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RE: BioRDF [Telcon]

From: Nigam Shah <nigam@stanford.edu>
Date: Fri, 15 Dec 2006 14:09:51 -0800
To: "'June Kinoshita'" <junekino@media.mit.edu>, "'Kashyap, Vipul'" <VKASHYAP1@PARTNERS.ORG>
Cc: <public-semweb-lifesci@w3.org>
Message-ID: <002201c72095$be96d380$082041ab@stanford.edu>

Hi June,

... Comments in line ...

> In answer to Vipul's question about posting hypotheses and
> querying the SWAN knowledge base, we are planning to manually
> curate hypotheses. Each major hypothesis will be broken down
> into claims, or scientific assertions, and linked to
> supportive evidence, additional supportive, refuting or
> alternative claims, etc. We've been mainly focused on creating
> a scientific discourse ontology and defining the relationship
> terms among the different SWAN objects, but we are planning
> for each claim or type of evidence to be tagged with terms
> from shared ontologies. We'll be thinking a lot about the
> ontologies that will support the type of querying we envision.

Have you looked at the HyBrow project? www.hybrow.org. HyBrow contains
an ontology that lets you describe a hypothesis about gene regulation.
It then breaks down the hypothesis into individual assertions and for
each assertion, will examine the available evidence (gene annotation,
mRNA expression, protein expression, TFBS, prior-curated-literature
etc) and tells you wether the assertion is supported or contradicted
by the data.
(It also tries to "fix" the contradiction by modifying the assertion
in simple ways)

There is 25 slide presentation at: www.hybrow.org/Docs/ISMB04 if you
want more details.

> This is an area where many of the HCLSIG community have far
> greater expertise than we have, and we will very much welcome your
> help! 

Do let me know if you have anything specific in mind (in terms of help
you want/wish you had).

Received on Friday, 15 December 2006 22:10:06 UTC

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