W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > June 2007

Clinical semantics and coverage in OBI / OBO - was Re: HCLS SW "Web Metro Map"

From: Chimezie Ogbuji <ogbujic@ccf.org>
Date: Tue, 05 Jun 2007 16:53:45 -0400
To: samwald@gmx.at
cc: kei.cheung@yale.edu, public-semweb-lifesci@w3.org, Kerstin.L.Forsberg@astrazeneca.com
Message-ID: <1181076825.31344.33.camel@otherland>

On Tue, 2007-06-05 at 20:53 +0200, samwald@gmx.at wrote:
> > Very nice diagrams (I'd like to know what tools were used to create
> > them), but I can't help but notice that the clinical realm is very much
> > under-represented - with the exception of the HCLS 'ecosystem' diagram.
> 
> Yes, unfortunately the clinical side has become quite under-represented recently. 

Absolutely, and I've been concerned about this for some time.

> I think we should try to put more emphasis on the connection of the research side to the clinical side. Of course, the clinical aspects will be represented in the HCLS map.
> Maybe you could give an update on your Problem-Oriented Medical Record ontology and make some suggestions on where it would fit into the landscape of other resources we have recently developed?

Frankly, there is not much fitting to do if the motivating usecases and
datasets don't span the clinical realm to begin with.  

>  Since the infrastructure starts to crystallize around the OBO Foundry/Relation Ontology/BFO - based ontologies, 
> some ontologies that are based on different foundations (like your Medical Record ontology) become a bit separated, it seems.

Sure, but this is very much dependent on what aspects of DOLCE are not
covered by BFO / OBI (from my vantage, only a small portion of DOLCE is
accounted for).  I've always wondered if correspondence with DOLCE  is a
criteria for building these foundations.  DOLCE covers quite a bit of
ground and in a very thorough manner - as ontologies go.

Theoretically, it should mostly be a matter of names not semantics.  
At the top-most levels there seems to be a strong correspondence.  
Since, the POMR ontology only uses a handful of DOLCE terms, I'll take
 a stab at trying to find equivalence in OBI / BFO.  This way, we can
easily determine where these foundations do not account for the kind of
semantics you need for clinical data (such as diagnostic actions, their interpretations, etc.).
I had already made an attempt (in the most recent revision) to use the OBO relations wherever it made sense to.

> cheers,
> Matthias
-- 
Chimezie Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Foundation
9500 Euclid Avenue/ W26
Cleveland, Ohio 44195
Office: (216)444-8593
ogbujic@ccf.org


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Received on Tuesday, 5 June 2007 20:54:11 GMT

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