an introduction to biomedical ontology
DESCRIPTION
AN INTRODUCTION TO BIOMEDICAL ONTOLOGY. Barry Smith University at Buffalo http://ontology.buffalo.edu/smith. Uses of ‘ontology’ in PubMed abstracts. The problem. There are many ways to create databases, creating silos Multiple terminologies will not solve these silo problems - PowerPoint PPT PresentationTRANSCRIPT
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AN INTRODUCTION TO BIOMEDICAL ONTOLOGY
Barry SmithUniversity at Buffalo
http://ontology.buffalo.edu/smith
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Uses of ‘ontology’ in PubMed abstracts
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The problem
There are many ways to create databases, creating silos
Multiple terminologies will not solve these silo problems
We need to constrain terminologies so that they converge
How?
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Evidence-based terminology development
Q: What is to serve as constraint?
A: Reality, as revealed by experimentally based science
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The Gene Ontology
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an example fromthe Gene Ontology
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particulars
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how link differentontologies together?
how ensure that they are developed in tandem?
One aspect of the problem
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Things and processes exist in time in different ways
substance
t i m
e
process
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Continuants vs occurrents
In preparing an inventory of reality
we keep track of these two different kinds of entities in two different ways
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The very top
ContinuantOccurrent
(always dependent on one or more
independent continuants)
IndependentContinuant
DependentContinuant
molecular function
cellular component
biological process
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Continuant entities
- have continuous existence in time
- preserve their identity through change
Occurrent entities
- have temporal parts
- exist only in their phases/stages
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You are a substance
Your life is a process
You are 3-dimensional
Your life is 4-dimensional
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Dependent entities
require independent continuants as their bearers
There is no run without a runner
There is no grin without a cat
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Dependent continuants
Functions, qualities, roles …
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Qualities
are dependent continuants
temperature
weight
height
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Realizable dependent continuants
function
role
disposition
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Realizations are processes
the expression of a function
the exercise of a role
the realization of a disposition
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All occurrents are dependent on their bearers/participants
One-place vs. relational processes
One-place processes:
a thing’s getting warmer
a thing’s getting hungrier
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Relational processes
fusings, signallings, capturings
bearers joined together into collectives of greater or lesser duration
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Part-Whole
Basic relation on the level of particulars
John’s heart is part of JohnJohn’s death is part of John’s dying
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Relations crossing the continuant-occurrent border are never part-relations
John’s lifeJohn
physiological processes
sustaining in existence
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Parts of processes are always processes
thing process
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meningitis is_a disease of the nervous system
unicorn is_a one-horned mammal
cancer documentation is_a cancer
is_a
A is_a B =def.
‘A’ is more specific in meaning than ‘B’
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The problem
We need to constrain terminologies so that they converge
How?
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Integration of biomedical data
will never be achieved through integration of meanings or concepts
because different user communities use different concepts
and express them in uncontrolledly different ways
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Kinds of relations
<type, type>: is_a, part_of, ...
<particular, type>: this explosion instance_of the type explosion
<particular, particular>: Mary’s heart part_of Mary
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part_of
as a relation between particulars
as a relation between types
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part_offor continuant types is time-
indexed
A part_of B =def.given any particular a and any time t, if a instantiates A at t,then there is some particular b such that b instantiates B and a is an part_of b at t on the level of particulars
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C
c at t
C1
c1 at t1
C'
c' at t
derives_from (ovum, sperm zygote ... )
time
particulars
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Advantages of the methodology of enforcing commonly accepted
coherent definitions
promote quality assurance (better coding)
promote automatic reasoning across ontologies and across data at different granularities
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Are pathways continuants or occurrent?
what happens if we take the definitions from google and classify the biologically relevant cases into two groups, according to whether they implied that pathways are continuants (roughly: the road travelled) or occurrents (the actual travelling event)?
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continuant1. nerve pathway: a bundle of myelinated nerve fibers following a path
through the brain 2. a trodden path (wordnet.princeton.edu/perl/webwn )3. Network of interacting proteins used to carry out biological functions
such as metabolism and signal transduction. www.inproteomics.com/nwglospq.html
4. The physical course a chemical or pollutant takes from its source to the exposed organism. www.waterquality.de/hydrobio.hw/PTERMS.HTM
5. The "route" a hazardous substance takes from its point of release (the "target") to a person, plant or animal (the "receptor"). www.deq.state.or.us/wmc/cleanup/glossary.htm
6. A series of consecutive valid linkages in a Pathways Diagram. www.ceaa-acee.gc.ca/013/0001/0004/a_e.htm
7. Potential route for exposure to radioactive or hazardous materials. www.comrad.org/glossary/glos2.htm
8. The path traced as movement proceeds through space. A pathway may be either on the floor or through the air and is constructed of straight and/or curved lines. www.ncpublicschools.org/curriculum/artsed/scos/dance/glossary
9. The route along which a chemical substance or hazardous material moves in the environment www.ec.gc.ca/etad/csmwg/pub/fed_aprch/en/glossary_e.htm
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occurrent
1. A series of related biochemical reactions. www.genpromag.com/Glossary~LETTER~P.html
2. Process for how patient moves through continuum of care. There may be multiple guidelines for a patient, depends on what you are managing. Workflow management describes what is done, how, by whom, and with what means.
informatics.medicine.dal.ca/w4/glossary.html