Beta 14 of SciPlore MindMapping is out: Import comments & highlighted text; more BibTeX attributes, Export works now, …

Published by Joeran Beel on

We added some new features to SciPlore MindMapping Beta 14 that should help you a lot in managing your academic literature: Many users told us they would like not only to import bookmarks but comments and highlighted text from PDFs to their mind maps. Well, this is now possible :-). However, importing highlighted text is pretty… far from being perfect. Currently, it works only with PDFs edited with Skim. Anyway, importing comments works quite well. In addition, more BibTeX attributes are shown in the mind map (journal, year and authors in addition to bibtexkey and title). Also the BibTeX processing is more tolerant which makes it easier to use SciPlore MindMapping with manually created BibTeX files and other reference mangers than JabRef. And, we fixed several bugs. As a consequence all export formats should work now (e.g. HTML, XHTML, Java Applet, Flash, PNG, PDF, …). Here is the complete list of our changes:

  • New: Comments in PDFs and highlighted text can be imported
  • New: Show more BibTeX attributes in mind map (author, year, journal/conference)
  • New: Icons for most important actions in incoming folder window added
  • Improved: BibTeX processing is more tolerant
  • Improved: Incoming folder window remembers width
  • Fixed: Update reference keys did not work if one BibTeX key in BibTeX file was empty
  • Fixed: Some export formats did not work properly
  • Fixed: Status window lost focus on click on background
  • Fixed: If monitoring directory was non-existent, an exception occured
  • Fixed: Reference key was not assigned if file name had special chars

7 Comments

Mr. Drive · 19th July 2011 at 21:12

I tried with Skim because I thought Skim was awesome. However, I just figured that with Mac OSX’s Preview 5.0.3 you can do the same types of annotations done with Skim. So I tried importing these annotations to SciPlore Beta 16 Build 360, et violá, Bookmarks, Text items and Note items were successfully imported to SciPlore on Mac OS X Snow Leopard. So long for Skim, I still love it and we had great times together, but I have to let it go now…

I am still struggling with Bibdesk imports for publication data though. If you could shine some light on how the link is done between the bibtex file and the current pdf added through a monitored folder, it would be of great help.

Great Job in Creating and Sharing Sciplore, I will try to document my experiences with it on my website and I will try to keep you guys posted!!!!

    Joeran · 25th July 2011 at 08:45

    hello,

    thank you for letting us know about the MacOS preview function. this sounds really nice.
    Regarding Bibdesk: it seems, Bibdesk is using a binary encoding in its bibtex file. if you like, create a “wish” for bibdesk-support in our feedback forum http://docear.uservoice.com/ and if some other users also would like this feature we implement it.

AB · 28th January 2011 at 03:18

Thanks for this excellent software – I’ve been trialling Sciplore for a PhD lit review and it’s generally working very well for me. I’m using a Mac, and adding bookmarks to the pdfs using Foxit Reader running under Parallels. Under the Mac OS, I use Skim as my default pdf reader.

I’ve now downloaded the Beta 14 release of Sciplore, and was keen to use the new ‘comments in PDFs and highlighted text can be imported’ feature. I tried using Skim as recommended, but there’s no ‘add comments’ feature in Skim, and text that I highlight is not importing into my map.

I’d be grateful for any suggestions on this.

    Joeran · 1st February 2011 at 13:40

    All I can tell you is the same I answered M@rtin (see above):

    We are not using Skim our selves but only had some PDFs a user sent us. This user told us that you have to export the PDFs in Skim and you can select that annotations shall be written into the PDF (annotations stored in Skim’s standard format in a separate file will not work). If you find out how to do it exactly, I would be glad if post a short description here in the Blog.

M@rtin · 16th January 2011 at 09:05

Great!
I was quite excited to read that the import of notes mad with SKIM now could be supported, so I downloaded Beta14 and tried.

Could you please clarify, how to do it correctly?
I tried to drag a pdf file, where I had highlighted text with Skim into the Mindmap, but I only see the structure of the Bookmarks (which existed already in the original PDF), but none of the skim note.

Questions:
Can the skim notes be stored in a separate “.skim” file? (does SciPlore Mindmapping search for this separate file?)

Are there any other preferences to set up before it works?

Kind regards

Martin

    Joeran · 1st February 2011 at 13:39

    We are not using Skim our selves but only had some PDFs a user sent us. This user told us that you have to export the PDFs in Skim and you can select that annotations shall be written into the PDF (annotations stored in Skim’s standard format in a separate file will not work). If you find out how to do it exactly, I would be glad if post a short description here in the Blog.

      M@rtin · 2nd February 2011 at 11:30

      Thanks Joeran for your reply!

      I’m avoiding storing the Skim notes directly in the PDF, as I want to leave the (mostly) scientific articles untouched.
      So I’ll try if it works with “embedded” comments, but I would stronlgy prefer SciPlore to also be able to import the notes from separate .skim files.
      Do you have any plans to support that?

      (some minutes later…)

      I’ve tried, and yes:
      Even if I export a pdf in Skim to “PDF with embedded notes” (I hope that’s the correct name in the English version), only the bookmarks (which did already exist in the PDF) were imported and not the highlighted text and inserted notes.
      🙁

      Furthermore, even if it worked:
      this would have the big disadvantage, that the notes are in this case really fixed in the pdf. Skim can open the pdf, but you can not edit or remove the existing notes any more!

      So the workflow would be to have the original pdf with the editable notes and each time, something was edited again, to export it to a “pure” pdf which then is imported in SciPlore.
      If you read and edit only once, that’s ok – but nevertheless it would require to keep the original pdf (twice the disk space and source for errors…)

      Are there improvements planned?
      And could publish some example pdf files where Skim notes can be imported?

      Thank you,
      Kind regards

      Martin

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