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Reference management for research group
greenlaser3 #1
Member since Aug 2014 · 3 posts
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Subject: Reference management for research group
So I'm exploring the idea of creating a DokuWiki for my research group. Currently our research workflow mostly involves annotating papers (we have about 17000 stored in Endnote) and creating documents stored separately. It's a bit messy. The idea with DokuWiki would be to try to provide a "one stop shop" for exploring the literature and then developing/incubating ideas. A really critical part of that is reference management. I'm not exactly sure what the best way to do that is, and I was hoping for some advice.

Here's the functionality I would like to see on DokuWiki's end:
  * Easily find references in a database and cite them in a page.
  * Easily access the pdf file associated with a reference. (I.e., when I see a citation on a page, I would like to get to the pdf in one or two clicks)
  * Add annotations to said pdf, which can be seen by other people.

Is it possible to access an Endnote database through DokuWiki, and do the things I mentioned above? From looking around, it seems like I would have to use the RefNotes plugin to make a reference database within DokuWiki, and then make a script or something to sync that with our Endnote database. Seems a bit unwieldy...

I thought about eliminating Endnote entirely and just using DokuWiki + RefNotes for reference management. The problem is, I don't see an easy way to import citations from the internet and export them into various journal formats without a lot of manual work. Again, not ideal...

Is there perhaps another reference manager (other than Endnote) which can be more seamlessly integrated with DokuWiki? Maybe the reference manager would be used simply for importing/exporting papers, and then Dokuwiki would be used to organize and comment on those papers.

Or maybe there's another solution I'm missing altogether? Sorry for the long post, but I would appreciate any advice.
User title: Scott Ferguson
Member since Dec 2014 · 366 posts · Location: Canberra, Australia
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You might want to take a look at wikindx which is a Virtual Research Environment with support for EndNotes. There is a DokuWiki plugin, wikindx, for it.

You may also find the docsearch, yabibtex, and, bibtex plugins useful.

Adding annotations to the original pdf is interesting, I'm not sure how you'll manage that but I'll be interested in reading the results. Have you considered not putting the annotations into the pdfs and just linking instead?
jackdaniels #3
Member since Oct 2016 · 2 posts
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If you have more than ~500 references, Refnotes is a bad option. You'd have to post-process any bibtex file (ad pre and post syntax), and since refnotes has no database it just searches a bunch of files for your key. I tried it with a file containing 800 bibtex entries exported from zotero. For whatever reason, it would not render at all. I trimmed the file down to 100 and it worked.
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