Download UMIT_July_2003 - Buffalo Ontology Site

VT
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Medical Ontology
Barry Smith
http://ifomis.de
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IFOMIS
Institute for Formal Ontology and Medical
Information Science
Faculty of Medicine
University of Leipzig
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Reference Ontology
An ontology is a theory of a domain of
entities in the world
Ontology is outside the computer
seeks maximal expressiveness and
adequacy to reality
and sacrifices computational tractability for
the sake of representational adequacy
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Reference Ontology
a theory of the tertium quid
– called reality –
needed to hand-callibrate
database/terminology systems
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Methodology
Get ontology right first
(realism; descriptive adequacy; rather
powerful logic);
solve tractability problems later
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The Reference Ontology
Community
IFOMIS (Leipzig)
Laboratories for Applied Ontology (Trento/Rome,
Turin)
Foundational Ontology Project (Leeds)
Ontology Works (Baltimore)
Ontek Corporation (Buffalo/Leeds)
Language and Computing (L&C)
(Belgium/Philadelphia)
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Domains of Current Work
IFOMIS Leipzig: Medicine, Bioinformatics
Laboratories for Applied Ontology
Trento/Rome: Ontology of Cognition/Language
Turin: Law
Foundational Ontology Project: Space, Physics
Ontology Works: Genetics, Molecular Biology
Ontek Corporation: Biological Systematics
Language and Computing: Natural Language
Understanding
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Ontologie als Zweig der
Philosophie
die Wissenschaft von den Arten und
Strukturen von Objekten, Qualitäten,
Prozessen, Ereignissen, Funktionen
und Relationen in allen Bereichen der
Wirklichkeit
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Aristotle
Der erste Ontologe
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Eine biologische Ontologie
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Linné
1763: Genera Morborum
(Nosologie
oder
Ontologie der Krankheitsarten)
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Q: Warum “Ontologie” in der
medizinischen Informatik?
A: Das Turm von Babel-Problem
der Informationssysteme
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Turm von Babel
Jedes Informationssystem basiert auf einer
eigenen Terminologie
Wie können wir die Inkompatibilitäten
lösen, die entstehen, wenn Daten aus
verschiedenen Quellen kombiniert werden?
Vgl. Wie können wir Anatomie und
Physiologie integrieren?
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Wie lösen Medizinstudenten dieses
Problem?
Vielfach erst durch die
Begegnung mit dem Patienten
Der Patient und die in ihm ablaufenden
Prozesse dienen als Kristallisationspunkt
für eine sinnvolle Ordnung sonst isoliert
stehender (gelernter) Fakten.
(Aus Wissen-dass wird Wissen-wie)
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Dem Computer fehlt praktisches
Wissen
Wie können in Medizininformationssystemen isolierte Datenartefakte zu
konsistentem und anwendbarem Wissen
integriert werden?
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Ursprünglicher Traum der
Ontologie in der Informatik
Eine einzige allumfassende Taxonomie
aller Gegenstandsarten, die als zentrales
integrierendes Kategoriensystem für alle
Informationssysteme dient.
Dieser Traum ist ausgeträumt ...
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Gegenwärtige Lösungen
Standardisierte Terminologien
UMLS
SNOMED
ICD-10
Gene Ontology
Digital Anatomist
usw.
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Standardisierte Terminologien
sollen Zugriff auf biomedizinische Literatur
und Faktendatenbanken erleichtern
Beispielsweise um Verbindungen
zwischen spezifischen Genen und
spezifischen Körperreaktionen auffindbar
zu machen
Eine neue Art medizinischer Forschung
soll dadurch ermöglicht werden
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Database and terminology
standardization
is desparately needed in medical and
bioinformatics
to enable the huge amounts of existing
data to be fused together automatically
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To reap the benefits of standardization
we need to make ONE SYSTEM out of
many different terminologies
But how?
Through government edict? (Scandinavia)
Through efforts of international standards
bodies (ISO, CEN …)?
Through UMLS Metathesaurus?
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Zentrale Schaltstelle
UMLS
Universal Medical Language System
National Library of Medicine
Bethesda, MD
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UMLS Metathesaurus
eine riesige Kombination verschiedener
maschinenlesbarer Quellterminologien
800,000 Begriffe
10 Mio. Beziehungen
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Beispiele für Quell-Terminologien
SNOMED-RT
Systematized Nomenclature of Medicine
MeSH
Medical Subject Headings
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is_a trees
hormone
peptide hormone
adrenocorticotropin
digestive hormone
glycopeptide hormone
follicle-stimulating hormone
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is_a = ist ein / ist von der Art
Diabetes Melletus is_a Disease
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Bad Coding
deriving from over-simplification
and from failure to pay attention to
ontological principles
Z.B. SNOMED
both_testes is_a testis
(beide_Hoden ist_ein Hoden)
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Terminological Incompatibilities
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Representation of Blood in SNOMED
Blood is_a Tissue
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Representation of Blood in MeSH
Blood is_a Bodily Fluid
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Bad Coding
Incompatibilities
Context-Dependence
Standardized Terminologies
must be used properly
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people are lazy and idiosyncratic
Sie machen Schreibfehler
Jeder pflegt seine eigene Terminologie,
die sich mehr oder weniger von der
anderer Akteure unterscheidet
Sie verwenden verschiedene natürlichsprachliche Darstellungen der gleichen
medizinischen Phänomena
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The codes are not formulated on
the basis of clear principles
Therefore inconsistent
Unintuitive
Difficult to train people to use them
Application often depends on contextdependent knowledge
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The IFOMIS Contribution
help to improve standardizations through
constructive criticism based on robust
ontological principles
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UMLS Metathesaurus
eine riesige Kombination verschiedener
maschinenlesbarer Quellterminologien
UMLS Semantic Network
bestehend aus 134 Semantic Types
soll Ordnung in diesem Wust schaffen
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UMLS Semantic Network
entity
physical
entity
event
conceptual
entity
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conceptual entity
Organism Attribute
Finding
Idea or Concept
Occupation or Discipline
Organization
Group
Group Attribute
Intellectual Product
Language
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conceptual entity
Organism Attribute
Finding
Idea or Concept
Occupation or Discipline
Organization
Group
Group Attribute
Intellectual Product
Language
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Idea or Concept
Functional Concept
Qualitative Concept
Quantitative Concept
Spatial Concept
Body Location or Region
Body Space or Junction
Geographic Area
Molecular Sequence
Amino Acid Sequence
Carbohydrate Sequence
Nucleotide Sequence
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INNSBRUCK
is an Idea or Concept
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Idea or Concept
Functional Concept
Qualitative Concept
Quantitative Concept
Spatial Concept
Body Location or Region
Body Space or Junction
Geographic Area
Molecular Sequence
Amino Acid Sequence
Carbohydrate Sequence
Nucleotide Sequence
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Confusion of Ontology and Epistemology
Physical Entity
Chemical Entity
Chemical
Viewed
Structurally
Chemical
Viewed
Functionally
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Confusion of Ontology and Epistemology
the hydraulic equation:
BP = CO*PVR
arterial blood pressure is directly
proportional to the product of blood flow
(cardiac output, CO) and peripheral
vascular resistance (PVR).
Cardiac Output in UMLS = A Finding
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UMLS-Semantic Types:
blood pressure is an Organism Function,
cardiac output is a Laboratory or Test Result
or Diagnostic Procedure
BP = CO*PVR thus asserts that
blood pressure is proportional either to a
laboratory or test result or to a diagnostic
procedure
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The goal
Formulate clear principles for building
ontologies
Reconstitute the UMLS Semantic Types on
the basis of these principles
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Zusammenarbeit mit der National
Library of Medicine
Revision der UMLS Semantic Types und der
Gene Ontology
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GO: the Gene Ontology
3 large telephone directories of
standardized designations for gene
functions and products
organized into hierarchies via is_a and
part_of
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GO
can in practice be used only by trained
biologists (with know how)
whether a GO-term truly stands in the is_a
relation depends e.g. on the type of
organism involved
glycosome is part-of cytoplasm only for
Kinetoplastidae
Computers have no counterpart of such
context-dependent know-how
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GO divided into three disjoint
term hierarchies
the cellular component ontology,
e.g. flagellum, chromosome, cell
the molecular function ontology,
e.g. ice nucleation, binding, protein
stabilization
the biological process ontology,
e.g. glycolysis, death
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Definition of Molecular Function
“the action characteristic of a gene product.”
On March 2003 all nodes in the Molecular
Function ontology (except the root) had
‘activity’ added to their names
-- confusion of function with functioning
(how deal with dormant/suppressed
functions?)
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Definition of Biological Process
“A phenomenon marked by changes that
lead to a particular result, mediated by one
or more gene products”
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How are the 3 ontologies
related?
Function = “the action characteristic of a
gene product.”
Process = “phenomenon marked by
changes that lead to a particular result,
mediated by one or more gene products”
No part-whole relations across ontologies?
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The GO isa relation
in its intended meaning indicates a
necessary relationship.
That is, when we say “eukaryotic cell isa
cell”, we mean that every eukaryotic cell is
a cell.
Confusion of necessarily, universally, and
permanently
(No time in GO)
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part_of
The Relation part-of: The intended
meaning of part-of as explained in the GO
Usage Guide is: “can be a part of, not is
always a part of”
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Uses of part_of
– membrane part-of cell, intended to mean “a membrane is
a part-of any cell”
– flagellum part-of cell, intended to mean “a flagellum is
part-of some cells”
– replication fork part-of cell cycle, intended to mean: “a
replication fork is part-of the nucleoplasm only during
certain times of the cell cycle”
– regulation of sleep part-of sleep, should be corrected to:
“regulation of sleep is co-located with and is causally
involved with the sleep process”.
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Need to find ways to deal with time
in medical informatics
Functions vs. Realizations of Functions
Function is still there even when not being
realized
need to be clear about the distinction
between continuants and occurrents
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SNAP and SPAN
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SNAP and SPAN
Substances and processes
Continuants and occurrents
In preparing an inventory of reality
we keep track of these two different
categories of entities in two different ways
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Substances and processes
exist in time in different ways
process
substance
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Need for different perspectives
Not one ontology, but a multiplicity of
complementary ontologies
Cf. Quantum mechanics: particle vs. wave
ontologies
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SNAPshot
ontology
Video (SPAN)
ontology
process
substance
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SNAP and SPAN
stocks and flows
commodities and services
product and process
anatomy and physiology
synchrony and diachrony
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SNAP and SPAN
SNAP entities
- have continuous existence in time
- preserve their identity through change
- exist in toto if they exist at all
SPAN entities
- have temporal parts
- unfold themselves phase by phase
- exist only in their phases/stages
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SNAP: Entities existing in toto at a time
MedO Draft 0.0004
Enduring Entity
[Exists in space and time,
has no temporal parts]
Dependent Entity
[±Relational]
Spatial Entity
Occupied
Spatial region of 3
dimensions
occupied by organism
Spatial region of 2
dimensions *
occupied by burn, bruise
SNAP
Unoccupied
Quality
[Sometimes form qualityregions or scales]
Tunnel
Alimentary Canal
Hollow
Nostril
Cavity
Interior of Lung
Requisite
[Have determinable/
determinate structure]
Temperature. height
Optional
Diabetes
State
Being pregnant, being thirsty
Independent Entity
Role, Function, Power, Disposition
[Have realizations, called processes]
To circulate blood, to secrete hormones
Substance
Organism, organ
Fiat part of substance *
Extremity, upper body
Boundary of substance *
Surface of skin or hide
Aggregate of substances *
Family, mother and fetus
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Three kinds of SNAP entities
•
•
•
Substances
Dependent SNAP entities
(qualities, functions, roles,
powers …)
Spatial regions, Contexts, Niches
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0.0004
Enduring Entity
[Exists in space and time,
has no temporal parts]
SNAP
Dependent Entity
[±Relational]
Quality
[Sometimes form qualityregions or scales]
Requisite
[Have determinable/
determinate structure]
Temperature. height
State
Being pregnant, being thirsty
Role, Function, Power, Disposition
[Have realizations, called processes]
To circulate blood, to secrete hormones
Functions
The function of the
heart is to pump blood
Optional
Diabetes
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Spatial Entity
Occupied
Spatial region of 3
dimensions
occupied by organism
Spatial region of 2
dimensions *
occupied by burn, bruise
Unoccupied
Qu
[Sometimes
regions
Tunnel
Alimentary Canal
Hollow
Nostril
Requisite
[Have determinable/
determinate structure]
Temperature. height
Cavity
Interior of Lung
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NAP
Independent Entity
Role, Function, Power, Disposition
[Have realizations, called processes]
To circulate blood, to secrete hormones
SNAP
Substance
Organism, organ
Fiat part of substance *
Extremity, upper body
Fiat part of substance
Extremity (hand, arm)
Bodily System
Boundary of substance *
Surface of skin or hide
Aggregate of substances *
Family, mother and fetus
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SPAN: Entities extended in time
Entity extended in time
Processual Entity
[Exists in space and time, unfolds
in time phase by phase]
Portion of Spacetime
Spacetime worm of 3 + T
dimensions
occupied by life of organism
Temporal interval *
projection of organism’s life
onto temporal dimension
SPAN
Process
[±Relational]
Circulation of blood,
secretion of hormones,
course of disease, life
Fiat part of process *
First phase of a clinical trial
Aggregate of processes *
Clinical trial
Temporal boundary of
process *
onset of disease, death
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SPAN: Entities extended in time
Entity extende
Portion of Spacetime
Proce
Spacetime worm of 3 + T
dimensions
occupied by life of organism
Temporal interval *
projection of organism’s life
onto temporal dimension
[±Relatio
Circulation o
secretion of h
course of dis
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SPAN: Entities extended in time
Entity extended in time
SPAN
Processual Entity
[Exists in space and time, unfolds
in time phase by phase]
Process
[±Relational]
Circulation of blood,
secretion of hormones,
course of disease, life
Fiat part of process *
First phase of a clinical trial
Aggregate of processes *
Clinical trial
Functioning
The heart’s pumping
of blood
Temporal boundary of
process *
onset of disease, death
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Granularity
spatial region
substance
parts of substances are always substances
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Granularity
spatial region
substance
parts of spatial regions are always spatial regions
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Granularity
process
parts of processes are always processes 74
MORAL
Relations crossing the SNAP/SPAN
border are never part-relations
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Relations crossing the SNAP/SPAN border
are never part-relations
substance John
John’s life
physiological
processes
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DIGESTIVE
SYSTEM
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RESPIRATORY
SYSTEM
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URINARY
SYSTEM
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IMMUNE
SYSTEM
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CIRCULATORY
SYSTEM
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CIRCULATORY
SYSTEM
(Principal Organs)
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The autonomous part of the nervous system
(regulatory links to other systems)
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ENDOCRINE
SYSTEM
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Bodily Systems are Component Parts
of Bodies
digestive
respiratory
skeletal
musculatory circulatory
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immune
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A system for keeping your jewels
safe
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Bodily Systems interconnect
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Systems are SNAP entities
They are dependent continuants
We can take photographs of them
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The Monarchic System of Government
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