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Representing Phenotypes in OWL
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Representing Phenotypes in OWL

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Short presentation on design patterns for representing phenotypes using PATO and OBO Foundry ontologies in OWL. Includes issues with temporal modeling in OWL

Short presentation on design patterns for representing phenotypes using PATO and OBO Foundry ontologies in OWL. Includes issues with temporal modeling in OWL

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  • 1. Representing phenotypes in OWL Chris Mungall Lawrence Berkeley Laboratory NCBO GO
  • 2. red eye curly wing high blood pressure Invaginated placode thorax lacks wings ectopic leg Delayed chemotaxis
  • 3. 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
  • 4. Enumeration Class: CurvatureValue EquivalentClass: {flat curved} Individual: flat TYPE CurvatureValue DifferentFrom: curved Individual: fly-wing-00001 TYPE (Wing THAT hasCurvature VALUE curved) Individual: curved TYPE CurvatureValue DifferentFrom: flat FunctionalProperty: hasCurvature Range: CurvatureValue Alan Rector Representing 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
  • 5. Value partitions Class: CurvatureValue EquivalentClass: Flat OR Curved Disjoint: Flat Curved FunctionalProperty: hasCurvature Range: CurvatureValue Class: CurvedWing EquivalentClass: Wing THAT hasCurvature SOME Curved Individual: fly-wing-00001 TYPE CurvedWing Alan Rector Representing 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
  • 6. Value partitions Class: CurvedWing EquivalentClass: Wing THAT hasCurvature SOME Curved Individual: fly-wing-00001 TYPE CurvedWing ValuePartition: Curvature hasCurvature [Flat Curved] Alan Rector Representing 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
  • 7. PATO: An ontology of biological qualities
    • 949 textually defined classes
    • Limitations
      • Lacks disjointness and closure axioms
      • Lacks GCIs
    FunctionalProperty: inheresIn Domain: Quality
  • 8. 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
  • 9. 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
  • 10. 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
  • 11. 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 support not fully satisfactory Intermediate representation / information model 