Information architecture

This is about my own project, Science 2.0 for more general links

Current state

Citations in Dokuwiki

  • the built-in refnotes is really unreliable
    • find someone who can make it more reliable?
  • using Pandoc and inserting links
    • possible to do it automatically for all single citations, impossible for combined citations
    • having a look at source, or having someone to help me do it in the source


  • currently kindle-mount.rb runs every time a new volume is mounted, and imports new clippings.
  • clippings from Skim already work perfectly
  • any other input sources?

BibDesk integration

  • BibDesk can send automatically to Kindle by e-mail (Ctrl+Alt+Cmd+K) (still need to experiment a bit with exporting - pdftotext better than directly using ebook-convert for columns?)
  • BibDesk can automatically generate a detail page and open it on wiki (Cmd+E)
  • You can easily copy+paste citation in DokuWiki format
    • only link to citation if it exists? (see problem with citations above)
  • Script that batch-processes Bibliography.bib and generated ref:bibliography, already works
    • enhance with lists of authors, and keywords - how to do this - not have them indexed?
    • this is nice, because it means that we still have all the citations, without having to create detail pages for every single paper


  • Move all author pages to their own namespace (a:?), and create nice alphabetical page list (template with link to publications etc)
  • Exclude sub-page fragments from search, but include all the text in ref: pages
  • Integrating with Multi-Markdown and Pandoc, so that papers published on wiki link to detail pages (if they exist)
  • embed COinS
    • some plugins for WordPress etc. generalized library for generating COinS (citeproc)? CitationStyles? (Zotero has some support)
  • already have easy interlinking from blog to wiki. ability to color/display icon next to links to distinguish them from other external links?
  • using graphviz to visualize relationships between wiki pages (might already be plugins / software to do that?)
  • interesting example of wiki with pages generated from bibtex file, citation management, notes, etc. (HCI/design research stuff)


How to use blogs and wiki together with other offline tools, citation management etc.



  • use SkimNotes to automatically extract annotations
    /Applications/ get -format text gunn2008creating.pdf

    generates gunn2008creating.txt

  • Automatically import to DokuWiki
  • Create system service to import notes to DokuWiki automatically

Integrating bibdesk with Firefox

  • zot2bib seems to work well, sends citations directly to Bibliography.bib, automatically appear in BibDesk… BUT
    • don't show up as “last imported”
    • don't take files with them !!!
    • should I also import into Zotero or not? pros/cons?



  • standard format for describing references, and formatting templates
  • Citeproc-js
    • Demo, very impressive. How can this be used? WordPress? Integration with BibTex database?
    • Citeproc-js on node.js running a local CiteProc server, to be used by DokuWiki etc?



Own workflow

  • Look at integrating Pandoc better with Scrivener, including bibliography export