    And there is no field to add page number, which is still pretty important for people who work with printed texts, as opposed to online sources.
    I'll let other people discuss this. I generally agree with Bruce that this could just be solved by semantic markup (probably aided by some UI magic), but wanting to sort by page number is a legitimate concern. I wouldn't rule out the possibility of manual ordering of notes—that seems potentially more useful than manual ordering of items within collections (which we might eventually support too). I guess a workaround would be to put the page number at the beginning of the note...
  • edited April 13, 2007
    Dan--many thanks for such a thorough reply.
    But I guess something like "[Letter from Henry D. Thoreau to Ralph Waldo Emerson]", with all but the names auto-filled, could work... You'd have to have proper localization and handle multiple participants somehow, though.
    Ideally it would be [Thoreau letter to Emerson, 5 Jan 1859] and, for interview, [Thoreau interview by Emerson, 5 Jan 1859] with et al. added if there are more senders/recipients or interviewees/interviewers. You need the date also because people who work with letters would usually have more than one with the same correspondents. Not sure how to deal with localizations though.
    The best approach may be to display matching top-level items, matching children, and non-matching parents of matching children in gray. I'm not sure about non-matching siblings—on the one hand, if all siblings displayed in gray they could make browsing through search results quite tedious, but if they weren't shown that could be confusing/alarming and also require you to switch to the library to view them and therefore lose your place in the results.
    I really like this approach with the caveat that matching children appear as child items of greyed out parent items (as you probably meant to do). On greyed out siblings--I think there should be some way to indicate that there are more child items linked to the same parent item--maybe something like [...] which would then expand to show all child items if you click on it, as you do for abstracts in the right pane. But I would not mind just seeing a list of greyed out child items if that's easier.
    Beta 4 offers a "Child Note" search condition that lets you search for content in child notes and display just the parent items, so you might want to consider using that instead of just "Note".
    I just tried this--this is a great idea, but what you get back is the parent item with all notes attached with no way to tell which note has the phrase you're looking for. What would be great to have instead is something like "Parent Title" and "Parent Author" search for when you need to find a particular phrase in your notes from a particular book or article. So you could search for Parent Author contains Geertz & Parent Title contains Bazaar & Note contains "clinical interests" and then the results would be Geertz, "Bazaar Economy" greyed out with a not-greyed out child note that contains this particular phrase.
    "If I start clicking on tags to further narrow down my saved search, additional records start appearing--item types with this tag that were not found in my saved search originally. What i need to see instead is only the notes from my saved search that have this tag."

    Not clear on this, or at least can't reproduce it. Can you provide an example, including the search conditions on the saved search?
    This problem disappeared after the latest dev update, so never mind. Sorry.
    We have no (remotely efficient) way of supporting regular expressions for note content until Mozilla supports user-defined SQLite functions in mozStorage—the REGEXP function in SQLite is just a placeholder for a UDF.
    Ok, I didn't know this. I meant regexp search not available in notes rather than phrase--I was surprised to see that option for snapshots but not notes. This makes sense.
    I generally agree with Bruce that this could just be solved by semantic markup (probably aided by some UI magic)
    If IU magic could be done, putting page number in the beginning of the note, say, in brackets, makes sense. But in the long run, people would want to link notes to map coordinates and timecodes of media files (you know I'd like to do the latter) so some IU/data extraction magic will need to be done for that too.

    Thanks again for replying, Elena
  • If IU magic could be done, putting page number in the beginning of the note, say, in brackets, makes sense. But in the long run, people would want to link notes to map coordinates and timecodes of media files (you know I'd like to do the latter) so some IU/data extraction magic will need to be done for that too.
    Hmm ... interesting.

    This gets at some big design issues, actually. For example, when you say "links notes to ..." that might suggest some real modeling, rather than just simple annotations. In RDF terms, you'd be linking to the page/corrdinate/etc, which is then attached to the main item.

    But I suppose allowing flexible key/values (which is more than a tag of course) to be attached to notes would help this. Perhaps that flexible key/value approach could also be integrated into the in-content markup too.

    Just thinking out loud ...
  • Bruce--well, if I understand you correctly, yes--Zotero annotations are linked to the snapshot, not the parent item. Not sure what RDF for annotations to snapshots/images would look like, but perhaps Zotero will be adding "related item" tags to the attachment.

    But if you don't have the actual attachment/map/video file/book, then you'd only have the parent item and notes. What would then RDF look like? A use case would be annotating a dvd of a film, then exchanging timecoded notes with another user, who could load his own copy of the same dvd and map the annotations to particular moments in the film. Same model as books, only for video. Map coordinates could be exchanged in this way also in theory.
  • Example:

    <x:Note>
    <x:annotates rdf:resource="urn:isbn:23988734#page=23"/>
    <rdf:value>blah, blah, blah ...</rdf:value>
    </x:Note>

    <x:Segment rdf:about="urn:isbn:23988734#page=23">
    <dcterms:isPartOf rdf:resource="urn:isbn:23988734"/>
    </x:Segment>

    <x:Book rdf:about="urn:isbn:23988734">
    ...
    </x:Book>

    Do you see what I'm getting at?
  • got it--thanks!
  • edited April 16, 2007
    On the dev branch, child items now appear in context in search results, with non-matching rows appearing in gray. The tag selector should also now display tags from child items.

    Folks running a dev build should give both a try and let me know how it works out. There might be bugs, so testing would be appreciated.

    Didn't implement Elena's ellipsis idea for non-matching child items yet, though I might—I could see that potentially working well.
  • edited April 16, 2007
    Thanks! This works great in the main My Library collection, but when I try to work with other collections the tag selector seems to act as if I'm still in My Library folder:

    When I'm in a collection I still see all tags available (not greyed out), whereas I should be seeing only tags linked to the documents in this particular collection.

    If I do a quick search within a collection, the documents shown in middle pane are correct--only the items matching the search criteria in this collection show up. But the tags available in the tag selector match all items in the entire library with these search criteria--some of these tags do not belong to the items in the middle pane.

    Many thanks for this change and also for drag-and-drop from the file system--that works fabulously as well.
  • edited April 16, 2007
    More on this:
    "But I guess something like "[Letter from Henry D. Thoreau to Ralph Waldo Emerson]", with all but the names auto-filled, could work... You'd have to have proper localization and handle multiple participants somehow, though."

    Ideally it would be [Thoreau letter to Emerson, 5 Jan 1859] and, for interview, [Thoreau interview by Emerson, 5 Jan 1859] with et al. added if there are more senders/recipients or interviewees/interviewers. You need the date also because people who work with letters would usually have more than one with the same correspondents. Not sure how to deal with localizations though.
    Here is a possible localization-free way of indicating letters and interviews above the note:

    [Sender Last{ et al.}; Receiver Last{ et al.}; Item Type, Date], for example:

    [Thoreau; Emerson; Letter, 5 Jan 1859], or for interviews:

    [Thoreau; Emerson; Interview, 5 Jan 1859]

    If it's hard to distinguish between senders and receivers for auto-generation, just listing last names of all authors would work ok--there are usually only one of each and if there are more presumably the researcher can figure it out from the context in the note.
  • edited April 16, 2007
    Another notes-related request: it would be great to have a way to find and select a word or phrase within a note. Right now when I find a set of notes/snapshots containing a particular phrase, I can then use Firefox search function to locate and select this phrase in a snapshot, but I have to read through the entire note to find it. If notes could be loaded into the browser as html pages, they could be word-searched in the same way as snapshots.
  • When I'm in a collection I still see all tags available (not greyed out), whereas I should be seeing only tags linked to the documents in this particular collection.
    OK, should be fixed now. Thanks.
  • edited April 16, 2007
    More bugs: When I select a bunch of records through the tag selector or the quick search, I can't get to any related items that are not in the found set. It seems users should be able to get to related items by clicking on them in the "related" tab, even if that breaks up the found set.

    Also, the quick search for a phrase (using quotation marks) doesn't seem to find phrases in attachments, even when searching for the same phrase in the advanced search (using the pulldown menu) does.
  • Fixes for the last two bugs checked in.

    I also updated the items pane to properly gray out non-matching items when viewing a saved search. This does raise one problematic issue of how the quicksearch and tag selector should work, however. Currently, the scope they use to search (and display tags from, in the case of the tag selector) comprises solely the non-gray items. This means that if you have a child note "Foo" on item "Bar" and do a quicksearch in the Library for "foo", only the tags on "Foo" (which is black) will show up in the tag selector, not the tags on "Bar" (which is gray). That's probably the expected behavior. However, it also means that if you have a saved search that searches for notes containing "foo", typing "bar" into the quicksearch will find no items, since "Bar" is just a gray context item and isn't included in the quicksearch scope. While that makes sense on a theoretical level, it probably has the potential to be confusing for users who are used to using the quicksearch bar to find anything in the current view. It also means that if you had, say, a saved search for recently modified items, and some of those were child notes, and those notes pulled in their parent items as (gray) context items, you wouldn't be able to find the parent items with the quicksearch.

    Should the quicksearch behave differently within a saved search and include all siblings, parents and children of in-scope items? If so, when you match a gray item, does it remain gray, since it still doesn't match the saved search? How then do you know that it was what the quicksearch matched?

    Alternatively, might there just be an advanced search option along the lines of "Match item sets" that would display all siblings, parents and children of matched items in black, which could then be filtered via the quicksearch normally?

    Other ideas?
  • edited April 17, 2007
    Alternatively, might there just be an advanced search option along the lines of "Match item sets" that would display all siblings, parents and children of matched items in black, which could then be filtered via the quicksearch normally?
    This option makes most sense to me--it would also be great to toggle any "saved search" to "work with entire item set" and then back to actual found items. If I have over 200 found items in the found set I currently cannot find a note by the author "Bar" through quick search if the parent item "Bar" is not in the found set--it would be great to have that option. (this would be an equivalent of "parent author" advanced search)

    But it would also be great to show the actual found items within the entire "matching set", and I don't see how to do that without color coding found and not found items--say, green for found items and blue for other items in the entire "matching set." Then in this case above:
    This means that if you have a child note "Foo" on item "Bar" and do a quicksearch in the Library for "foo", only the tags on "Foo" (which is black) will show up in the tag selector, not the tags on "Bar" (which is gray).
    You'd see tags for "Foo" in green, and tags for "Bar" in blue and all other tags greyed out.

    And in this case:
    if you have a saved search that searches for notes containing "foo", typing "bar" into the quicksearch will find no items
    You will find the "bar" items but they will remain blue--not in the original found set for the saved search.

    Also, in light of this discussion perhaps it does make sense to use ellipsis for extra greyed-out notes--to make the view simpler at least initially.
  • edited April 19, 2007
    another bug: if i create a saved search for a particular tag, and a parent item has this tag, then all its child items appear in black, even when some child items do not have the tag. Instead, I should only see in black the parent item and the child items that have the tag, and all other child items grayed out. This does not happen if I do a quick search or even in the search results window for the advanced search, but only happens when I save the search.
  • edited April 19, 2007
    more oddities: It looks like saved-search reports print matching notes both under matching parent items and as stand-alone items. As a result, in the report some notes appear twice, but for others there is no way to tell which parent item they belong to (if the parent item is grayed out).
  • The new handling of child items in searches is now available in 1.0.0b4.r3. Some of the things discussed here haven't yet been implemented, but this should be an improvement.
  • edited April 28, 2007
    It seems that now saved-search reports only display found parent items with ALL the linked notes and attachments. As a result, the report doesn't reflect the found set at all: If a parent item is found, there is no way to tell which of the child items are in the found set, since all of the child items are printed. It may be more logical to omit child items that are not in the found set.

    More importantly, if a note is found but its parent item is not, the note does not appear at all. The only way to fix this I can think of is to add a short reference for the parent item which would be printed together with each found note, along the lines described earlier in this thread for an interview or letter (i.e. Author Last[, et. al]; Short Title [Item Type if no Title], Date).

    If anyone has other thoughts on how to make reports correspond to found sets let me know.
  • edited May 8, 2007
    a related reports issue: "generate report on selected item" on right-click doesn't work for child notes. i suspect the reason for this is that currently reports ignore notes, so when i select a child note without selecting its parent and choose the "generate report" option, i just get an empty screen. i know logically why this happens, but this will probably look like a bug to a new user.
  • I'm awed by Zotero's bibliographical functionality. But I have to agree with erazlogo, I don't think I'll be able to use the note-taking features.

    For notes, I'm now using my own crude build of Filemaker. By tagging notes with outline rubrics and dates, I'm able to sort them into "narrative outline" and "timeline" views, showing many notes (from different sources) in sequence, on the same page. These views are very useful as conceptual scaffolds during the writing process.

    On the bibliog side, I do record each source in my Filemaker build (in the old grueling, manual fashion) before I enter notes based on it. I also include a bibliog field on each note so that I know which source it came from.

    BUT -- and I think this is whence Zotero's weakness on notes stems -- I treat bibliog items and notes as "equals," i.e. all are individual, independent "items" or database entries. I then sort these into views that segregate them *as if* they were different types of items. So, my various bibliog views show only those items tagged as bibliog sources. The outline and timeline views show only those items tagged as notes.

    Zotero, by contrast, seems to treat a note as an attribute of a bibliog-item. One can manipulate bibliog items through searches, sorts, etc., but notes remain slaved to bibliog items.

    As such, Zotero seems great for creating annotated bibliography. But I can't figure out how I would use it to manipulate notes into the thematic and chronological patterns one needs during the writing process.

    I haven't spent a lot of time playing with Zotero. If I'm misspeaking, I beg your pardon -- and would LOVE to hear how I might unleash these as-yet undiscovered note-taking functions! Assuming I'm right, though, then my feature requests would include: sorting, searching, exporting and generating reports *on notes* as independent database items.

    It occurs to me (as a newbie and non-programmer) that this may not be possible due to some technical differences in the way, say, Filemaker and Firefox do databases. Is this the case? If not is something like this on the horizon for Zotero? If not, does anyone know of a single software that does a serviceable job both of automating bibliog entry and robust note manipulation of the type I describe? (I'm assuming *someone* has done this for their own individual Filemaker build. But then one lacks the excellent community problem solving that you guys have created here.)
  • It occurs to me (as a newbie and non-programmer) that this may not be possible due to some technical differences in the way, say, Filemaker and Firefox do databases. Is this the case?
    No. Zotero has a relational database underneath (so same technology), and notes are full fledged items in the database. You can create top-level notes that are unattached to specific bibliographic resources.

    I tend to think notes are in fact different, and need to be modeled so in the database if Zotero wants to support the kinds of features some people are calling for (such as ordering).
  • Zotero, by contrast, seems to treat a note as an attribute of a bibliog-item. One can manipulate bibliog items through searches, sorts, etc., but notes remain slaved to bibliog items.
    "Standalone" notes are quite possible in Zotero! And you can reassociate a particular note with a (different) citation or remove the association so that it becomes standalone. Searches, sorting, etc. do work on standalone notes.
    As such, Zotero seems great for creating annotated bibliography. But I can't figure out how I would use it to manipulate notes into the thematic and chronological patterns one needs during the writing process.
    There is a button to create a standalone note. The first line of the note is the title. You can use it for crude sorting.
    Assuming I'm right, though, then my feature requests would include: sorting, searching, exporting and generating reports *on notes* as independent database items.
    This, by-and-large, already exists.
    It occurs to me (as a newbie and non-programmer) that this may not be possible due to some technical differences in the way, say, Filemaker and Firefox do databases. Is this the case?
    No, it isn't the case.
  • edited June 29, 2007
    "Assuming I'm right, though, then my feature requests would include: sorting, searching, exporting and generating reports *on notes* as independent database items."

    This, by-and-large, already exists.
    Well, not really, because Zotero users can neither export child notes by themselves, nor mix child notes from different sources in a sort.
    is something like this on the horizon for Zotero? If not, does anyone know of a single software that does a serviceable job both of automating bibliog entry and robust note manipulation of the type I describe?
    Well, older CHNM software, Scribe, does all of this, plus it has an outline and timeline feature, and it's based on Filemaker. However, Zotero should have something like this also--ticket created. Not sure what the solution will be, but this functionality will be added somehow.
  • How about keeping Scribe alive, rather than trying to reinvent the wheel, and updating it to integrate more tightly with Zotero? A starting point would be making MySQL, rather than Filemaker the database. Next, synchronization instead of import/export (although this may be moot if they use the same database).
  • edited July 24, 2007
    Well, Zotero already has an sql database backend, and it only needs a few tweaks to work as well with notetaking, as I explain here.
  • edited July 25, 2007
    I know about the sql database. I've successfully accessed it using OpenOffice Base. Maybe that's the way to add some of the capabilities being discussed in the forum.
  • I definitely and strongly support the independent child note feature, WITH dedicated heading columns that are sortable (or allow custom renaming of the title, creator, year, call number columns that are used in the source records).
    Please, please, please give ticket 672 higher priority. Working with both scribe and Zotero is really a pain, and the crude workaround, starting standalone (or child) notes with the page numbers (including leading zeros!! 008-014) is the kind of thing computers and software are supposed to do for users, not the other way around.
    Thank you.
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