Extract PDF notes

AlbertoM1
Hi there,
When attaching a pdf file to a new element, Zotero extracts automatically all in-file pdf annotations (e.g. Adobe acrobat highlighted sentences) as annotations impossible to delete.

How to avoid this automatic extraction?
  • dstillman
    What's the actual problem? Zotero shows embedded annotations like any other PDF reader. If you want those to be editable, go to File → Import Annotations to transfer them from the PDF file into Zotero itself, where they'll be editable.
  • AlbertoM1
    Hi. I am referring to when pdf is still closed. Zotero shows annotations taken with Adobe in the list among annotations taken with Zotero. This is a mess. All Underlining and highlighting previously done on Adobe become notes. Unacceptable. I need Zotero to show only annotation
    https://s3.amazonaws.com/zotero.org/images/forums/u17619333/e6wxd4jhki0mzxtjf09w.png
  • AlbertoM1
    I need Zotero to show only annotations (notes, nor highlithing) done with Zotero as Mendeley does
  • dstillman
    Why wouldn't Zotero show you the existing annotations in the file? If you don't want your previous work for some reason, use File → Import Annotations from the reader and delete them before annotating with Zotero.
  • AlbertoM1
    I want to keep my previous work. What I dont want is my highlightings to be considered among Zotero notes. I dont want 106 notes listed for every Underlining and highlighting previously done on Adobe. I dont understand what are you suggesting: File + import and then? See my screenshot
    https://s3.amazonaws.com/zotero.org/images/forums/u17619333/a61g1gaihq9kl9hfygal.png
  • dstillman
    They're not notes. They're standard PDF annotations that Zotero is showing you, as any PDF reader would.

    File → Import Annotations is in the reader. Open the PDF first.
  • AlbertoM1
    edited 13 days ago
    Ok I try
  • dstillman
    edited 13 days ago
    Again, this is in the Zotero reader — in a reader tab, not the main library tab. You have to open the PDF and then look in the File menu.
  • AlbertoM1
    Ok. Sorry. Done. Now?
  • AlbertoM1
    Do I have to manually delete 110 annotations? A part from the time wasted in this way, the solution is not acceptable. It will remove annotations. Have you ever used Mendeley? Mendeley keeps all annotation done on the pdf with Adobe but when you add a note with Mendeley or highlight something, in the Mendeley list of notes it will show on the right of the file only that single note or only the notes created with Mendeley. Plus, if you click on the note it will open the pdf file exactly at that page.
  • dstillman
    edited 12 days ago
    I think you may be misunderstanding something here. Your screenshot shows the Annotations section of the item pane. The whole point is to show you the annotations you've made on the PDF — which includes highlights, underlines, note annotations, ink annotations, etc. That's going to show annotations you made in Zotero as well as other PDF readers, because they're all annotations. It would make no sense to show highlights created in Zotero but not show highlights made in Acrobat — people would complain, rightly, that Zotero couldn't display standard PDF annotations.

    If you just want to take notes — not annotations — about the document, you can create Zotero notes on the parent item, either from the library tab or by opening the Notes pane in the reader. Zotero notes aren't annotations and don't appear in the section you showed.

    If you don't want to see the list of PDF annotations in the item pane, you can just collapse that section.

    If for some reason you want to actually remove the annotations you created in another PDF reader, you can use File → Import Annotations from the reader, open the Annotations tab of the left sidebar, select all annotations, and delete them.
  • AlbertoM1
    edited 12 days ago
    we reached some point here. You mean that I can create a note on page 5 of my pdf (with pdf opened) and it will be listed in a different list (with pdf closed) with respect to annotations?
    It can still be acceptable. How to do this please? I do not see any option to do this nor see any area of the right menu dedicated specifically to notes
  • dstillman
    edited 12 days ago
    No, notes are just notes. They're child items of the parent item. There's a Notes button in the side navigation bar in the reader that will open up an editor on the right.

    Annotations — of all the kinds I listed above, including highlights, underlines, and location-specific note annotations — are annotations on the PDF, and those are going to appear in the Annotations tab of the reader sidebar and the Annotations section of the item pane in the library view, no matter where they were created. Again, it would make absolutely no sense for a highlight that you create in Acrobat and a highlight you create in Zotero not to appear in the same list of annotations. Zotero has a built-in PDF reader. It supports many standard annotation types. You create them the same way as in other PDF tools. They happen to not be stored in the file while using Zotero, but that's a technical implementation detail — if you export the PDF, they'll all be embedded in the file as standard PDF annotations. I don't know why you have this idea that PDF annotations created in Zotero and PDF annotations created in another tool are somehow fundamentally different, but there's just no basis for that, and it's not what the vast majority of users would expect. This isn't going to change.
  • AlbertoM1
    A part from what you think is correct or not, which I totally disagree (as all users I think, since Mendeley works in this way sonce ages, separating pdf in-file notes (not highlightings) created with Mendeley (put in a separate list) from the one created with Adobe (not listed by Mendeley). I am just speaking of the top player in the market used by millions of users...), the conclusion is that I cannot create any note (not highlightings) to page 5 that will be listed separately from Adobe notes?
  • dstillman
    They're not "Adobe notes". They are PDF annotations, created and read by any PDF reader, including Zotero. It's a specific technical thing, and the fact you don't understand that and keep insisting that there's some difference means you kind of have trust us when we tell you that what you're suggesting would not make sense. Mendeley failing to support PDF annotations in a standards-compliant way is just an example of their app being shoddy, not something to emulate.
  • AlbertoM1
    I think you are messing up things.
    Simple questions, simple answers, no escape:
    1) can I create a note to page 5 with Zotero that is listed separately from highlightings in the right menu of Zotero? YES or NO
    2) can I create a note to page 5 that when I click on it (in the right menu of Zotero) will open the pdf directly at that page? YES or NO
  • dstillman
    "no escape"? I'm not sure why you're making this so contentious? Our sole goal here is to help you. You've been using terms like "Adobe notes" that suggest a misunderstanding of the technical details, and I've been trying to clarify what's actually involved here, which has implications for how you should expect this to work.

    You asked whether annotations created with Adobe would be displayed separately from annotations created with Zotero, and the answer is no and will remain no.

    For your new questions:
    1) can I create a note to page 5 with Zotero that is listed separately from highlightings in the right menu of Zotero? YES or NO
    Currently, no. As I've said, the section is called Annotations, and it will show all annotations of any type. It may become possible to filter different types of annotations there in some way. That will definitely become possible in the Annotations tab of the reader's left sidebar, where there are already other filtering options (tag, color, etc.) at the bottom of the pane, and we'll be adding annotation type as a filter there. That wouldn't work as well in the item pane, which is already contextual based on what's selected in the items list, but we'll see what makes sense there. Annotations will be displayed directly in the items list in the next major version of Zotero, and it will likely become possible to filter the items list by annotation type in some way, which would accomplish the same thing.

    Just to be clear, it is standard for PDF readers to display annotations in a sidebar without any sort of filtering options, and that's what Zotero does now. We go beyond that already in the reader sidebar, and we'll be adding other features to both the reader sidebar and item pane Annotations section, but you should understand that what you're asking for is not a standard thing. Mendeley not displaying the standard PDF annotations that are already in the file isn't a feature — that's just a limitation of the software. Mendeley has not historically demonstrated a lot of care for standards or interoperability.
    2) can I create a note to page 5 that when I click on it (in the right menu of Zotero) will open the pdf directly at that page? YES or NO
    Currently, no, but that's just because the display of annotations there was added recently. You can do this in the Annotations tab of the reader's left sidebar.

    In a future version, it will be possible both to jump directly to the PDF page as well as to edit annotations directly in the item pane. In the Zotero beta, you can also already double-click on annotations in the items list to jump to the PDF page.
  • AlbertoM1
    Hi.
    I wasn't contentious at all.
    I appreciate your help, thanks.
    Just please avoid comments on all users' needs if you don't have statistical data on hand. The same for comments on Mendeley: dont define limitations something that maybe you dont understand. In particular when Mendeley has navigation through pdf notes pointing to pdf pages that Zotero still doesnt have.

    However, again, thanks.

    Turning to the 2 answers.
    They are both NO, as expected.
    But I see some useful indications there.

    Your answer to question 1) "Annotations will be displayed directly in the items list in the next major version of Zotero. it will likely become possible to filter the items list by annotation type in some way, which would accomplish the same thing." When this will be possible? Future week or more?

    Your answer to question 2) why beta has this feature and main version not? When this will be implemented? Very soon or weeks time? And if I use beta I will not encounter any other problems?
  • AlbertoM1
    Plus I just tested Beta version and it does create notes to navigate to pdf pages. You just need to select "turn annotations to notes" by clicking directly on the file in Zotero menu.
    Great... but it does this only with zotero pdf reader. With your custom pdf reader(e.g. Adobe) doesnt work: you click on navigating note and it opens pdf without bringing you to the page of the note...
    So... for annotations it collects annotations from adobe and zotero pdf reader while for "navigation option" it treats adobe differently from zotero pdf reader... Complete nonsense to me.

    Can you please report this problem to developers so to be fixed in the next update?

    (Since the program mixes Zotero and Adobe annotations, to use Adobe as pdf reader is the only reasonable option.)

    Plus you can't select which annotation turn into navigation notes.
    No filtering
    You have to delete manually the entries in the note file created. But everytime you add a pdf annotation and create a new note from annotations again you will find all annotations there..

    Another problem is lags.Extremely long lags.

    Extremely long lag (in the end you need to close program and reopen it or it will not work) to recognize an annotation taken with adobe and to report it in the Zotero right menu.
    No lags with Zotero pdf reader annotations recognition....

    Extremely long lag (in the end you need to close program and reopen it or it will not work) to turn an annotation taken with adobe to a note
    No lags with Zotero pdf reader annotations recognition....

    Can you please report also this lags to developers?

    Why creating integration with adobe and to mix notes Adobe-Zotero if Adobe integration has not yet been perfected and Adobe then becomes an inferior option as pdf reader?

    I understand this is beta but these are normal operations. Why so difficult to perfect them at the 7th version of the program?
  • tim820
    @AlbertoM1 you have been talking to the lead developer all along.
    https://www.zotero.org/support/forum_guidelines#etiquette

  • AlbertoM1
    Ah ok. Great! I directly indicated to the developer the things not working. I didnt know. Great.
    Thanks
    In this way he can give me also indications of how much time for these changes to be applied.
    I will wait for his answer. Thanks
  • mjthoraval
    @AlbertoM1: The people in this forum are doing their best to help you use Zotero in the most efficient way. Please keep in mind that the way to perform a task you were used to in Mendeley may not be the best way to do it in Zotero. Take the time to understand how it works in Zotero before asking to transpose what you were used to.

    Here are a few pages that I have found useful when I migrated from Mendeley:
    Getting Help: https://www.zotero.org/support/getting_help
    How Zotero Support Works: https://www.zotero.org/support/zotero_support
    Reporting Zotero Problems: https://www.zotero.org/support/reporting_problems
    Forum Guidelines: https://www.zotero.org/support/forum_guidelines

    To reply to your questions:
    (Since the program mixes Zotero and Adobe annotations, to use Adobe as pdf reader is the only reasonable option.)
    Zotero simply displays all annotations, both Zotero Annotations and Embedded Annotations. The difference between them is described in the link provided by dstillman: https://www.zotero.org/support/kb/annotations_in_database
    Mendeley is not able to display Embedded Annotations.

    I understand that you would like to be able to hide the Embedded Annotations in Zotero, in the same way as you were used to in Mendeley. Dstillman has replied that this will likely be possible in the future:
    It may become possible to filter different types of annotations there in some way. That will definitely become possible in the Annotations tab of the reader's left sidebar, where there are already other filtering options (tag, color, etc.) at the bottom of the pane, and we'll be adding annotation type as a filter there. That wouldn't work as well in the item pane, which is already contextual based on what's selected in the items list, but we'll see what makes sense there. Annotations will be displayed directly in the items list in the next major version of Zotero, and it will likely become possible to filter the items list by annotation type in some way, which would accomplish the same thing.
    Most users just keep their annotations in Zotero, or more seldom as embedded annotations, so this is not a common request from users to keep annotations both in Zotero and embedded. Can you explain why you want to keep two separate sets of annotations?
    Plus I just tested Beta version and it does create notes to navigate to pdf pages. You just need to select "turn annotations to notes" by clicking directly on the file in Zotero menu.
    You do not need to create notes to navigate to the annotation in the Zotero PDF Reader. You can simply "double-click on annotations in the items list to jump to the PDF page":
    https://s3.amazonaws.com/zotero.org/images/forums/u265723/t9hu69074gwdfb051k86.png

    For other problems like the lag problems you experience, please open separate threads following the Reporting Problems guidelines.
  • AlbertoM1
    Hi. Thank you.
    Yes, I appreciate all the help given. Thanks

    To reply to your question, I would like to be able to hide/separate the Embedded Annotations in Zotero right menu or item list since otherwise they will saturate all the the item list (e.g
    100 underlines) reducing visibility of other key annotations (e.g. notes)

    Referring to the jump page option I confirm you that is not present in main version for both Zotero and other pdf readers.
    And also in beta is not working for all Adobe pdf readers/acrobat

    Where is your screenshot coming from? Which version? Which commands did you use?
  • mjthoraval
    Where is your screenshot coming from? Which version? Which commands did you use?
    This is in latest Zotero beta, where this feature has recently been added:
    https://forums.zotero.org/discussion/123884/available-for-beta-testing-annotations-in-the-items-list

    The screenshot is taken from the centre pane of the main library tab (the "items list" mentioned in the post above).
    The first line "Test item" is a "parent item" storing the metadata.
    The next line "PDF" is a PDF "attachment". This is the PDF file attachment to the parent item "Test item". This is what is visible in the stable version of Zotero.
    The next two lines, with yellow and blue symbols are the annotations in the PDF file. This is only visible in Zotero beta at the moment.

    You can expand the parent item "Test item" by a click on the > symbol at the beginning of the line of "Test item", or by selecting that line, and pressing the right-arrow key on your keyboard.
    You can also expand all the items in the items list by pressing + on your keyboard (- to collapse).
    https://www.zotero.org/support/tips_and_tricks
    https://www.zotero.org/support/kb/keyboard_shortcuts
  • AlbertoM1
    Yes, in beta you will see that. But it will not work with any pdf reader (exept zotero).

    Should I have to report it somewhere? I think this is evident and crucial so maybe no need to report, right?
    Plus I spoken directly to lead developer so he will take care of it, right?
  • mjthoraval
    edited 10 days ago
    reducing visibility of other key annotations (e.g. notes)
    Notes are attachments, at the same level as the PDF files.
    The annotations are nested within the PDF file.
    If you only want to see the attachments, you can only expand the top-level item and keep the annotations collapsed.

    As mentioned above, the ability to hide or filter the annotations in the items list will likely be implemented in the future, which has been raised in the testing of the beta.
    Should I have to report it somewhere? I think this is evident and crucial so maybe no need to report, right?
    Yes, please open a new thread, explaining what you want to achieve and why this is useful for you.
    But it will not work with any pdf reader (exept zotero). [...] Plus I spoken directly to lead developer so he will take care of it, right?
    Zotero receives a very large number of feature requests daily. They listen to all feedback received and constantly implement new features to make it the best reference manager available for a wide variety of users with different needs.
    They do not give timelines to implement new features. The best way to ask for a new feature is to write a clear post explaining what you would like to achieve.

    In the meantime, people in this forum will suggest some other way to workaround the problem you are facing. In your case, I would recommend you to try the Zotero annotations, and eventually move all your annotations in Zotero if that works for you. As you have observed, this is the most convenient way to work with annotations in Zotero.
    Why do you want to keep them as embedded annotations?
    Keep an open mind. Different people use Zotero in different ways. Not everybody shares your priorities, sometimes you're the only person experiencing a particular problem, or maybe you just didn't discover the best way to perform a task. Avoid generalizing statements like “it's obvious that without this feature, Zotero is useless for anybody”.
    https://www.zotero.org/support/forum_guidelines#etiquette
  • AlbertoM1
    Thanks.
    I prefer adobe annotations for many reason, aesthetics and practical. I feel Adobe more solid and robust and annotations are more widely customizable. Plus I have 1000 pdf with hundreds of annotations and I cant move all of them to zotero pdf reader annotations. Too much time.

    Regarding the problem with jump pages impossible with adobe pdf readers also in beta, so I have to write to
    Reporting Zotero Problems?
    https://www.zotero.org/support/reporting_problems
    This is the best way right?
  • mjthoraval
    Yes, simply make a new post here in the Zotero Forums following the instructions in the link.
  • AlbertoM1
    Ok, just done, thanks.
    Hope this will lead to a solution
  • AlbertoM1
    Plus, regarding adobe another advantage of using adobe reader is that if you have a specific version of adobe installed its interface will always remain the same (if you stay on that version) while when updating zotero maybe zotero pdf reader interface will change in the future to an interface/color panel/instruments menu different and maybe not anymore liked by a specific user.
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