I received an email from Andrew Su at GNF today, reminding me about the Wikipedia Gene Wiki project and asking if I wouldn’t mind publicising their efforts. No worries Andrew.
I happened to stumble upon your blog, and I thought you might be interested in an ongoing project that I’ve been spearheading over at Wikipedia. The goal is to create gene stubs for every gene in the human genome. The stubs will have some minimal amount of structured content – links to important databases, GO annotations, PDB structures, etc. It’s our hope/expectation that these stubs will then seed contributions from experts in the field, specifically the “free-text” and unstructured sort of knowledge for which there really isn’t a great resource available.
If you’re interested, check out this link (warning – large page with long load time!):
which lists the ~8000 (and counting) pages at Wikipedia that have incorporated structured content from our effort. The top of the list is biased toward gene pages which were already established and were supplemented with content from our “bot”. Near the middle-to-bottom of the list are pages which were created de novo in our effort.
In any case, wiki efforts of course are dependent on having a large cohort of readers/editors, so if you saw fit to blog about the project, we would certainly welcome the additional eyeballs. Deepak at BBGM also blogged about it a while back, but the more the merrier!
11 thoughts on “Gene Wiki”
Let the flame wars begin!
Thanks Neil. Could be coincidence, but I think I noticed a small blip in the number of edits overnight. Readers checking in on their favorite gene?
Paulo, is your favorite gene really so controversial as to incite a flame war? Global warming maybe, but COX5B?
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Does this gene wiki uses some kind of templates and automated import scripts to publish the gene based info or is it completely manual (hand written).
@pj – you’d have to ask Andrew for the details. I would suspect that templates are used, but entries are by hand.
We’re hoping for a hybrid model. The “stubs” are created from all the structured content we harvest from the usual sources (Entrez Gene, Ensembl, PDB, etc.). Stub creation is *mostly* automated (a little manual supervision is required from time to time when content needs to merged into an existing page). Check out this page, for example: http://en.wikipedia.org/wiki/NUP214. This one was created completely using an automated “bot”.
After gene stubs are created automatically by the bot, our hope, of course, is that the legions of scientists will come through and manually add all the really interesting information about the gene’s function. The sort of stuff that can’t be harvested (or pigeon-holed) into a database.
Oh, and as evidence that this could be working as planned, we have created/amended about 8500 gene pages now. When searching by gene symbol, 60% show up on the first page of google.
So everyone should go on over to Wikipedia now and add one sentence about their favorite gene… ;)
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