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Use Case: Releasing Taqman Data

From: John Wilbanks <wilbanks@w3.org>
Date: Tue, 17 Aug 2004 13:57:31 -0400
Message-ID: <4122470B.6010601@w3.org>
To: public-semweb-lifesci@w3.org


Here is a use case derived from a conversation I had recently with a 
computational biologist.

1. I am a researcher with a killer set of taqman data - and I want to 
share it with the world.
2.  I am busy, and perhaps don't understand the data issues inherent in GO.
3.  I overlay onto GO assignments for the gene.
4.  However, what I've really found is a complex transcriptional region, 
and what GO has looked at is coding regions with clear functions to 
5.  My taqman data is looking at a different exon which is proximal to 
GO annotation.
6.  I release my data with the GO annotation, but its utility is 
comprimised, as the annotation does not apply to my data

My question is:  what are the best ways to go after this type of 
problem, which in many ways is derived from the conflicting perceptions 
of what "gene" means?  Should the W3C be thinking about standards for 
overlaying ontologies onto raw data, with those standards determined for 
given entity classes or ontological classes?  Should we simply look at 
making sure our recommended technologies *support* the scientifically 
accurate overlay of ontological classification onto binary data?  The 
central point is that imprecise usage of ontologies for functional 
annotation can actively undermine the utility of the information...

Please discuss!


John Wilbanks
W3C Fellow
Semantic Web - Life Sciences
617-253-5845 (direct)
617-838-6333 (mobile; best voicemail #)
Received on Tuesday, 17 August 2004 17:56:59 UTC

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