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Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering...
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![Page 1: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/1.jpg)
Ontological Foundations of Biological Continuants
Stefan Schulz, Udo Hahn
Text Knowledge Engineering LabUniversity of Jena (Germany)
Department of Medical InformaticsUniversity Hospital Freiburg (Germany)
International Conference on Formal Ontology in Information Systems
![Page 2: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/2.jpg)
Representation of Continuants in Bio-ontologies
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 branch
Size: 103 (Adult Mouse) – 105 (FMA)
![Page 3: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/3.jpg)
![Page 4: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/4.jpg)
Semantic framework for biological structure…
Foundational Relations
General Attributes
Theories
![Page 5: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/5.jpg)
Semantic framework for biological structure…
Foundational Relations
General Attributes
Theories
![Page 6: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/6.jpg)
Semantic framework for biological structure…
Foundational Relations
General Attributes
Theories
![Page 7: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/7.jpg)
Classes
Individuals
Is-A
Instance-of
part-of, has-locationhas-branch, bounds,
connectshas-developmental-form
Some Foundational Relations between Biological Continuants
x
y Rel(x,y)
Classes Individuals
![Page 8: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/8.jpg)
Classes
Classes
Individuals
Is-A
Instance-of
part-of, has-locationhas-branch, bounds,
connectshas-developmental-form
Some Foundational Relations between Biological Continuants
Individualsx
y Rel(x,y)
![Page 9: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/9.jpg)
Is-A, Part-Of, Has-Location Bounds,Has-Branch, Connects
Has-Developmental-Form
Instance-of
part-of, has-locationhas-branch, bounds,
connectshas-developmental-form
Some Foundational Relations between Biological Continuants
x
y Rel(x,y)
Classes Individuals
Classes
Individuals
![Page 10: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/10.jpg)
Class-Level Relations (I)
“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 ?
![Page 11: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/11.jpg)
Class-Level Relations (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
cells 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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Class-Level Relations (III)
A, B: classes, inst-of: class membershiprel: relation between instances Rel: relation between classes
Rel (A, B) =def
x: inst-of(x, A) y: inst-of (y, B) rel (x, y)cf.Schulz (AMIA 2001)Schulz & Hahn (KR 2004, ECAI 2004)Rosse & Smith (MEDINFO 2004)
![Page 13: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/13.jpg)
Semantic framework for biological structure…
Foundational Relations
General Attributes
Theories
![Page 14: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/14.jpg)
General Attributes (top level categories)
Point 1-D 2-D 3-D
Solids Holes Boundaries
Pluralities Masses Count Objects
cf. Schulz & Hahn, FOIS 01
![Page 15: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/15.jpg)
Semantic framework for biological structure…
Foundational Relations
General Attributes
Theories
![Page 16: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/16.jpg)
“Heart”
![Page 17: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/17.jpg)
Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
![Page 18: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/18.jpg)
Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
epistemiological
ontological
![Page 19: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/19.jpg)
Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
![Page 20: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/20.jpg)
Granularity
Classification(level of detail of class distinction)
Cell
Blood Cell
Cell
Blood Cell
WBC
Lymphocyte
T-Lymphocyte
T4-Lymphocyte
(taxonomy)
![Page 21: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/21.jpg)
Granularity
Classification(level of detail of class distinction)
Dissection(focus on organism, tissue, cell, molecule)
Cell
Cell Nucleus
Cell
Cell Nucleus
Chromosome
DNA
Nucleotide
-NH2
(partonomy)
![Page 22: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/22.jpg)
Granularity of DissectionChange in Granularity level may be non-monotonous
Change of sortal restrictions:3-D 2-D boundary
Plurality Mass object
Change of relational attributions:disconnected connected
![Page 23: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/23.jpg)
Granularity
Classification(level of detail of class distinction)
Dissection(focus on organism, tissue, cell, molecule)
Relations(relation hierarchy vs. few foundational relations)
included-by included-by
part-of
proper-part-of
functionalpart-of
![Page 24: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/24.jpg)
included-by(CellNucleus, Cell)part-of(CellNucleus, Cell)included-by(VirusProtein, Cell)part-of(VirusProtein, Cell) ??
Virus
Cell
Granularity of Relations
![Page 25: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/25.jpg)
Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
![Page 26: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/26.jpg)
http://tolweb.org
Linnean Taxonomy of Species
![Page 27: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/27.jpg)
http://tolweb.org
Linnean Taxonomy of Species
![Page 28: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/28.jpg)
http://tolweb.org
Linnean Taxonomy of Species
![Page 29: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/29.jpg)
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
![Page 30: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/30.jpg)
Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
![Page 31: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/31.jpg)
Development Represents time-dependent
“snapshots” from the life cycle of an organism, e.g.,zygote, embryo, fetus, child, adult
Development stages are species-dependente.g. metamorphosis
![Page 32: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/32.jpg)
Theories
A set of formal axioms which describe a restricted (local) domain.
Four orthogonal theories for Biological Structure
GranularitySpeciesDevelopment Canonicity
![Page 33: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/33.jpg)
Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure
![Page 34: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/34.jpg)
Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure Structural Variations
![Page 35: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/35.jpg)
Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure Structural VariationsPathological Structure
congenital
acquired
![Page 36: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/36.jpg)
Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure Structural VariationsPathological StructureLethal Structure
![Page 37: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/37.jpg)
Canonicity
Degrees of “Wellformedness” of Biological Structure:Canonic structure Structural VariationsPathological StructureLethal StructureDerivates of biological
structure
![Page 38: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/38.jpg)
Canonicity
Five canonicity levels: each level introduces axioms valid for higher levels
![Page 39: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/39.jpg)
Examples
Granularity
Species
Development
Canonicity
low high
general specific
embryo adult
low high
![Page 40: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/40.jpg)
Coverage:Foundational Model of Anatomy
Granularity
Species
Development
Canonicity
low high
general specific
embryo adult
low high
![Page 41: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/41.jpg)
Coverage:Gene Ontology
Granularity
Species
Development
Canonicity
low high
general specific
embryo adult
low high
![Page 42: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/42.jpg)
Coverage:Mouse Anatomy
Granularity
Species
Development
Canonicity
low high
general specific
embryo adult
low high
![Page 43: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/43.jpg)
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
![Page 44: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/44.jpg)
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
![Page 45: Ontological Foundations of Biological Continuants Stefan Schulz, Udo Hahn Text Knowledge Engineering Lab University of Jena (Germany) Department of Medical.](https://reader035.fdocuments.in/reader035/viewer/2022070410/56649f085503460f94c1d3c4/html5/thumbnails/45.jpg)
Ontological Foundations of Biological Continuants
Stefan Schulz, Udo Hahn
Text Knowledge Engineering LabUniversity of Jena (Germany)
Department of Medical InformaticsUniversity Hospital Freiburg (Germany)
International Conference on Formal Ontology in Information Systems