Igor - a Google Wave robot to manage your references
(Google Wave hasn't been released yet but if you're interested in working with the preview you can request a developer account on the sandbox here)
Google Wave is a new open source project from Google that holds a lot of promise as a platform for scholarly communication. It's a little bit like email but allows for collaborative document editing, versioning and real time conversation within groups - check out Cameron and Martin's archives for more.
Igor is a proof of concept Wave robot that allows Wave users to pull in citations from Pubmed or their libraries on Connotea and CiteULike as they type.
To use it invite helpmeigor@appspot.com to join a wave.
Say you'd like to cite 'Chaperonin overexpression promotes genetic variation and enzyme evolution' by Nobuhiko Tokuriki and Dan Tawfik from last month's Nature.
In the Wave you'd write:
... as shown by Tokuriki et al. (cite chaperonin tokuriki)
Igor will notice the (cite x), connect to PubMed, search for articles where the title, authors or journal contain "chaperonin" and "tokuriki" and then pull in the relevant citation. The (cite x) will be replaced with a number and the citation will be appended to the end of the document.
... as shown by Tokuriki et al. [1]References
1. Chaperonin overexpression promotes genetic variation and enzyme evolution. Tokuriki et al 2009 Nature
(http://www.ncbi.nlm.nih.gov/pubmed/19494908)
If Igor comes up empty handed or multiple articles match the cite query then it'll tell you by dropping in a message after the relevant part of the document.
To cite a web page just do
Google Wave (cite http://wave.google.com)
To switch to using your Connotea or Citeulike library you can use the (cite from x) command.
e.g.
(cite from citeulike dullhunk)
(cite from connotea euanadie)
(cite from pubmed)
You can switch between citation libraries in the same session:
candidate genes include NRG1 (cite from connotea euanadie)(cite schizophrenia neuregulin) and (cite from pubmed)DISC1 (cite PDE4B evans schizophrenia)
Commands are processed in order of appearance so Igor will search Connotea for "schizophrenia neuregulin" and PubMed for "PDE4B evans schizophrenia".
References are always numbered in order of their first appearance in the text. If you move a reference from the bottom of the article to the top then reference numbers will be change accordingly.
Igor is written in Java and runs on App Engine. It's almost inevitable that you'll experience some turbulence, especially when introducing him to a new Connotea or CiteULike account for the first time - Wave robots are very unforgiving of sites timing out. If something looks broken try leaving the wave and coming back to it later or reloading the page. Let us know how you get on!
Comments
I think your going down the wrong path here in tying citations to particular record ids, in particular accounts. I think the better path is to have global identifiers (URIs) embedded in the Waves, and for the robot to be configured with one-or-more trusted sources, which could include those accounts.
Posted by: Bruce D'Arcus | July 27, 2009 08:47 AM
Hi Bruce,
Sorry for the confusion - although I tend to type (cite from ) right before citations in the video the commands are parsed completely independently; the only things tied together on the Wave are a position (first, second, third ref etc.) and formatted citations.
"I think the better path is to have global identifiers (URIs) embedded in the Waves"
I think I agree - will hopefully speak to you about it in a different forum.
Posted by: Euan | July 27, 2009 12:48 PM
Really nice! Now I'm even more longing to play with GW!
Posted by: Egon Willighagen | July 29, 2009 06:15 AM
Euan, I just signed up and requested a GW account too... let's hope I may finally end up on the Google radar...
Anyway, where's the source code? I like to adapt it for Wikipedia/DBpedia support for chemistry... thinks typing (wp formula benzene)...
Posted by: Egon Willighagen | July 31, 2009 08:18 AM
Just put it up at:
http://code.google.com/p/helpmeigor/
I like the (wp) idea!
Posted by: Euan | July 31, 2009 08:45 AM
I see this is working in the Preview, but Igor's initial reply references a sandbox URL that is broken:
http://ghastlyfop.com/igor for more details.
Posted by: Eric Hellman | October 22, 2009 11:47 AM
This is an awesome idea, I really like it. Since you have put up the source code, maybe you'd like to put it in the samples gallery? It will give the idea more visibility and help other developers on the same path.
Are you using annotations or data documents to keep track of the citations?
Posted by: Pamela Fox | December 30, 2009 12:11 AM