representing phenotypes in owl
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Representing phenotypes in OWL
Chris Mungall
Lawrence Berkeley LaboratoryNCBO
GO
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curly wing
high blood pressure
Invaginatedplacode
thorax lacks wings
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ectopic leg
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Delayed chemotaxis
Describing phenotypes in OWL
• OBO Foundry http://www.obofoundry.org– OWL translations of all ontologies– Different ontologies for kinds of bearer entities at
different scales and granularities
• Characteristics (qualities)– Inhere in bearer entities– PATO - ontology of qualities
• Composing phenotype descriptions– Pre or post compose– Representing Specified Values in OWL
• value partitions and value sets
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Enumeration
Class: CurvatureValue EquivalentClass: {flat curved}
Individual: flat TYPE CurvatureValueDifferentFrom: curved
Individual: fly-wing-00001 TYPE (Wing THAT hasCurvature VALUE curved)
Individual: curved TYPE CurvatureValueDifferentFrom: flat
FunctionalProperty: hasCurvatureRange: CurvatureValue
Alan RectorRepresenting specified values in OWL: “value partitions” and “value sets”. W3C note, W3C, May 2005. http://www.w3.org/TR/2005/NOTE-swbp-specified-values-20050517
Value partitionsClass: CurvatureValue EquivalentClass: Flat OR Curved
Disjoint: Flat Curved
FunctionalProperty: hasCurvature Range: CurvatureValue
Class: CurvedWing EquivalentClass: Wing THAT hasCurvature SOME Curved
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Individual: fly-wing-00001 TYPE CurvedWing
Alan RectorRepresenting specified values in OWL: “value partitions” and “value sets”. W3C note, W3C, May 2005. http://www.w3.org/TR/2005/NOTE-swbp-specified-values-20050517
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Value partitions
Class: CurvedWing EquivalentClass: Wing THAT hasCurvature SOME Curved
Individual: fly-wing-00001 TYPE CurvedWing
ValuePartition: Curvature hasCurvature [Flat Curved]
Alan RectorRepresenting specified values in OWL: “value partitions” and “value sets”. W3C note, W3C, May 2005. http://www.w3.org/TR/2005/NOTE-swbp-specified-values-20050517
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PATO: An ontology of biological qualities
• 949 textually defined classes
• Limitations– Lacks
disjointness and closure axioms
– Lacks GCIs
FunctionalProperty: inheresIn Domain: Quality
Applications and uses
• Translational medicine: NCBO– Phenote annotation tool
• Genotype-phenotype annotation for disease genes in human and model organisms
– Database• Sesame• OBD-SQL
– Defining classes in pre-coordinated phenotype ontologies
• Evolution: NESCENT– Coding phylogenetic character statements– Relational databases & phylogenetic software
Relational Qualities
• Monadic– Inheres in and
depends on a single individual
• Relational– Inherence takes
additional arguments
– “Adhesivity”– “Sensitivity to
light”
Sensitive that towards some UVLight and inheresIn some Skin
inheresIn(sensitive,skin,UVLight)
N-ary relation
Pseudo-reified
Temporal durations and non-rigid qualities
OpticPlacode that hasQuality some (Flat that during some Stage11) and hasQuality some (Invaginated that during some Stage12)
OpticPlacode that hasTimeSlice some (Slice that hasQuality some Flat and during Stage11) and hasTimeSlice some (Slice that hasQuality some Invaginated and during Stage12)
??????OpticPlace that (hasQuality some Flat at Stage11) and (hasQuality some Invaginated at Stage12)??????
OrganismPart subClassOf (hasQuality exactly 1 Curvature) Slice subClassOf (hasQuality exactly 1 Curvature)
X
Higher level representations
hasQuality some ?Q at ?Int
hasTimeSlice some (Slice that hasQuality some ?Q and during ?Int)
Syntax support: macro expansion
FOL semantics - fluents
(=> (hasQuality ?bearer ?quality ?interval) (and (hasTimeSlice ?bearer ?slice) (during ?slice ?interval) (hasQuality ?slice ?quality)))
not reusable
Tool supportnot fully satisfactory
Intermediate representation / information model
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