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Representingthe UMLS Semantic Network
using OWL
Vipul Kashyap1 and Alex Borgida2
1 LHCNBC, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 208942 Department of Computer Science, Rutgers University, New Brunswick, NJ 08903
Seminar Prinzipien des Ontological Engineering Leipzig, 15.01.2004
Kristin Lippoldt
Email: [email protected]
Outline
• The UMLS Semantic Network (SN)
• Representation of SN using OWL
• Multiple interpretations of „link“
• Evaluation of the interpretation variants
• Methodology for choosing the „right“ representation variant (first steps)
The UMLS Semantic Network
• nodes = semantic types• links = semantic relationships• two high level is-a hierarchies
Entity, Event
• is-a hierarchie of relationshipsphysically_related_to, spatially_related_to, temporally_related_to, functionally_related_to, conceptually_related_to
functionally_related_to
affects
manages
is-a
is-a
The UMLS Semantic Network (excerpt)
OrganismAttribute
AnatomicalStructure
EmbryonicStructure
AnatomicalAbnormality
CongenitalAbnormality
AcquiredAbnormality
Fully FormedAnatomical
Structure
Finding
Laboratory orTest Result
Sign orSymptom
BodySubstance
Body System
part of
part of
part of part of
part of
Body Part, Organ orOrgan Component
Tissue Cell CellComponent
Gene orGenome
Injury orPoisoning
property of
evaluation of
Body Spaceor Junction
conceptualpart of
Body Locationor Region
conceptualpart of
produces,contains
disrupts
disrupts
process of
conceptualpart of
evaluation of
isa linksnon-isa relations
conceptualpart of
BiologicFunction
PhysiologicFunction
Organ orTissue
Function
CellFunction
MolecularFunction
OrganismFunction
GeneticFunction
MentalProcess
PathologicFunction
Cell orMolecular
Dysfunction
Experimentalmodel
of Disease
Disease orSyndrome
Mental orBehavioral
Dysfunction
NeoplasticProcess
location of
adjacent to
location of
co-occurs with
Organism
Alga
Fungus Virus Rickettsiaor
Chlamydia
Bacterium Animal
Invertebrate Vertebrate
Amphibian Bird Fish
PlantArchaeon
ReptileMammal
Human
OrganismAttribute
AnatomicalStructure
EmbryonicStructure
AnatomicalAbnormality
CongenitalAbnormality
AcquiredAbnormality
Fully FormedAnatomical
Structure
Finding
Laboratory orTest Result
Sign orSymptom
Laboratory orTest Result
Sign orSymptom
BodySubstance
Body System
part of
part of
part of part of
part of
Body Part, Organ orOrgan Component
Tissue Cell CellComponent
Gene orGenome
Injury orPoisoningInjury orPoisoning
property of
evaluation of
Body Spaceor Junction
conceptualpart of
Body Locationor Region
conceptualpart of
produces,contains
disrupts
disrupts
process of
conceptualpart of
evaluation of
isa linksnon-isa relationsisa linksnon-isa relations
conceptualpart of
BiologicFunction
PhysiologicFunction
Organ orTissue
Function
CellFunction
MolecularFunction
OrganismFunction
GeneticFunction
MentalProcess
PathologicFunction
Cell orMolecular
Dysfunction
Experimentalmodel
of Disease
Disease orSyndrome
Mental orBehavioral
Dysfunction
NeoplasticProcess
Mental orBehavioral
Dysfunction
NeoplasticProcess
location of
adjacent to
location of
co-occurs with
Organism
Alga
Fungus Virus Rickettsiaor
Chlamydia
Bacterium Animal
Invertebrate Vertebrate
Amphibian Bird Fish
PlantArchaeon
ReptileMammal
Human
Organism
Alga
Fungus Virus Rickettsiaor
Chlamydia
Bacterium Animal
Invertebrate Vertebrate
Amphibian Bird Fish
PlantArchaeon
ReptileMammal
Human
Mammal
Human
OWL
• Web Ontology Language• Based on DAML+OIL• Description of classes, properties (e.g. relations
between classes (e.g. disjointness), cardinality (e.g. "exactly one"))
• Sublanguages:– OWL Lite (lower formal complexity than OWL DL, only
cardinality values of 0 or 1)– OWL DL (maximum expressiveness, computational
completeness )– OWL Full (maximum expressiveness, syntactic freedom of
RDF with no computational guarantees)
Description Logic - OWL
Bacterium ODER Virus
<owl:Class>
<owl:unionOf rdf:parseType=“Collection”>
<owl:Class rdf:about=“#Bacterium”/>
<owl:Class rdf:about=“#Virus”/>
</owl:unionOf>
</owl:Class>
Representation of SN using OWL
• Semantic Types OWL classes– Fungus Organism– Virus Organism
• Semantic Relationships OWL properties– part_of physically_related_to– affects functionally_related_to
• Properties of Semantic Network Relationships– Asymmetric relationships
• has_part ≡ part_of
– Symmetric relationships• adjacent_to ≡ adjacent_to
Semantics of a „link“ in the UMLS SN
Two operators and :
(causes) = { x Bacteria (y)(y Infection causes(x,y)) }DL notation: (causes) ≡ causes.T
(causes) = { y Infection (x)(x Bacteria causes(x,y)) }DL notation: (causes) ≡ causes.T
Bacteria Infectioncauses
Interpretation 1: / equals
• axioms: causes.T ≡ Bacteria, causes.T ≡ Infection
• All Bacteria have to “cause” and all Infections have to“be-caused” (no others can participate in “causes”)
b1 i1b2 i2
b3 i3b4
Interpretation 2: / subsumed
• axioms: causes.T Bacteria, causes.T Infection
• Not all bacteria need to “cause” not all infections have to “be-caused” (However no others can participate)
i1b2 i2
b3 i3b4
Interpretation 3: / subsumes
• axioms: Bacteria causes.T, Infection causes.T
• All bacterias have to “cause” and all infections have to “be-caused”, but – A bacteria can cause a “non-infection” as well!– A “non-bacteria” can cause an infection as well!
i1b2 i2
b3 i3b4
x1
y1
Interpretation 4: All/Some
• axiom: Bacteria causes.Infection
• All bacteria must “cause” some infection, but– A bacteria can cause a “non-infection” as well!– A “non-bacteria” can cause an infection as well!
i1b2 i2
b3 i3b4
x1
y1
Interpretation 5: All/Only
• axiom: Bacteria causes.Infection
• All bacteria, if they “cause”, can cause only infections, but– Not all bacteria have to participate in the “causes”
relationship– A non-bacteria can still cause an infection!
i1b2 i2
b3 i3b4
y1
Interpretation 6: All/Each
• axiom: Bacteria causes.Infection
• Similar to a cross product, but– A bacteria can still cause a non-infection!
i1b2 i2
b3 i3b4
x1
Interpretation 7: Some/Some
• axiom: 1 (Bacteria causes.Infection)
• There is at least one bacteria that “causes” at least one infection, but– A bacteria can still cause a non-infection!– A non-bacteria can still cause an infection!
i1b2 i2
b3 i3b4
x1
y1
Interpretation 8: Some/Each
• axiom: 1 (Bacteria causes.Infection)
• There is at least one bacteria that “causes” all infections, but– A bacteria can still cause a non-infection!– A non-bacteria can still cause an infection!
i1b2 i2
b3 i3b4
x1
y1
Summary of Interpretations
1) equals: causes.T ≡ Bacteria, causes.T ≡ Infection
2) subsumed: causes.T Bacteria, causes.T Infection
3) subsumes: Bacteria causes.T, Infection causes.T
4) all/some: Bacteria causes.Infection
5) all/only: Bacteria causes.Infection
6) all/each: Bacteria causes.Infection
7) some/some: 1 (Bacteria causes.Infection)
8) some/all: 1 (Bacteria causes.Infection)
and Inheritance
inheritance P(A,B) C A P(C,B)
inheritance P(A,B) D B P(A,D)
Example: process_of(BiologicFunction,Organism)C = PhysiologicFunctionD = Animal
1) equals: no support of inheritance , A ≡ C
2) subsumed: no support of inheritance A
C process_of.T
and Inheritance
3) subsumes: supports both
4) all/some: supports inheritance,but not inheritance
5) all/only: supports inheritance,but not inheritance
A
C
process_of.T
B
D
process_of-.T
A
C
process_of.B
B
D
process_of-.D
process_of.B
A
C
and Inheritance
6) all/each: supports both
7) some/some: no support of inheritance
8) some/all: doesn’t supports inheritance, but inheritance
A
C
process_of. B
process_of. D
Blocking of Inheritance
Example:Process_of(BiologicFunction,Organism)Process_of(MentalProcess,Plant)
Modifying axioms:
subsumes: P(A,B)C1 A and D1 BA C1 (P) and B D1
(P)
Ergebnis
Interpretation Encoding /Inheritance
Inheritance Blocking PolymorphicRelations
/ equals (P) A (P) B No/No N/A No
/ subsumed (P) A(P) B No/No N/A Missed model
/ subsumes A (P) B (P) Yes/Yes
Exceptions + compensation
Unintended model
all / some A P.B Yes/No Exception in axiom ok
all / only A P.B Yes/No Exception in axiom Modification
some / some 1(A P.B) No/No N/A ok
some / all 1(AP.B) No/Yes Exception in axiom ok
all / each A P.BYes/Yes
Exceptions + compensation
ok
Methodologie für die Kodierung von Wissen im Semantic Web
• Wahl der Kodierung– Unterstützung von Inferenz– Unterstützung der intendierten Anwendung– Nachvollziehbares Domänenmodell– Repräsentation in der Ontologiesprache
Unterstützung von Inferenzen
• Welche Kodierung unterstützt Inferenz?– All/each und subsumes
• Unterstützt die Kodierung nicht-intendierte Inferenzen?– Some/some unterstützt Aufwärts-Vererbung von Links
• Kann etwas aus der Abwesenheit eines Links geschlussfolgert werden?– A P. B verbietet nicht, dass A in Relation zu B
steht
Unterstützung der intendierten Anwendung
• Ist es wichtig Inkonsistenzen zu erkennen?
• Was sind Inkonsistenzen?
• Wird die Kodierung diese Inkonsistenzen erkennen?
Nachvollziehbarkeit des Domänenmodells
• Konzepte sind Kollektionen von Instanzen– Causes(Bacteria,Infection)
• Was ist die intuitive Kodierung?– All/some and all/only wird von medizinischen
Ontologien genutzt– All/each und some/some wurden abgelehnt
• Gibt es alternative Interpretationen?– Aber: all/each erfüllt alle UMLS SN Anforderungen
Repräsentation in der Ontologiesprache
• Grenzen von OWL– Negation und Disjunktion von Rollen– Kardinalität von Konzepten
• Kann man weniger „teure“ Konstrukte verwenden?– Ressourcen fließen in die Komplexität der DL
Operatoren
Conclusions and Future Work
• Experiences in representing a real world “ontology”, the UMLS Semantic Network
– Has been used very successfully– Requirements: / inheritance, inheritance blocking, polymorphic relationships
• Presented multiple interpretations and encodings and evaluated their support for the UMLS Semantic Network requirements
– Ontology developers and encoders on the Semantic Web might encounter similar requirements and possible encodings
• Identified criteria for choosing between the various encodings– First steps towards a methodology which might be useful to ontology developers
• Ongoing and Future Work– Semantic Vocabulary Interoperation Project
• http://cgsb2.nlm.nih.gov/~kashyap/projects/SVIP – Use of OWL, RDF for improvement in Medical Information Retrieval