Third-Party Mac Apps to import/export PDFs

Peter100
Is anyone aware of any third-party Mac reference managers/apps that easily imports/exports Zotero BibTeX or RDF (with PDFs)? I managed to import to Qiqqa (Windows) to see what its analytical tools can do but will not use it as my main ref mgr. (interface is clunky and buggy). I am considering BibDesk and/or Sente to work alongside Zotero for annotating/tagging with OpenMeta. However I have not been able to include my 1000+ PDFs. I have also tried Bookends and Paper2 unsuccessfully. Any work-around solutions would be greatly appreciated!

I'm also curious to know why there are so may export formats in Zotero but I have trouble finding third-party apps that use these. Instead many seem to have their own preferred format, with possible exception of BibTeX or RIS (which doesn't include PDFs using Zotero export).

I have been experiencing import/export issues for the past X number of years, not only with Zotero but all the ref mgr apps I have tried. I just cannot understand why somebody doesn't just come up with ONE universal standard format that is multi-platform and WORKS, with PDFs! A PDF for PDFs! I would but my programming skills are nil. Perhaps the Open Source community has cooked up something that I am unaware of?
  • Peter100
    edited August 13, 2012
    Couldn't some kind of translating export/import algorithm/code/plugin be developed that uses text analyses - whether from the citation file itself (e.g. rdf, ris) or the attached ocr'd text and/or rtf docs? It could make "smart" guesses as to which fields the text belongs (author, date, etc) and also checked against an online database (like the title database for iTunes) for each export/attached file. It could also be made trainable (like voice recognition software) so it "learns" e.g. proper names, dates, titles of each publication with user corrections. I have in mind something like the "magic wand" used to analyze the metadata of a pdf. (Simply magical!) However this would sit in between export-import as a kind of translation device. It could use a database of all existing software and the exact import/export format of the app's "own" format to see if variations occur from the expected format. Perhaps this could be created by using a dummy reference that is first imported to the third-party app and then exported back out so Zotero can check for any adjustments/translations that need to be made first. So when I click "export" in Zotero I just have to choose to which app I need to export into (Endnote, Bibdesk, Whatever) and presto! A pipe dream? What about a babel fish!
  • mronkko
    Keeping two reference management software in sync by importing and exporting is asking for trouble. What is the problem that you are trying to solve with this kind of setup? (Or what is the problem that you want to solve by using OpenMeta)

    Many software vendors want to maintain their users locked into proprietary formats so that the users cannot switch to less expensive or better alternatives, but must keep on purchasing new versions of their software. EndNote for example has sued Zotero for trying to be compatible: http://en.wikipedia.org/wiki/Zotero#EndNote_lawsuit

    Making something that you suggests would be a huge effort. Unlikely to happen unless someone put a lot of money in the table and hired a team of developers to do it.
  • Peter100
    edited August 13, 2012
    The first issue is the my more pressing problem: finding a way to annotate pdfs with searchable tags for use in other apps like DevonThink. Sente is set up to work this way for instance (with an external pdf database).

    Apparently the Zot2Bib plugin works between Zotero and Bibdesk for people who want the slick keyless magic of Zotero combined with the annotation powers of Bibdesk (http://mackerron.com/zot2bib/) ... but as I understand it this only works for NEW references. I want to set this up too but first I need to get my +1000 pdfs into Bibdesk.

    The second idea was offered as a provocative "what if" challenge. Curious if it sparks any ideas. This forum seems like a good place to put it. I understand that there are politics involved but ideally that's what a user like me needs. It isn't rocket science, is it?
  • mronkko
    Why do you want to use two different software for managing the PDFs? Would it be simpler to store the files in Zotero and use Zotero's tagging feature?

    What you are asking is rocket science. It would be a huge effort and difficult to get right.
  • Peter100
    Yes, Zotero does tag, but can it search the annotated notes of a pdf and are these annotations available for searching for outside Zotero, from for example Spotlight?

    Here is an example of Bibdesk and Skim (based on OpenMeta) working together: http://jenniferclaro.wordpress.com/2011/08/12/a-simple-academic-workflow/

    (Okay, I'll give up on rocket science then.)
  • Peter100
    edited August 13, 2012
    As I mentioned, I still wish to use Zotero because it has superior metadata identification function and word plugins. It's also the program I know best.

    At the same time, I'm in the mood to experiment with my workflow and hoping to tweak it and see if something better emerges...
  • mronkko
    edited August 13, 2012
    So the problem that you are trying to solve is to search PDFs based on tags and annotations?

    There are several solutions:
    1 Make Zotero write tags as OpenMeta tags, use Spotlight for searching
    2 Implement a spotlight plugin for Zotero so that Spotlight uses Zotero metadata
    3 Make Zotero use Spotlight index when searching for PDFs. (The current full text search is not nearly as useful as Spotlighth)
    4 Export the annotated notes as Zotero notes. (ZotFile plugin does this.)
    5 And the combination of software that you are suggesting.

    I would say that none of these are currently easily possible. 1-3 would be possible to code in a reasonable time. I have been thinking about coding 2 myself, but have not had the free time to do that.
  • Peter100
    edited August 13, 2012
    Well, I'd be happy for any solution, or at least the attempt. As I mentioned, I am no programmer and don't have the time to learn (perhaps when I retire).

    I should also mention that Bibdesk, as far as I know, is for use with LaTeX so in that sense it is not really a Zotero competitor.

    On the other hand Sente does have some interesting features that Zotero could learn from. However Sente is proprietary, so there you go.
  • mronkko
    If you think that Zotero does not do something that some other software does, that's a good case to write in the feature requests forum.

    I for one would love to see Zotero using Spotlight index for searching PDFs.
  • Peter100
    I will enter a link to this discussion but assume they monitor this category too ...
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