stefan schulz, martin boeker, holger stenzhorn: how granularity issues concern biomedical ontology...
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![Page 1: Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration Stefan Schulz, Martin Boeker, Holger Stenzhorn](https://reader036.vdocuments.net/reader036/viewer/2022062714/56649d235503460f949fa2f1/html5/thumbnails/1.jpg)
Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Stefan Schulz , Martin Boeker, Holger Stenzhorn
University Medical Center Freiburg, Institute of Medical Biometry and Medical Informatics
Freiburg, Germany
How Granularity Issues Concern Biomedical Ontology Integration
MIE 2008
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction
• Background: emerging biomedical ontologies: standard descriptions of types of bio(medical) entities
• Challenge: interlink ontologies and enable interoperability
• Goal: share data both within and across disciplinary boundaries
• Proposal: BioTop, an integrative domain top level ontology for life scienceE Beisswanger, U Hahn, H Stenzhorn, S Schulz: BioTop: A Life Science Upper DomainOntology. Forthcoming in Applied Ontology 2008
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Biomedical Ontologies…
DomainOntologies
…are artifacts whose representational units are
intended to designate classes of biomedical entities, their properties,
and their interrelations
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
• Transcription • DNA-dependent transcription
• antisense RNA transcription• mRNA transcription• rRNA transcription• tRNA transcription • …(from Gene Ontology)
Biomedical Ontologies…
DomainOntologies
OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …)
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
• Transcription • DNA-dependent transcription
• antisense RNA transcription• mRNA transcription• rRNA transcription• tRNA transcription • …(from Gene Ontology)
Upper Ontologies…
DomainOntologies
OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …)
Onto-logies
limited to domain-
independent categories
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
• Transcription • DNA-dependent transcription
• antisense RNA transcription• mRNA transcription• rRNA transcription• tRNA transcription • …(from Gene Ontology)
Upper Ontologies
DomainOntologies
OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …)
UpperOntology BFO
DOLCE
• Entity• Continuant• Dependent Continuant• Realizable Entity• Function• Role• Independent Continuant • Object• Object Aggregate• Occurrent
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
• Transcription • DNA-dependent transcription
• antisense RNA transcription• mRNA transcription• rRNA transcription• tRNA transcription • …(from Gene Ontology)
Middle-level ?
DomainOntologies
OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …)
UpperOntology BFO
DOLCE
• Entity• Continuant• Dependent Continuant• Realizable Entity• Function• Role• Independent Continuant • Object• Object Aggregate• Occurrent
•Organism• Body Part• Cell• Cell Component• Tissue• Protein• Nucleic Acid• DNA• RNA• Biological Function• Biological Process
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
• Transcription • DNA-dependent transcription
• antisense RNA transcription• mRNA transcription• rRNA transcription• tRNA transcription • …(from Gene Ontology)
Top Domain Ontologies
DomainOntologies
OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …)
UpperOntology BFO
DOLCE
• Entity• Continuant• Dependent Continuant• Realizable Entity• Function• Role• Independent Continuant • Object• Object Aggregate• Occurrent
•Organism• Body Part• Cell• Cell Component• Tissue• Protein• Nucleic Acid• DNA• RNA• Biological Function• Biological Process
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
BioTop
Lower-level alignment
UpperOntology
TopDomainOntology
DomainOntologies
BFO
OBO (Gene Ontology, Sequence Ontology, Cell Ontology, OBI, ChEBI, Mouse Anatomy, FMA …)
GENIA Ontology
GFO-Bio
Simple Bio Upper Ontology
DOLCE
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
BioTop
Upper-level alignment
BFO
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
BioTop
Upper-level alignment
BFO
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
Object or FiatObjectPart?IndependentContinuant
ObjectFiat
ObjectPart
ObjectAggregate
Continuant
An independent continuant entity that is spatially extended, maximally self-connected and self-contained (the parts are not separated from each other by spatial gaps), and possesses an internal unity; the identity of substantial objects is independent of that of other entities and can be maintained through time and through loss and gain of parts and qualities.
Examples: an organism, a chair, a cell, a lung, an apple.
An independent continuant entity that is part of a object but is not demarcated by any physical discontinuities.
Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Copenhagen, the lower right portion of a human torso.
BFO
FiatObjectPart
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
Object or FiatObjectPart?IndependentContinuant
ObjectFiat
ObjectPart
ObjectAggregate
Continuant
Bodily OrganBioTop
?
FiatObjectPart
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Lung Surface vs.Pleural Space:Bona Fide Boundary(physical discontinuity)
Lung Hilus: Entry of Bronchi, veins and arteries. Fiat Boundary(no physical discontinuity)
Object or FiatObjectPart?
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
Object or FiatObjectPart?IndependentContinuant
ObjectFiat
ObjectPart
ObjectAggregate
Continuant
SiameseTwinBioTop …before separation
BFO
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
Object or FiatObjectPart?
BFOIndependentContinuant
ObjectFiat
ObjectPart
ObjectAggregate
Continuant
SiameseTwinBioTop …after separation
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
Object vs. ObjectAggregate
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
Object vs. ObjectAggregate
BFO
Continuant
IndependentContinuant
ObjectFiat
ObjectPart
ObjectAggregate
An independent continuant entity that is spatially extended, maximally self-connected and self-contained (the parts are not separated from each other by spatial gaps), and possesses an internal unity; the identity of substantial objects is independent of that of other entities and can be maintained through time and through loss and gain of parts and qualities.
Examples: an organism, a chair, a cell, a lung, an apple.
An independent continuant entity that is a mereological sum of separate objects.
Examples: a heap of stones, a group of commuters on the subway, a collection of bacteria, a flock of geese, the patients in a hospital, a symphony orchestra.
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
Object vs. ObjectAggregate
Continuant
IndependentContinuant
ObjectFiat
ObjectPart
ObjectAggregate
BioTop BiologicalObject
?
BFO
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
E.coli
Object
An independent continuant entity that is spatially extended, maximally self-connected and self-contained (the parts are not separated from each other by spatial gaps), and possesses an internal unity; the identity of substantial objects is independent of that of other entities and can be maintained through time and through loss and gain of parts and qualities.
Examples: an organism, a chair, a cell, a lung, an apple.
Introduction Problem 1 Problem 2 Problem 3 Conclusion
Object vs. ObjectAggregate
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
E.coli
Object vs. ObjectAggregate
ObjectObject
Aggregate
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
E.coli
Object vs. ObjectAggregate
ObjectObject
Aggregate
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
H
H
H
Object vs. ObjectAggregate
ObjectObject
Aggregate
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
H
H
H
H
H
H
H
H
H
H
H
H
Object vs. ObjectAggregate!
ObjectAggregate
Object
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
HH
H
H
H
H
H
H
H
0,0001% nuclei99,9999% empty space “filled”by probability distributions of electrons
Every Biological Object is an ObjectAggregate!
ObjectAggregate
Object
Introduction Problem 1 Problem 2 Problem 3 Conclusion
An independent continuant entity that is a mereological sum of separate objects.
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Problem 3: What are “separate objects”?
E.coli
ObjectObject
Aggregate
An independent continuant entity that is a mereological sum of separate objects.
Examples: a heap of stones, a group of commuters on the subway, a collection of bacteria, a flock of geese, the patients in a hospital, a symphony orchestra.
E.coli
An independent continuant entity that is spatially extended, maximally self-connected and self-contained (the parts are not separated from each other by spatial gaps), and possesses an internal unity; the identity of substantial objects is independent of that of other entities and can be maintained through time and through loss and gain of parts and qualities.
Examples: an organism, a chair, a cell, a lung, an apple.
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
strength ofconnection
mechanicadhesion
HydrogenBridges
surfaces chemical bonds
Van-der-Waals
Metallic
Non PolarCovalent
PolarCovalent
Ionic
Continuum of physical connection
electro-staticadhesion
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
BFO 3rd level categories challenged by
• Granularity-dependent notion of self-containedness and unity of objects
• Granularity-dependent view of objects as collection of particles
• Continuum of physical connection
• BFO uses ill-defined criteria of highest-level ontological distinctions
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Consequences for upper ontology integration
• Critique of domain level ontology (BioTop) by applying the rigor of an upper level ontology
• Critique of the upper level ontology by assessing the appropriateness of upper level categories from the perspective of the domain level
• Practical conclusion for BioTop: exclude subclasses of BFO:IndependentContinuant
Introduction Problem 1 Problem 2 Problem 3 Conclusion
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
Introduction Problem 1 Problem 2 Problem 3 Conclusion
Consequences for upper ontology integration
Continuant
ObjectFiat
ObjectPart
ObjectAggregate
BioTop
BFO
BioTop
IndependentContinuant
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Stefan Schulz, Martin Boeker, Holger Stenzhorn: How Granularity Issues Concern Biomedical Ontology Integration
BioTop• Metrics:
• BioTop is freely available at: http://purl.org/biotop
• BioTop discussion forum: [email protected]• BootSTREP (FP6 - 028099 ) project: http://www.bootstrep.eu
Introduction Problem 1 Problem 2 Problem 3 Conclusion