Ontological Foundations of Biological Continuants

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Ontological Foundations of Biological Continuants
International Conference on Formal Ontology in
Information Systems

• Stefan Schulz, Udo Hahn

Text Knowledge Engineering LabUniversity of Jena
(Germany)
Department of Medical InformaticsUniversity
Hospital Freiburg (Germany)
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Representation of Continuants in Bio-ontologies

• Human Anatomy
• Foundational Model of Anatomy (FMA)
• Portions of SNOMED, OpenGalen, MeSH
• Other Organisms
• Open Biological Ontologies (OBO)
• Mouse (developmental stages), Zebrafish,
  Drosophila,
• Species-Independent
• Gene Ontology Cellular Component branch

Size 103 (Adult Mouse) 105 (FMA)
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(No Transcript)
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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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Semantic framework for biological structure

• Foundational Relations
• General Attributes
• Theories

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Some Foundational Relations between Biological
Continuants
y
Classes
Individuals
Rel(x,y)
x
Classes
Is-A
Individuals
Instance-of
part-of, has-location has-branch, bounds,
connects has-developmental-form
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Some Foundational Relations between Biological
Continuants
Classes
Individuals
y
Rel(x,y)
x
Classes
Is-A
Individuals
Instance-of
part-of, has-location has-branch, bounds,
connects has-developmental-form
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Some Foundational Relations between Biological
Continuants
y
Classes
Individuals
Rel(x,y)
x
Is-A, Part-Of, Has-Location Bounds, Has-Branch,
Connects Has-Developmental-Form
Classes
Instance-of
part-of, has-location has-branch, bounds,
connects has-developmental-form
Individuals
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Class-Level Relations (I)

• Cell has-part Axon (Gene Ontology)
• Do cells without axons exist ?
• Do axons withoutcells exist ?

• Neuron has-part Axon (FMA)
• Does every neuron has an axon?

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Class-Level Relations (II)
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

• Cell has-part Axon (Gene Ontology)
• Do cells without axons exist ?
• Do axons withoutcells exist ?

• Neuron has-part Axon (FMA)
• Does every neuron has an axon?

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)
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Semantic framework for biological structure

• Foundational Relations
• General Attributes
• Theories

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General Attributes (top level categories)

• Point 1-D 2-D 3-D

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Semantic framework for biological structure

• Foundational Relations
• General Attributes
• Theories

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Heart
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Theories

• A set of formal axioms which describe a
  restricted (local) domain.
• Four orthogonal theories for Biological Structure

• Granularity
• Species
• Development
• Canonicity

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Theories

• A set of formal axioms which describe a
  restricted (local) domain.
• Four orthogonal theories for Biological Structure

• Granularity
• Species
• Development
• Canonicity

epistemiological
ontological
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Theories

• A set of formal axioms which describe a
  restricted (local) domain.
• Four orthogonal theories for Biological Structure

• Granularity
• Species
• Development
• Canonicity

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Granularity

• Classification(level of detail of class
  distinction)

Cell
Cell
Blood Cell
Blood Cell
WBC
Lymphocyte
T-Lymphocyte
T4-Lymphocyte
(taxonomy)
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Granularity

• Classification(level of detail of class
  distinction)
• Dissection(focus on organism, tissue, cell,
  molecule)

Cell
Cell
Cell Nucleus
Cell Nucleus
Chromosome
DNA
Nucleotide
-NH2
(partonomy)
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Granularity of Dissection

• Change 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

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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
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Granularity of Relations

• included-by(CellNucleus, Cell)
• part-of(CellNucleus, Cell)
• included-by(VirusProtein, Cell)part-of(VirusProte
  in, Cell) ??

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Theories

• A set of formal axioms which describe a
  restricted (local) domain.
• Four orthogonal theories for Biological Structure

• Granularity
• Species
• Development
• Canonicity

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Linnean Taxonomy of Species
http//tolweb.org
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Linnean Taxonomy of Species
http//tolweb.org
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Linnean Taxonomy of Species
http//tolweb.org
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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

• Granularity
• Species
• Development
• Canonicity

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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

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Theories

• A set of formal axioms which describe a
  restricted (local) domain.
• Four orthogonal theories for Biological Structure

• Granularity
• Species
• Development
• 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 Variations
• Pathological Structure

acquired
congenital
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Canonicity

• Degrees of Wellformedness of Biological
  Structure
• Canonic structure
• Structural Variations
• Pathological Structure
• Lethal Structure

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Canonicity

• Degrees of Wellformedness of Biological
  Structure
• Canonic structure
• Structural Variations
• Pathological Structure
• Lethal Structure
• Derivates of biologicalstructure

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Canonicity

• Five canonicity levels each level introduces
  axioms valid for higher levels

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Examples
low
high
Granularity
general
specific
Species
embryo
adult
Development
low
high
Canonicity
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CoverageFoundational Model of Anatomy
low
high
Granularity
general
specific
Species
embryo
adult
Development
low
high
Canonicity
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CoverageGene Ontology
low
high
Granularity
general
specific
Species
embryo
adult
Development
low
high
Canonicity
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CoverageMouse Anatomy
low
high
Granularity
general
specific
Species
embryo
adult
Development
low
high
Canonicity
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Examples

• Connects (RightVentricle, Left Ventricle)

Granularity normal Species
mammal Development adult Canonicity 4-5
false
Granularity any Species vertebrate Developmen
t early embryo Canonicity any
true
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Conclusion

• Integration of bio-ontologies requires
• Uncontroversial semantics of relations and
  attributes
• Clear 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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Ontological Foundations of Biological Continuants
International Conference on Formal Ontology in
Information Systems

• Stefan Schulz, Udo Hahn

Text Knowledge Engineering LabUniversity of Jena
(Germany)
Department of Medical InformaticsUniversity
Hospital Freiburg (Germany)