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RE: HCLS Demo at ISMB/ECCB, How to contribute to the demo?

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Tue, 14 Aug 2007 15:17:43 -0400
To: Nigam Shah <nigam@stanford.edu>, Matthias Samwald <samwald@gmx.at>, brandizi@ebi.ac.uk, Eric Neumann <eneumann@teranode.com>
Cc: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>, "M. Scott Marshall" <marshall@science.uva.nl>
Message-id: <AB349814F1ECB143A5D4CD29C7A64569019ED1F4@CCSEXB10.CUNET.CARLETON.CA>

Fantastic material Nigam (and co)!  I hope you don't mind if I use some
for my 4th year bioinformatics class :-)

Couple of points:

Problem: Asserting disjointness between classes that are definable.
Example (slide 100): Rural Area and Urban Area are disjoint; Woomera is
initially asserted to be a rural area, and it is later develops into an
urban area. How do you intend to manage this change? Will you then
create a new instance of Woomera, assert it as an urban area, and link
it to the rural Woomera? Better to not make these disjoint....

Problem: Ontology normalization.
Slide 108: "An InfectiousPneumonia is either a BacterialPneumonia or a
ViralPneumonia." An infectious pneumonia is a pneumonia caused by an
infectious agent. Rather that asserting the union of specific agent
caused pneumonia, one should instead define a class of infectious
agents. Thus, we can automatically discover whether the agent is in fact
infectious. Moreover, this is easier to maintain. 

Slide 115: providing definitions for property characteristics would be
useful here - the difference between functional/inverse function may not
be clear from these examples (as a SIN is also functional - at least in

Great job!

> From: public-semweb-lifesci-request@w3.org
> request@w3.org] On Behalf Of Nigam Shah
> Sent: Tuesday, August 14, 2007 12:49 PM
> To: 'Matthias Samwald'; brandizi@ebi.ac.uk; 'Eric Neumann'
> Cc: 'W3C HCLSIG hcls'; 'M. Scott Marshall'
> Subject: RE: HCLS Demo at ISMB/ECCB, How to contribute to the demo?
> >Matthias Samwald wrote:
> >... but the result is much
> >more useful when some basic ontology design criteria are met and the
> >information in the source databases is re-interpreted to form a
> >meaningful ontology. Unfortunately I cannot point you to a short,
> >comprehensive document that would describe the design philosophy I am
> >thinking of -- this is something that still needs to be written, I
> >guess.
> >
> >
> >[1] http://www.obofoundry.org/ro/
> >[2] http://www.ifomis.uni-saarland.de/bfo/
> >[3] http://obofoundry.org/
> Barry Smith and I did a tutorial on how to make and use Biomedical
> Ontologies at ISMB 2007. The handout is at http://tinyurl.com/3dxeg8.
> Section 5, do's and don't's of ontology creation summarizes a lot of
> the design criteria. (Section -5 contains materials provided by Barry
> Smith and Andrew Spear).
> Cheers,
> Nigam.
Received on Tuesday, 14 August 2007 19:18:14 UTC

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