I have collected some 9 papers using wiki technologies in bioinformatics, ranging from collaborative authoring, ontology-based annotation, to sharing data, and lab reporting. What is your favorite paper describing the use of wikis in bioinformatics?
I have used the following wiki based bioinformatics resources in different scenarios:
Edit: WikiPathway is added. Thanks for the tweet from Chris Evelo.
This isn't a paper but i watched a very interesting/persuasive talk at the recent Genome Informatics conference. It was by Alex Bateman about how they have used Wikipedia to store all of their Rfam descriptions.
They seem to have benefited from non-biologists doing their editing for them. Without suffering from too much vandalism. http://xfam.wordpress.com/2009/02/20/rfam-rna-biology-and-wikipedia-in-the-news/
Gene Wiki because I just love the way I was enrolled in this project via FriendFeed. :-P (thank you Andrew ! )
I use OpenWetWare as a notebook (cited in http://www.ncbi.nlm.nih.gov/pubmed/18444327)
Comment: a list of biological wikis is available from this FF thread.
Another answer: is the 'History of Sciences' related to Bioinformatics ?(*) I've played with http://www.freebase.com to insert the biographies of some famous scientists (http://blog.freebase.com/2008/02/18/new-application-freebase-and-the-history-of-science/). My site is now down but I really enjoyed the powerful API and the ability to select/update/insert some JSON-based structured data.
(*) yes
Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database
Proteopedia
Big data: Wikiomics: Nature 455, 22-25 (2008)
http://biodatabase.org/index.php/Main_Page
Open Notebook Science
OpenWetWare
TOPSAN project
To Add:
Does any one explored Google's "Knol - a unit of knowledge" as a wiki alternative?
There was an interesting discussion of what has/hasn't worked so well in terms of community annotations recently at a GMOD satellite meeting:
Community Annotation Satellite Meeting
I remain unconvinced that wikification of curation is a good and effective model, though. Unless paired with something like a requirement for publication (as the Rfam one did), I don't think that the quality, evenness, and breadth will be adequate. I prefer professional curation. But I also know that's not valued as much by end users or funding agencies in some ways.
Mary, two thoughts... First, your comment implies that "quality, evenness, and breadth" are not problems with professional curation, but I think the evidence suggests otherwise. Curators do a great job, but asking them to handle the 850K new PubMed-indexed articles every year is drinking from the proverbial fire hose. Second, I think wikis vs professional curation is a false choice. One area of emphasis for the Gene Wiki moving forward is how to partner with professional curators to make their workflows more efficient and accurate. I'm very excited about that line of work...
Oh, I know, you and I have gone 'round this before. I still contend that wikis will draw people with deep interest in some topics, and zero interest in others. So to get people to curate genes they aren't that personally interested in we need to pay them. And I'm willing to support that, I value that. There may be some partnerships that work, sure. I'd be interested to see the data on the effectiveness.
It's not a wiki as such but my experiment is a virtual research environment. It is mainly for sharing and exchange of workflows. This is a video showing a case study. It does have its own wiki
You might considering joining the Google group on the matter.
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Pierre, sure you meant to say that you love the Gene Wiki also because it's the coolest bio-wiki around, right? ;)