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RE: [hcls] Harmonization of labels, descriptions and definitions

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Mon, 28 May 2007 09:28:11 -0400
Message-ID: <DBA3C02EAD0DC14BBB667C345EE2D124428503@PHSXMB20.partners.org>
To: <samwald@gmx.at>, "William Bug" <William.Bug@DrexelMed.edu>, <public-semweb-lifesci@w3.org>
Cc: <cjm@fruitfly.org>, <olivier@nlm.nih.gov>


Matthias,

This is a very important problem and an early harmonization effort could save a
lot of pain later on (A stitch in time saves nine).

An interesting point to be noted here is that the UMLS and NCI metathesauri 
seek to do a similar thing for medical vocabularies.

Wondering if there's a similar effort being undertaken for biological
ontologies? I know that Gene Ontology is now "linked in" to the UMLS
Metathesaurus.

Maybe Olivier can tell us something more about this.

Cheers,

---Vipul

=======================================
Vipul Kashyap, Ph.D.
Senior Medical Informatician
Clinical Informatics R&D, Partners HealthCare System
Phone: (781)416-9254
Cell: (617)943-7120
http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik
 
To keep up you need the right answers; to get ahead you need the right questions
---John Browning and Spencer Reiss, Wired 6.04.95
> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-
> request@w3.org] On Behalf Of samwald@gmx.at
> Sent: Friday, May 25, 2007 11:45 AM
> To: William Bug; public-semweb-lifesci@w3.org
> Cc: cjm@fruitfly.org
> Subject: [hcls] Harmonization of labels, descriptions and definitions
> 
> 
> > [2] For instance, definitions in the PATO OWL file (quality.owl) are
> > not visible in Protege.  The OWL version of PATO has an
> > AnnotationProperty called "oboInOwl:hasDefintion" that has the value
> > "@_:A4843".
> 
> I and some other people have already nagged Chris about the representation
> of defintions and synonyms in the OWL versions of OBO ontologies.
> This is partly related to a larger problem, namely the inhomogeneous
> representation of labels, descriptions and definitions among biomedical
> Semantic Web ontologies. I have started a Wiki page on this topic:
> 
> http://esw.w3.org/topic/HCLS/Labels_and_Definitions
> 
> The page is intended to contain the following (please add to it /
> discuss!):
> 
> * Examples from biomedical ontologies of non-standard constructs to
> represent Labels, names, descriptions and definitions of entities.
> 
> * An analysis of the motivations behind the creation of these constructs
> 
> *A description of the problems that arise through a lack of harmonization
> (e.g. for queries and user interfaces)
> 
> * A review of the basic constructs in the RDF, RDFS and OWL vocabularies
> and their intended usage for labels, descriptions and definitions
> 
> * An informal recommendation for the representation of labels,
> descriptions and definitions and suggestions for the harmonization of
> biomedical ontologies in this regard.
> 
> 
> I have started comparing the constructs from a few ontologies, but there
> are many additional ontologies that have created their own style for the
> representation of this information. We should try to find the smallest
> common denominator between all these approaches, because this really is a
> large hindrance to practical interoperability between our ontologies.
> 
> cheers,
> Matthias Samwald
> 
> ----------
> 
> Yale Center for Medical Informatics, New Haven /
> Section on Medical Expert and Knowledge-Based Systems, Vienna /
> http://neuroscientific.net
> 
> 
> 
> .
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Received on Monday, 28 May 2007 13:29:22 UTC

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