Multiple entries per PDF, Annotating and Mind-mapping

1) I have drag and dropped many PDFs to a collection in Zotero. It was an easy drop and all PDFs were nicely lined up in Zotero. I then selected all of them and right-clicked and selected 'retrieve meta data'. Almost all of them now have an additional entry in addition to the PDF link which is not nested. When I use the add a note, it makes another nested entry. Even with a few PDFs it all of a sudden looks so very cluttered with more than one entry per PDF. I just need one entry per PDF. Am I doing something wrong? I am trying to transition from Mendeley and this is not helping.

2) Can you export all of your notes and annotations in multiple selected PDFs instead of having to export one by one? Mendeley hasn't got this feature.

2) Is there anyway to have a mind-mapping tool integrated to Zotero? In order to go from managing articles + making notes to formal writing I need a visual middle-man so I can organise my research writing and jot down ideas and have a look at how everythings fits in before I actually start formal writing. Any software that would help me do this please? I tried Qiqqa and Docear - they both have the functions I need but their GUI is SOOO user-unfriendly and ugly!

Thanks in advance.
  • 1) I'm not 100% sure I understand, but I _think_ this is just a different GUI and data model: In Zotero the main entry is the "parent item" which can have multiple notes, PDFs, webpage snapshotes, etc. attached to it. Normally you would look at your library with all those attached items collapsed (you can toggle that with the - and + keys on your keyboard)

    If that's not it, could you take a screenshot, upload it to a free image hosting site (e.g., dropbox) and link to it here? Retrieve metadata should never add _additional_ top-level items.

    2) That question doesn't really make sense in the context of Zotero. Since Zotero doesn't have built-in PDF annotation, you would typically annotate with a standard PDF reader such as adobe acrobat, which write annotations and notes directly to the file, so there's no need to export them.

    3) Nothing in sight, no.
  • Many thanks for your responses.

    1) Yes, that's exactly what I am talking about. Thanks.
    2) But Zotero has a fantastic feature in the Notes tab with decent of word processing functions! If I were to opt for Zotero, I plan to use Notes to summarise each article in my own words and then if were able to export all of these notes of more than one article as a batch that would be amazing!
    3) What a shame :(
  • oh, the actual notes, absolutely you can export those in batch. I think the most elegant way to do this would be to create reports:

    If you don't want all item information, you can select multiple attached notes using ctrl+click and then just generate a report for those.
  • edited January 22, 2018
    Depending on the metadata/formatting you need in the export, you can also just select multiple notes and drag them to a text editor, though that's probably less appropriate for notes from multiple items.
  • I'm also trying to mind map my Zotero data and looking for a method to do this dynamically so that if I update an entry in Zotero (such as adding a note) it also updates in my mind map. I've spent considerable time looking for a mind mapping program that will allow me to import Zotero data and then, within the map, allows me to link an item to multiple parent items, which I've found ( But it takes about 30 minutes to prep the Zotero CSV file for the transfer to contain everything I need, and unfortunately it's a one-time transfer which means it no longer updates as I change Zotero (for what it's worth, once the transfer is complete, the map does what I want in that each Zotero item can be linked to as many parent or child items I want and when I select an item it gives me the option to see web hyperlinks and the local PDF version when one exists.)
  • I can see a few options:

    1) Rather than exporting from Zotero, just copy "Zotero select links" to your clipboard and add these to your mindmap. You can then click this link from your mindmap to open the item in Zotero. You can use the Zutilo plugin to add a "Copy Zotero select link" option to the right-click menu.

    2) If you want all of Zotero item data as well, can you set up to refer to a local JSON file instead of CSV? And can you set to keep itself up-to-date with a local file? If so, then you can use the BetterBibTeX plugin to keep an export of a collection to CSL-JSON always up-to-date. You can control what variables are included in the export. You should also be able automate the process of exporting to BibTeX or CSL-JSON and converting to CSV.

    3) You can import the Zotero SQLite database directly into Microsoft Visio and use this as a mind-map program:
  • Thanks! I don't think I can copy "Zotero select links" because I would like to use the mind mapping program's import will automatically classify and tag imported items if pre-tagged. Unfortunately, I'm not a computer programmer and so options #2 and #3 are way beyond my expertise. I know the mind mapping tool's website says there is not an API which I think means it doesn't not work easily with third-party programs. Thanks.
  • What formats can your program import? And can it be set to automatically reimport any of them as the source file changes?
  • These are the formats to which it will accept imported data:
    1. Text Outline (which I'm currently using but very crude)
    2. MindManager
    3. FreeMind
    4. Folders
    5. TheBrain 8 XML (their program says "TheBrain 8 XML format is still supported. If you are using custom scripts or third party software that generates this XML, you can continue to use it." (the actual program is currently on v10.

    Are you suggesting can export Zotero data as XML and have someone write code that would allow me to import it? If so, where would I find such a person?
  • No, Zotero XML won’t work. Honestly, this program doesn’t seem designed to work with a sort of system where you have a continuously updated local file feeding it information. I don’t think there is going to be any method that will be more efficient trying to work with it when it doesn’t have that functionality.
  • Hi everyone,

    I am just curious whether there is any development in the mind mapping world that can be integrated with Zotero.

  • I would second that curiosity. Especially since all the other solutions stop working.
  • Yeah, it would be so cool to be able to drop items to a map, connect them, and stick short notes to the connections and the items like 'this item develops this and this', 'these two items contradict each other', etc.
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