A Preliminary Draft Ontology of Amphibian Morphology AmphibiaTree 2006 Workshop Sunday 1–1:15 A. Pugener

Building the Amphibian Ontology Top-down ApproachTop-down Approach –Based on anatomical systems –Modeled after the ZFIN Zebrafish Anatomical Dictionary Bottom-up ApproachBottom-up Approach –Instantiation by manually mining literature sources

Taxonomic Group  Amphibia  Lissamphibia  Lissamphibia  Order Anura  Order Anura  Pipidae  Pipidae  Xenopus laevis  Xenopus laevis  Order Caudata  Order Caudata  Salamandridae  Salamandridae  Salamandra salamandra  Salamandra salamandra  Order Gymnophiona  Order Gymnophiona  Caeciliidae  Caeciliidae  Dermophis mexicanus  Dermophis mexicanus

Elements of the Amphibian Ontology ClassClass –Definition: collection of distinct things considered as a whole; they may contain other classes, individuals, or a combination of both –Classes are abstract groups that exist in their respective instances

Elements of the Amphibian Ontology Instance / IndividualInstance / Individual –Definition: “ground-level” components of an ontology

Elements of the Amphibian Ontology AttributeAttribute –Definition: property, feature, characteristic, or parameter that describes an instance

Elements of the Amphibian Ontology AttributeAttribute –Definition: property, feature, characteristic, or parameter that describes an instance

Elements of the Amphibian Ontology RelationRelation –Definition: an attribute whose value is another instance in the ontology –Kinds of Relations: ObjectObject DatatypeDatatype AnnotationAnnotation

Elements of the Amphibian Ontology –Definition: binary relationship between two instances –Must have domain and range –Kinds of Object Relations: FunctionalFunctional Inverse_FunctionalInverse_Functional SymmetricSymmetric TransitiveTransitive Object RelationObject Relation

Elements of the Amphibian Ontology FunctionalFunctional –Definition: relation that is limited to having a single value

Elements of the Amphibian Ontology Example of a Functional Relation:Example of a Functional Relation: Optic_foramen is_bound_in Bone

Elements of the Amphibian Ontology Inverse_FunctionalInverse_Functional –Definition: relation that has an inverse

Elements of the Amphibian Ontology Example of an Inverse_Functional Relation:Example of an Inverse_Functional Relation:IF Inferior_perilymphatic_foramen is_lateral_to Jugular_foramen THEN Jugular_foramen is_medial_to Inferior_perilymphatic_foramen

Elements of the Amphibian Ontology Symmetric RelationSymmetric Relation –Definition: relation that is its own inverse

Elements of the Amphibian Ontology Example of a Symmetric PropertyExample of a Symmetric PropertyIF Zygomatic_ramus_of_squamosal articulates_with Dorsal_process_ of_ posterior_maxillary_process THEN Dorsal_process_of_posterior_maxillary_process articulates_with Zygomatic_ramus_of_squamosal

Elements of the Amphibian Ontology Transitive RelationTransitive Relation –Definition: relation that if the link holds between a 1 st element and a 2 nd and between the 2 nd element and a 3 rd, it holds between the 1 st and 3 rd elements

Elements of the Amphibian Ontology Example of a Transitive RelationExample of a Transitive RelationIF Stylus_of_stapes is_part_of Pars_media_plectri AND Pars_media_plectri is_part_of Plectral_Apparatus THEN Stylus_of_stapes is_part_of Plectral_Apparatus

Elements of the Amphibian Ontology Attributes –Are used to describe and define classes by creating restrictions that constrain the instances of a particular that class Quantifier Restriction: describes the existence of relations to instances of a particular classQuantifier Restriction: describes the existence of relations to instances of a particular class –for some values of / some –for all values of / only Cardinality Restriction: describes the set of instances that have a specified number of relations with other instances or datatype valuesCardinality Restriction: describes the set of instances that have a specified number of relations with other instances or datatype values –at least –at most –exactly has_Value Restriction: describes the set of instances that have at least one relations to a specific instancehas_Value Restriction: describes the set of instances that have at least one relations to a specific instance

Elements of the Amphibian Ontology Quantifier Restriction –Existential Restriction (  ) Definition: specifies the existence of a relation to an instance that is a member of a specified class Example: Frontoparietal is_in some Adult Frontoparietal is_in some Adult 

Elements of the Amphibian Ontology Quantifier Restriction –Universal Restriction (  ) Definition: specifies that the only relation that can exist must be to an instance that is a member of a specified class Example: Frontoparietal is_partially_homologous_with only (Frontal or Parietal) 

The Amphibian Ontology

Partonomy

Problematic Representations of Part_of part_of means can_be_part_of, not is_always_a_part_ofpart_of means can_be_part_of, not is_always_a_part_of Example: vomerine dentition is_a_part_of vomer part_of / has_part; but if part_of means located_in, thenpart_of / has_part; but if part_of means located_in, then part_of not inverse of has_part Example: occipital condyle is_part_of exoccipital exoccipital has_part occipital condyle exoccipital has_part occipital condyle jugular foramen is_part_of otic capsule jugular foramen is_part_of otic capsule jugular foramen is_located_in otic capsule jugular foramen is_located_in otic capsule otic capsule not has_part jugular foramen otic capsule not has_part jugular foramen

The Alternative Is_a Represents relations between types that are universally true (i.e., for all instances)Represents relations between types that are universally true (i.e., for all instances) Example: jugular foramen is_a cranial conduit tooth is_a organ with organ cavity tooth is_a organ with organ cavity Common Anatomy Reference Ontology (CARO)Common Anatomy Reference Ontology (CARO) –Based on the Foundational Model of Anatomy –Top-level, structural is_a –Objectives To facilitate queries within and between ontologiesTo facilitate queries within and between ontologies To integrate anatomical termsTo integrate anatomical terms

CARO Amphibian Ontology