Information architecture

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

• 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 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.

DokuWiki

• bibdesk plugin - generates on the fly detail pages, and links to those detail pages.
• improved bibdesk plugin - nice slide-down bibtex view
• bib2tpl - php library for converting bibtex to different templates (used by publist)
• improved bibtex with anchors

Skim

• use SkimNotes to automatically extract annotations

  /Applications/Skim.app/Contents/SharedSupport/skimnotes 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?

Bibdesk

• doesn't have option to copy as citation (maybe with LaTeX installed?)
  • templates for use in export?
• sync with citeulike
• integrate with Word

Citeproc

• standard format for describing references, and formatting templates
• Homepage
• Citeproc-js
  • Manual
  • 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?

Jabref

• Mark Schenk tools - nice outputs of sortable/searchable HTML bibliographies

• A Digital Workflow for Academic Research - Skim, DevonThink, BibDesk

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