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

From: Chimezie Ogbuji <ogbujic@ccf.org>
Date: Wed, 06 Jun 2007 10:02:44 -0400
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
cc: "Alan Ruttenberg" <alanruttenberg@gmail.com>, samwald@gmx.at, kei.cheung@yale.edu, public-semweb-lifesci@w3.org, Kerstin.L.Forsberg@astrazeneca.com
Message-ID: <1181138564.7850.29.camel@otherland>
So, I went ahead and composed a document which indicates correspondence
between terms in the POMR ontology and those in the relevant
'foundational' ontologies (GALEN, WordNet, DOLCE, OBI, and OBO-RO).  It
is attached from the Ontology Task Force Wiki for the POMR ontology:


I should start with the disclaimer that I am *not* a clinician by trade,
but the semantics I've tried to capture are completely derived from the
literature I've been exposed to. The mapping captures (mostly) what is
already expressed in the ontology, but the intent here is to make the
gaps and correspondence more visible to (perhaps) generate conversation
on how we can close these gaps.  I augmented the mapping with terms I
found in the OBI ontology which seemed to match directly with the
semantics the POMR terms attempt capture.  Where I wasn't sure about the
OBI terms I settled on, I have a question mark.  For instance: is a
cpr:clinical-description a obi:OBI_344?

I also have links (in context) to the relevant literature where the
formal definitions were derived.  Some of these citations need to be
augmented with more formal sources than Wikipedia and WordNet (although
in some cases these seem to do a decent job).

The XHTML document is generated from an XML document via an XSLT
transformation (both are attached).  

On Tue, 2007-06-05 at 22:59 -0400, Kashyap, Vipul wrote:
> > b) Putting some meat on the definition of what you are calling
> > "Clinical Process".  Just putting the two words together doesn't give
> > me a clear idea of what is being referred to.
> [VK] Will give some meat to the notion of "disease as a clinical process".
> Chime, help!

I'm not quite sure I understand the notion of a disease as a clinical
process.  The (general) definition of a disease in the POMR, follows
from the formal definition given in the OBR paper
(http://ontology.buffalo.edu/bio/OBR.pdf), which covers a disease
process and a disease as a material continuant.

The notion of a clinical process as defined in the POMR, follows from
Elisabeth Bayegan's workflow characterization
(http://www.idi.ntnu.no/~bayegan/pub/bayegan_ictai02.pdf) of the various
archetypes of clinical acts and their instantiations in the family-care
workflow.  She makes the distinction between a CareActType and the
instantiation of such CareActs documented within a patient record (as
recordings of a process).

I found her workflow characterization of clinical activities recorded in
a patient record quite useful.

> Maybe you and Matthias can give some meet to "Disease as a biological process"?

As indicated in the mapping, I settled on obi:OBI_155 and
galen:PathologicalPhenomenon as the authoritative definition of the
general notion of a disease.  Anything beyond this level of granularity
is outside my comfort zone (and is the kind of thing a first-class
disease ontology should model unambiguously).  Though I noticed (while
browsing OBI):

".. BS did not view disease as a process, and indeed it is now a child
of dependent continuant. rdfs:label (en) : disease editor_note (Datatype
http://www.w3.org/2001/XMLSchema#string) : rem1: BP - placed into
quality. needs to be discussed "

Chimezie Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Foundation
9500 Euclid Avenue/ W26
Cleveland, Ohio 44195
Office: (216)444-8593


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Received on Wednesday, 6 June 2007 14:03:10 UTC

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