towards a computational paradigm for biological structure stefan schulz department of medical...
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Towards a Computational Paradigm for Biological
Structure
Stefan SchulzDepartment of Medical Informatics
University Hospital Freiburg (Germany)
Udo HahnText Knowledge Engineering Lab
University of Jena (Germany)
First International Workshop on Formal Biomedical Knowledge Representation (KR-MED2004), June 1, 2004, Whistler (Canada)
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The World of Life Sciences…
Millions of Species
Evolutionof Life Morphology
MoleculesGenesCells
OrgansOrgan Systems
Function
Dysfunction
Tissues
Organisms
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Bio-ontologies
Occurrents: (Changes of) states of affairs
of the physical world:
Examples: process, state, event,…
Continuants: Entities of the physical world
(„Biomedical Structure“):
Examples: body, organ, tissue, molecule,..
…requires sophisticated organization
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What exists ?
Human AnatomyFoundational Model of Anatomy (FMA)Portions of SNOMED, OpenGalen, MeSH
Other OrganismsOpen Biological Ontologies (OBO)
Mouse (developmental stages), Zebrafish, Drosophila,…
Species-IndependentGene Ontology: Cellular Component
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Overlap
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Same name – different meaning“Motor Neuron instance-of Neuron”
(FlyBase)
“Motor Neuron narrower Neuron” (MeSH)
“Motor Neuron subclass-of Neuron” (FMA, OpenGALEN)
Neuron
MotorNeuron
Is-A ?
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Same name – different meaning
“Neuron has-part Axon” (FMA) Does every neuron
has an axon?
“Cell has-part Axon” (Gene Ontology) Do cells without
axons exist ? Do axons without
cells exist ?
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Deficiencies (II)
“Neuron has-part Axon” (FMA) Does every neuron
has an axon?
“Cell has-part Axon” (Gene Ontology) Do cells without
axons exist ? Do axons without
cell exist ?
“Keep in mind that part_of means can be a part of, not is always a part of “GO Editorial Style Guide, Oct 2003
“The part_of relationship (…) is usually necessarily is_part” GO Editorial Style Guide, Jan 2004
“A part_of B if and only if: for any instance x of A there is some instance y of B which is such that x stands to y in the instance-level part relation, and vice versa”.
Rosse & Smith MEDINFO 2004
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Conflicting and / or underspecified conceptualizations hamper sharing and integration of ontologies
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Semantic framework for biological structure…
Foundational Relations
General Attributes
Theories
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Semantic framework for biological structure…
Foundational Relations
General Attributes
Theories
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Foundational Relations between Biological Structure is-a instance-of part-of / has-part has-location / location-of has-branch / branch-of has-developmental-form /
is-developmental-form-of descends-from /
has-descendant connects bounds / bounded by
classify bydomain / range ?
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Individuals(Concrete Objects)
Universals(Concepts, Classes of
Individuals)
Domain Entities
•my left hand•a blood sample•a concrete cell
•Hand•Blood •Cell
Two kinds of entities
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Classification of Foundational Relations
Universals(Concepts, Classes of
Individuals)
Is-ADescends-From
instance-of
Individuals(concrete objects)
part-ofhas-locationhas-branchhas-developmental-formboundsconnects
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Classification of Foundational Relations
Universals(Concepts, Classes of
Individuals)
Is-ADescends-From
instance-of
Part-OfHas-LocationHas-BranchHas-Developmental-FormBoundsConnects
Individuals(concrete objects)
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From Instance-to-Instance relations to Class-to-Class Relations
A, B are classes, inst-of = class membershiprel: relation between instances Rel: relation between
classes
Rel (A, B) =def
x: inst-of (x, A) inst-of (y, B) rel (x, y) OR x: inst-of(x, A) y: inst-of (y, B) rel (x, y) OR
y: inst-of(y, B) x: inst-of (x, A) rel (x, y)
cf.Schulz & Hahn (KR 2004, June 2, 11am)Rosse & Smith (MEDINFO 2004)
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Semantic framework for biological structure…
Foundational Relations
General Attributes
Theories
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General Attributes (mutually disjoint classes)
Dimensionality: Point, 1-D, 2-D, 3-D
Solids vs. hollow spaces, vs. Boundaries
Collections vs. Masses vs. Count Objects
cf. Schulz & Hahn, FOIS 01
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Semantic framework for biological structure…
Foundational Relations
General Attributes
Theories
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Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
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Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
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GranularityLevel of detail
(molecular, cellular, tissue, organ)
Change in Granularity level may be non-monotonousChange of sortal restrictions:
3-D 2-D boundaryCount concept Mass concept
Change of relational attributions:disconnected connected
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Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
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http://tolweb.org
Linnean Taxonomy of Species
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http://tolweb.org
Linnean Taxonomy of Species
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http://tolweb.org
Linnean Taxonomy of Species
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Species
Introduction of Axioms at the highest common level
Has-Part Skull
Has-Part Skull Has-Part Vertebra
Has-Part Skull Has-Part Vertebra Has-Part Jaw
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Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
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Development Represents time-dependent
“snapshots” from the life cycle of an organism, e.g.,zygote, embryo, fetus, child, adult
Granularity stages are species-dependente.g. metamorphosis
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Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
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Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure
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Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure Structural Variations
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Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure Structural VariationsPathological Structure
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Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure Structural VariationsPathological StructureLethal Structure
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Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure Structural VariationsPathological StructureLethal StructureDerivates of biological
structure
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Canonicity
Five canonicity levels: each level introduces axioms valid for higher levels
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Examples
Granularity
Species
Development
Canonicity
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Coverage:Foundational Model of Anatomy
Granularity
Species
Development
Canonicity
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Coverage:Gene Ontology
Granularity
Species
Development
Canonicity
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Coverage:Mouse Anatomy
Granularity
Species
Development
Canonicity
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ExamplesConnects(RightVentricle, Left Ventricle)
false
true
Granularity = normalSpecies = mammalDevelopment = adultCanonicity = 4-5
Granularity = anySpecies = vertebrateDevelopment = early embryoCanonicity = any
Is-A(Membrane, 3-D object)
true
false
Granularity = normalSpecies = anyDevelopment = anyCanonicity = any
Granularity = lowestSpecies = anyDevelopment = anyCanonicity = any
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Conclusion
Integration of bio-ontologies requiresUncontroversial semantics of relations and
attributesClear commitment to theories, such as
granularity, species, development and canonicity
Redundancy can be avoided Encoding axioms at the highest common level
in the species taxonomy (e.g. vertebrates, arthropods, primates) and benefit from inheritance in subsumption hierarchies
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…requires sophisticated organizationFormalization and Standardization of
Clinical TerminologiesBasis for the Annotation of Genes and
Gene ProductsSemantic reference for scientific
communicationMachine-supported reasoning and
decision-support
Bio-ontologies !
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Upper level classification of entities
Individuals(concrete objects)
Universals(Concepts, Classes of
Individuals)
Continuants(physical objects,…)
• my left hand• a blood sample• a concrete cell
• Hand,• Blood• Cell
Occurrents(events, processes,
actions…)
• Peter’s diabetes• appendectomy of
Patient #12345• Diabetes mellitus• Appendectomy
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Mereotopological Quiz• Cranial Cavity has-location Head
Is Cranial Cavity part-of Head ?• Brain has-location Cranial Cavity
Is Brain part of Cranial Cavity ?
• Glioblastoma has-location BrainGlioblastoma part-of Brain?
• Brain metastasis has-location Brain Brain metastasis part-of Brain?
• Embryo has-location UterusEmbryo part-of Uterus ?
Images from: Sobotta CD-ROM
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HS
HP p
is-a
is-a
HL
has-location
Head
is-a
SS
SP p
is-a
is-a
SL
has-location
Skull
is-a
CS
CP p
is-a
is-a
CL
has-location
CranialCavity
is-a
BS
BP p
is-a
is-a
BL
has-location
Brain
is-a
HEHead(Solid)
SESkull(Solid)
CE
CranialCavity(Hole)
BE
Brain(Solid)
part-of has-location
is-a
is-a
is-a
transitive closure by taxonomic subsumption
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1. Taxonomy 2. Mereology 3. Topology
Thumbnail
Thumb
Hand
part-ofpart-of
part-of
„is-a“ „part-of“ „connection“
Subtheories of an Ontology of Biological Structure
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1. Taxonomy 2. Mereology 3. Topology„is-a“ „part-of“ „connection“
• Canonical relationships
X Y X Y X Y XY X Y Y X X Y Y X
(Schulz et al. AMIA 2000)
• Topological Primitives:
Subtheories of an Ontology of Biological Structure
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Structure of Talk
IntroductionFoundational RelationsFoundational AttributesTheories
GranularitySpeciesDevelopment“Canonicity”
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The World of Life Sciences…
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Generalized Representation of Living Systems: Top Level
Biological Entities
Biological Occurrents
process, state, event,…
Biological Continuants organism, organ, tissue,
cell, molecule,..
dependence
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Ontological Account for Biological Continuants
Foundational RelationsFoundational AttributesTheories
GranularitySpeciesDevelopment“Canonicity”
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Granularity
Taxonomic: degreeof specialization
Mereologic: degreeof dissection
{molecular level, cellular level, tissue level, organ level, population level}
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Change in Granularity level may be non-monotonous
Change of sortal restrictions: 3-D 2-D boundary Count concept Mass concept
Change of relational attributions:disconnected connected