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Re: Nature: A call for a public gene Wiki

From: Matthew Cockerill <matt@biomedcentral.com>
Date: Wed, 8 Feb 2006 23:04:18 +0000
Message-Id: <9E5C7AD6-15C2-4F97-B9F2-2C617D00697C@biomedcentral.com>
Cc: "hclsig-pub" <public-semweb-lifesci@w3.org>
To: "Tom Stambaugh" <tms@stambaugh-inc.com>

I agree that the details of gene function probably don't belong on  
Wikipedia.

However, as these two recent articles


Are the current ontologies in biology good ontologies?
Larisa N Soldatova & Ross (Nature Biotechnology)
htttp://dx.doi.org/10.1038/nbt0905-1095

Time to Organize the Bioinformatics Resourceome
Nicola Cannata, Emanuela Merelli, Russ B. Altman*
PLoS Comp Biol
http://dx.doi.org/10.1371/journal.pcbi.0010076


both discuss, one of the key problems with current biomedical  
ontologies is that they are not well embedded in a coherent set of  
higher level ontologies.

Biomedical ontologies need simple concepts such as "institution" and  
instances of those concepts.
e.g.
http://en.wikipedia.org/wiki/Harvard_Medical_School

Or as another example of a high level concept in need of a URI, the  
JPEG2000 file format
http://en.wikipedia.org/wiki/Jpeg2000

It's at least conceivable that Wikipedia may play an important role  
in providing widely accepted identifiers for such high level  classes  
and instances, since the high level of usage of wikipedia would tend  
to keep those high level concepts  far better maintained and curated  
than they would be in the backwaters of a specifically biomedical  
ontology.

Matt


On 8 Feb 2006, at 21:39, Tom Stambaugh wrote:

>
>
>> You raise important issues on this. But I take the converse  
>> position, I
>> think:
>> [snipped]
>>
> What he said ... and ...
>
> A more tightly focused Gene Function Wiki (or perhaps "interwiki"...)
> promises to provide specific benefits to the life science community  
> for the
> same reason that the existence of Encyclopedia Brittanica does not  
> preclude
> publication in "Nature" and "Science". Were we to begin posting the
> contemplated content into Wikipedia, I suspect it wouldn't take  
> long before
> we'd be accused -- at least by some -- of "wiki-squatting"
> (http://c2.com/cgi/wiki?WikiSquatting). Never mind how the wikipedia
> community might hear our proposals to add experimental semantic web  
> markup
> to wikipedia.
>
Received on Wednesday, 8 February 2006 23:04:16 GMT

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