I'm planning to move from Citavi to Zotero. The new highlighting and annotation feature seems to bring Zotero closer to the Citavi workflow, and it's fantastic news. I have a range of questions though (from the more specific to the more general):
1. Will/could there be an easy way to jump from Citavi to Zotero (maybe an importer) that also preserves the links between annotations and highlights in the PDF? I am aware of https://www.zotero.org/support/kb/import-from-citavi but that was before the new annotation system was introduced.
2. I understand how annotations exported in markdown retain a link to the file and the PDF annotation, but then how does the formatting work? I'm thinking in comparison to how the Zotero plugin works in MS Word (I am also new to markdown editors and how they play with Zotero).
3. Will there be options to customize the behaviour of the annotation system? I would like for example to have my higlight comments before the highlight, not after; specify how the citekey is formatted, export annotations with a simple click to a specified folder, etc. If yes, what is the best way to suggest features?
4. Are you considering an "atomic notes/Zettelkasten" system either by generating individual notes or some "blocks" in the annotation file, so the highlights/annotations can be manipulated individually (tagged, etc.)?
5. Along the same lines, is there any plan to introduce a way to categorize individual annotations in collections? Alternatively, are you planning to introduce more complex text editor possibilities in the annotation pane, such as an outliner function? Currently there is only one "level" in your annotation pane, thus there is no way to introduce hierarchy in the ideas and the annotations
6. Is there a long-term vision to make Zotero not only a reference manager but also a knowledge manager? The beauty of an app like Citavi (despite being closed source, and now sold off with an uncertain future) is the integration of all the different requirements of an academic workflow: Reference/Pdf management → Annotation → categorization of the annotations (tags and categories) → (basic) outlining function → word interface for further fine tuning.
1. Will/could there be an easy way to jump from Citavi to Zotero (maybe an importer) that also preserves the links between annotations and highlights in the PDF?
It's possible annotations can be imported if they're included in the Citavi XML. We don't have access to Citavi, though, so we'd need someone to share a backup (which could be of a simple test library) that contains annotations, created using the steps on Importing from Citavi.
2. I understand how annotations exported in markdown retain a link to the file and the PDF annotation, but then how does the formatting work? I'm thinking in comparison to how the Zotero plugin works in MS Word (I am also new to markdown editors and how they play with Zotero).
Exporting with pandoc citations is planned.
3. Will there be options to customize the behaviour of the annotation system?
Yes.
4. Are you considering an "atomic notes/Zettelkasten" system either by generating individual notes or some "blocks" in the annotation file, so the highlights/annotations can be manipulated individually (tagged, etc.)?
Annotations in the PDF reader can already be tagged and filtered on by tag and color.
5. […] Alternatively, are you planning to introduce more complex text editor possibilities in the annotation pane, such as an outliner function?
I'm not sure what you mean by "annotation pane", but you can add annotations to Zotero notes and create hierarchical lists there, and you can drag around paragraphs with a drag handle. We'll be making many more improvements to the note editor going forward.
[…] the integration of all the different requirements of an academic workflow: Reference/Pdf management → Annotation → categorization of the annotations (tags and categories) → (basic) outlining function → word interface for further fine tuning.
I'm happy to provide a backup to check if that's possible. what's the best way to send it to you? Should I just post a link here?
Best would be to create a sample library with examples of available annotations. You can post that publicly or email a link to support@zotero.org with a link to this thread. If you want to send a link to your actual backup, that's OK, but it's really just the annotations that are necessary here.
As for rest, first, just to clarify the terminology we use, Zotero has an "annotations sidebar" on the left-hand side of the PDF reader that shows all annotations in a PDF and "notes" (editable in the right-hand pane in the PDF reader and, obviously, elsewhere in Zotero).
As you've seen, annotations are already taggable in the PDF reader, and you can filter them there. In future versions you'll be able to view and filter annotations in the library view as well. Tags don't currently persist when annotations are added to notes. We can add an option for that, but we'd need to hear more about how people saw themselves using it.
Notes are the mechanism for organizing annotations for a given project. Once you add annotations to notes, you can use all the normal features of the note editor, including indented lists. We don't have any plans to add any sort of hierarchy to the annotations sidebar, since that's just showing a list of all the annotations in the PDF.
Thank you so much for your fast and thorough anwser, I really appreciate it.
I deleted my earlier comments because I realized I had not fully grasped how the interface worked, much of what I was responding to was based on my initial misconception. I'm really glad to see how it works, I note the distinction between the "annotation bar" on the left and the notes (on the right). Here are my comments:
1. Great, thanks a lot for checking how the Citavi XML works. I will send you that as soon as possible, and keep my fingers crossed that the highlight and highlight locations can be exported.
2. It seems to me that the currently workflow you envisage makes a lot of sense, but is perhaps missing a fundamental step: the need for categorization and classification of annotations irrespective of the project, in a durable way. PDFs of articles or books are generally anotated with a project in mind, but these annotations are often used for several projects in a a row. When working in a new project in the future, you may want to start by "recalling" all the annotations made in the past, on a specific dimension of previous projects. So rather than "annotation" -> "note" , I think "annotation" -> "categorization" -> "note" might be key for many researchers.
Tags, if made persistent, could be a good way to address that "categorization" part. But a flat tags structure is limiting, especially if you start to have hundreds of them. This is where I think a hierarchy comes to play, to organize the categorization of annotations into hierarchically strutured tags. Alternatively, "annotation collections" might be a more promising direction, and live together with tags.
Users who don't want to use the feature, could just ignore tags and collections and drop directly all annotations into a note file.
3. One more detail: great that you will be able to customize how annotations are represented in the notes file. For me, for example, the "comment" should come first, and possibly appear in bold, as this is the main idea that will help me undnerstand where the annotation fits in my project.
4. Finally about the outlining feature. I don't imagine it in the left bar, but in the right bar. Outlining, with collapsible headers, is really useful when dealing with a long writing project. Sometimes an article is based on 30, 40 or 50 annotations. Having them all in a row in a flat structure makes it difficult to navigate the document, to move them around and generally speaking to understand what the hell is going on in the project. The outline allows you to zoom in and zoom out easily and keep a perspective on the project.
4. Finally about the outlining feature. I don't imagine it in the left bar, but in the right bar. Outlining, with collapsible headers, is really useful when dealing with a long writing project.
Well that's the point, though — we view notes, which already appear in the right-hand pane, as the best mechanism for outlining. The current feature set of notes is just the initial implementation. We intend to add many more features to facilitate better outlining.
1. Great about the Citavi import possibilities. I think it would bring a large amount of disgruntled Citavi users to Zotero. You can see the unhappiness here : https://help.citavi.com/en/topic/203572-who-are-unhappyhappy-with-citavi-nowadays - I'll be lookign forward to importing my entire Citavi database (9,000 references, 11,000 notes) in the new Zotero.
2. Great to hear that you are planning to work in this direction.
Very much looking forward to the coming release and updates!
Searching pdf annotations by tags (categories/keywords) can be helpful as a partial solution for categorizing annotations. This does not replace Citavi's hierarchical categories system, but can somehow help .
You can install zotero's add-on "better notes" and use the template "search by tags" to compile all your annotations (from selected pdfs) with a specific tag into one note.
Many thanks to @hsiangyu_wong for developing this great add (and his other highly useful add ons).
For Hierarchy, you can manually create semi-hierarchical tags by adding parts to tags: ie: #Evaluation , #Evaluation_positive , #Evaluation-Negative, #Evaluation_ Neutral, #Evaluation_positive_Internal Dimensions and so on)..
@agam2222 Thank you for your efforts to help others! The Zotero community grows better because of enthusiastic people like you~
I’ve noticed a lot of recent replies to these discusses related to the Better Notes plugin. I’m happy to know it is liked by and useful to so many Zotero users!
I’m afraid that discussing plugins too much would make some more important discusses be ignored. Sorry if these discusses bothered anyone.
I regard my plugins just a unmatured way to realize some features that users need them now while Zotero group doesn’t have time to do, just like this ‘search annotations by tag’. I’m looking forward to the day when this could be officially supported by Zotero.
We can never thank too much to the Zotero development group. Thank you developers!
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I'm planning to move from Citavi to Zotero. The new highlighting and annotation feature seems to bring Zotero closer to the Citavi workflow, and it's fantastic news. I have a range of questions though (from the more specific to the more general):
1. Will/could there be an easy way to jump from Citavi to Zotero (maybe an importer) that also preserves the links between annotations and highlights in the PDF? I am aware of https://www.zotero.org/support/kb/import-from-citavi but that was before the new annotation system was introduced.
2. I understand how annotations exported in markdown retain a link to the file and the PDF annotation, but then how does the formatting work? I'm thinking in comparison to how the Zotero plugin works in MS Word (I am also new to markdown editors and how they play with Zotero).
3. Will there be options to customize the behaviour of the annotation system? I would like for example to have my higlight comments before the highlight, not after; specify how the citekey is formatted, export annotations with a simple click to a specified folder, etc. If yes, what is the best way to suggest features?
4. Are you considering an "atomic notes/Zettelkasten" system either by generating individual notes or some "blocks" in the annotation file, so the highlights/annotations can be manipulated individually (tagged, etc.)?
5. Along the same lines, is there any plan to introduce a way to categorize individual annotations in collections? Alternatively, are you planning to introduce more complex text editor possibilities in the annotation pane, such as an outliner function? Currently there is only one "level" in your annotation pane, thus there is no way to introduce hierarchy in the ideas and the annotations
6. Is there a long-term vision to make Zotero not only a reference manager but also a knowledge manager? The beauty of an app like Citavi (despite being closed source, and now sold off with an uncertain future) is the integration of all the different requirements of an academic workflow: Reference/Pdf management → Annotation → categorization of the annotations (tags and categories) → (basic) outlining function → word interface for further fine tuning.
Thank you very much!
As for rest, first, just to clarify the terminology we use, Zotero has an "annotations sidebar" on the left-hand side of the PDF reader that shows all annotations in a PDF and "notes" (editable in the right-hand pane in the PDF reader and, obviously, elsewhere in Zotero).
As you've seen, annotations are already taggable in the PDF reader, and you can filter them there. In future versions you'll be able to view and filter annotations in the library view as well. Tags don't currently persist when annotations are added to notes. We can add an option for that, but we'd need to hear more about how people saw themselves using it.
Notes are the mechanism for organizing annotations for a given project. Once you add annotations to notes, you can use all the normal features of the note editor, including indented lists. We don't have any plans to add any sort of hierarchy to the annotations sidebar, since that's just showing a list of all the annotations in the PDF.
Thank you so much for your fast and thorough anwser, I really appreciate it.
I deleted my earlier comments because I realized I had not fully grasped how the interface worked, much of what I was responding to was based on my initial misconception. I'm really glad to see how it works, I note the distinction between the "annotation bar" on the left and the notes (on the right). Here are my comments:
1. Great, thanks a lot for checking how the Citavi XML works. I will send you that as soon as possible, and keep my fingers crossed that the highlight and highlight locations can be exported.
2. It seems to me that the currently workflow you envisage makes a lot of sense, but is perhaps missing a fundamental step: the need for categorization and classification of annotations irrespective of the project, in a durable way. PDFs of articles or books are generally anotated with a project in mind, but these annotations are often used for several projects in a a row. When working in a new project in the future, you may want to start by "recalling" all the annotations made in the past, on a specific dimension of previous projects. So rather than "annotation" -> "note" , I think "annotation" -> "categorization" -> "note" might be key for many researchers.
Tags, if made persistent, could be a good way to address that "categorization" part. But a flat tags structure is limiting, especially if you start to have hundreds of them. This is where I think a hierarchy comes to play, to organize the categorization of annotations into hierarchically strutured tags. Alternatively, "annotation collections" might be a more promising direction, and live together with tags.
Users who don't want to use the feature, could just ignore tags and collections and drop directly all annotations into a note file.
3. One more detail: great that you will be able to customize how annotations are represented in the notes file. For me, for example, the "comment" should come first, and possibly appear in bold, as this is the main idea that will help me undnerstand where the annotation fits in my project.
4. Finally about the outlining feature. I don't imagine it in the left bar, but in the right bar. Outlining, with collapsible headers, is really useful when dealing with a long writing project. Sometimes an article is based on 30, 40 or 50 annotations. Having them all in a row in a flat structure makes it difficult to navigate the document, to move them around and generally speaking to understand what the hell is going on in the project. The outline allows you to zoom in and zoom out easily and keep a perspective on the project.
Thanks again!
Francesco.
1. Great about the Citavi import possibilities. I think it would bring a large amount of disgruntled Citavi users to Zotero. You can see the unhappiness here : https://help.citavi.com/en/topic/203572-who-are-unhappyhappy-with-citavi-nowadays - I'll be lookign forward to importing my entire Citavi database (9,000 references, 11,000 notes) in the new Zotero.
2. Great to hear that you are planning to work in this direction.
Very much looking forward to the coming release and updates!
Francesco.
Searching pdf annotations by tags (categories/keywords) can be helpful as a partial solution for categorizing annotations. This does not replace Citavi's hierarchical categories system, but can somehow help .
You can install zotero's add-on "better notes" and use the template "search by tags" to compile all your annotations (from selected pdfs) with a specific tag into one note.
You can find the discussion here
https://forums.zotero.org/discussion/96945/zotero-better-notes-a-knowledge-based-note-manager-in-zotero/p2
The "Better notes" add-on here:
https://github.com/windingwind/zotero-better-notes/issues/23
And the template to filter annotations by tag here:
https://github.com/windingwind/zotero-better-notes/issues/85
Many thanks to @hsiangyu_wong for developing this great add (and his other highly useful add ons).
For Hierarchy, you can manually create semi-hierarchical tags by adding parts to tags:
ie: #Evaluation , #Evaluation_positive , #Evaluation-Negative, #Evaluation_ Neutral, #Evaluation_positive_Internal Dimensions
and so on)..
Best regards
Thank you for your efforts to help others! The Zotero community grows better because of enthusiastic people like you~
I’ve noticed a lot of recent replies to these discusses related to the Better Notes plugin. I’m happy to know it is liked by and useful to so many Zotero users!
I’m afraid that discussing plugins too much would make some more important discusses be ignored. Sorry if these discusses bothered anyone.
I regard my plugins just a unmatured way to realize some features that users need them now while Zotero group doesn’t have time to do, just like this ‘search annotations by tag’. I’m looking forward to the day when this could be officially supported by Zotero.
We can never thank too much to the Zotero development group. Thank you developers!