Transcript Document

R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Bioinformatics and Technology Applications in
Medication Management.
Ontology: background and application to
Medication Management
Buffalo, NY, USA, June 13th, 2008
Werner CEUSTERS, MD
Center of Excellence in Bioinformatics and Life Sciences, and
National Center for Biomedical Ontology, University at Buffalo, NY, USA
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
‘Ontology’ is
popular
‘Ontology’ in
Buffalo is famous
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
‘Ontology’: one word, two meanings
• In philosophy:
– Ontology (no plural) is the study of what entities exist and how they
relate to each other;
• In computer science and (biomedical informatics)
applications:
– An ontology (plural: ontologies) is a shared and agreed upon
conceptualization of a domain;
• Our ‘realist’ view within the Ontology Research Group
combines the two:
– We use realism, a specific theory of ontology, as the basis for
building high quality ontologies, using reality as benchmark.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Realism-based ontology
• Basic assumptions:
1. reality exists objectively in itself, i.e. independent of
the perceptions or beliefs of cognitive beings;
2. reality, including its structure, is accessible to us,
and can be discovered through (scientific) research;
3. the quality of an ontology is at least determined by
the accuracy with which its structure mimics the
pre-existing structure of reality.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Three major views on reality
Realism
• Basic questions:
– What does a
general term
such as
‘clinical drug’
refer to?
– Do generic
things exist?
Conceptualism Nominalism
Universal
Concept
Collection
of
particulars
yes: in
particulars
perhaps: in
minds
no
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Dominant view in computer science is conceptualism
Realism
• Basic questions:
– What does a
general term
such as ‘tree’
refer to?
– Do generic
things exist?
Conceptualism Nominalism
Universal
Concept
Collection
of
particulars
yes: in
particulars
perhaps: in
minds
no
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Dominant view in computer science is conceptualism
Realism
Conceptualism Nominalism
concept
Embedded in
Terminology
Semantic
Triangle
object
term
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
‘Terminology’: one word, two meanings
• Terminology is the study of identifying and labelling
‘concepts’ pertaining to a subject field.
• Terminology related activities:
– analysing the concepts and concept structures,
– identifying the terms assigned to the concepts,
– establishing correspondences between terms, possibly in various
languages,
– compiling a terminology, on paper or in databases,
– managing terminology databases,
– creating new terms, as required.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
However …
• Terminology:
– solves certain issues related to language use, i.e. with respect to
how we talk about entities in reality (if any);
• Relations between terms / concepts
– does not provide an adequate means to represent independent of
use what we talk about, i.e. how reality is structured;
• Women, Fire and Dangerous Things (Lakoff).
• Ontology (of the right sort):
– Language and perception neutral view on reality.
• Relations between entities in first-order reality
This is the ‘terminology / ontology divide’
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
The semantic triangle revisited
Representation and Reference
concepts
concepts
terms
about
objects
terms
First Order Reality
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Terminology
Realist Ontology
Representation and Reference
terms
concepts
representational units
about
objects
universals
First Order Reality
particulars
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Terminology
Realist Ontology
Representation and Reference
terms
concepts
representational units
about
objects
universals
First Order Reality
particulars
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Terminology
Realist Ontology
Representation and Reference
representational units
terms
concepts
cognitive
units
communicative
units
about
objects
universals
First Order Reality
particulars
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Three
Terminology
levels of reality in Realist Ontology
Representation and Reference
representational units
(3) Representational units in various
forms about (1), (2) or (3)
cognitive
units
communicative
units
universals
particulars
(2) Cognitive entities which are our
beliefs about (1)
(1) Entities with objective existence
which are not about anything
First Order Reality
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
The three levels applied to medication management
Generic
3. Representation
2. Beliefs
(knowledge)
1.
First-order
reality
‘person’ ‘drug’ ‘penicillin’
CONTRA-INDICATION
INDICATION
PATHOLOGICAL
STRUCTURE
DRUG
MOLECULE
Specific
‘W. Ceusters’ ‘my pneumonia’
my doctor’s
work plan
my doctor
PERSON
DISEASE
PORTION OF
PENICILLIN
me
my doctor’s
diagnosis
my pharmacist’s
computer
my bronchitis
my toxic reaction
to penicillin
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Terminology is too reductionist
Generic
3. Representation
2. Beliefs
(knowledge)
1.
First-order
reality
‘person’ ‘drug’ ‘penicillin’
CONTRA-INDICATION
INDICATION
PATHOLOGICAL
STRUCTURE
DRUG
MOLECULE
Specific
‘W. Ceusters’ ‘my pneumonia’
my doctor’s
work plan
my doctor
PERSON
DISEASE
PORTION OF
PENICILLIN
me
my doctor’s
diagnosis
my pharmacist’s
computer
my bronchitis
my toxic reaction
to penicillin
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Terminology is too reductionist
What concepts do we need?
How do we name concepts properly?
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Terminological versus Ontological approach
• The terminologist defines:
– ‘a clinical drug is a pharmaceutical product given to (or taken
by) a patient with a therapeutic or diagnostic intent’. (RxNorm)
• The ontologist thinks:
– Does ‘given’ includes ‘prescribed’?
– Is manufactured with the intent to … not sufficient?
• Are newly marketed products – available in the pharmacy, but not yet
prescribed – not clinical drugs?
• Are products stolen from a pharmacy not clinical drugs?
• What about such products taken by persons that are not patients?
– e.g. children mistaking tablets for candies.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Why is this important ?
• Not as much for humans:
– Our ‘minds’ are very good in resolving ambiguities,
even at ‘unconscious’ levels.
• But for machines (computers, software):
– They can’t deal with imprecise, vague or ambiguous
statements.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
The power of realism in ontology design
Reality as benchmark !
1. Is the scientific ‘state of the art’
consistent with biomedical reality ?
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
The power of realism in ontology design
Reality as benchmark !
2. Is my doctor’s knowledge up to date?
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
The power of realism in ontology design
Reality as benchmark !
3. Does my doctor have an accurate
assessment of my health status?
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
The power of realism in ontology design
Reality as benchmark !
4. How can we use case studies better
to advance the state of the art?
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
The power of realism in ontology design
Reality as benchmark !
5. Is our terminology rich enough
to communicate about all three levels?
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
In summary
• Medication management involves many actors and IT
systems: semantic interoperability is thus a key issue.
• Ontologies (of the right sort) provide a deep level of
semantic interoperability between IT systems, thereby
keeping track:
– of what is the case;
– of what is known by some actor(s);
– of what has been and still needs to be done.
• Realism-based ontology, as a discipline, helps in creating
ontologies of the right sort.