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