a preliminary draft ontology of amphibian morphology amphibiatree 2006 workshop sunday 1–1:15 a....

A Preliminary A Preliminary Draft Ontology Draft Ontology

of Amphibian Morphologyof Amphibian Morphology

AmphibiaTreeAmphibiaTree 2006 Workshop 2006 WorkshopSunday 1Sunday 1–1:15–1:15

A. PugenerA. Pugener

Building the Amphibian OntologyBuilding the Amphibian Ontology

• Top-down ApproachTop-down Approach– Based on anatomical systemsBased on anatomical systems– Modeled after the Modeled after the ZFIN Zebrafish Anatomical DictionaryZFIN Zebrafish Anatomical Dictionary

• Bottom-up ApproachBottom-up Approach– Instantiation by manually mining literature sourcesInstantiation by manually mining literature sources

Taxonomic GroupTaxonomic Group

AmphibiaAmphibia

LissamphibiaLissamphibia

Order AnuraOrder Anura

PipidaePipidae

Xenopus laevisXenopus laevis

Order CaudataOrder Caudata

SalamandridaeSalamandridae

Salamandra salamandraSalamandra salamandra

Order GymnophionaOrder Gymnophiona

CaeciliidaeCaeciliidae

Dermophis mexicanusDermophis mexicanus

Elements of the Amphibian OntologyElements of the Amphibian Ontology

• ClassClass

– DefinitionDefinition: collection of distinct things : collection of distinct things considered as a whole; they may considered as a whole; they may contain other classes, individuals, or contain other classes, individuals, or a combination of botha combination of both

– Classes are abstract groups that exist Classes are abstract groups that exist in their respective instancesin their respective instances


• Instance / Individual Instance / Individual

– DefinitionDefinition: “ground-level” components of : “ground-level” components of an ontologyan ontology


• AttributeAttribute

– DefinitionDefinition: property, feature, : property, feature, characteristic, or parameter that characteristic, or parameter that describes an instancedescribes an instance


• RelationRelation

– DefinitionDefinition: an attribute whose value is : an attribute whose value is another instance in the ontologyanother instance in the ontology

– KindsKinds ofof RelationsRelations::• ObjectObject

• DatatypeDatatype

• AnnotationAnnotation


– DefinitionDefinition: binary relationship between : binary relationship between two instancestwo instances

– Must have Must have domaindomain and and rangerange

– KindsKinds ofof ObjectObject RelationsRelations::• FunctionalFunctional

• Inverse_FunctionalInverse_Functional

• SymmetricSymmetric

• TransitiveTransitive

• Object RelationObject Relation


• FunctionalFunctional

– DefinitionDefinition: relation that is limited to having a single value: relation that is limited to having a single value


• ExampleExample ofof aa FunctionalFunctional RelationRelation::

Optic_foramenOptic_foramen is_bound_inis_bound_in BoneBone


• Inverse_FunctionalInverse_Functional

– DefinitionDefinition: relation that has an inverse: relation that has an inverse


• ExampleExample o off anan Inverse_FunctionalInverse_Functional RelationRelation::

IFIF

Inferior_perilymphatic_foramenInferior_perilymphatic_foramen is_lateral_tois_lateral_to Jugular_foramenJugular_foramen

THENTHEN

Jugular_foramenJugular_foramen is_medial_tois_medial_to Inferior_perilymphatic_forInferior_perilymphatic_foraamenmen


• Symmetric RelationSymmetric Relation

– DefinitionDefinition: relation that is its own inverse: relation that is its own inverse


• ExampleExample ofof aa SymmetricSymmetric PropertyProperty

IFIF

Zygomatic_ramus_of_squamosalZygomatic_ramus_of_squamosal articulates_witharticulates_with Dorsal_process_Dorsal_process_

of_ posterior_maxillary_processof_ posterior_maxillary_process

THENTHEN

Dorsal_process_of_posterior_maxillary_processDorsal_process_of_posterior_maxillary_process articulates_witharticulates_with

Zygomatic_ramus_of_squamosalZygomatic_ramus_of_squamosal


• Transitive RelationTransitive Relation

– DefinitionDefinition: relation that if the link holds between a 1: relation that if the link holds between a 1stst element and a 2 element and a 2ndnd and and between the 2between the 2ndnd element and a 3 element and a 3rdrd, it holds between the 1, it holds between the 1stst and 3 and 3rdrd elements elements


• ExampleExample ofof aa TransitiveTransitive RelationRelation

IFIF

Stylus_of_stapesStylus_of_stapes is_part_ofis_part_of Pars_media_plectriPars_media_plectri

ANDAND

Pars_media_plectriPars_media_plectri is_part_of is_part_of Plectral_ApparatusPlectral_Apparatus

THENTHEN

Stylus_of_stapesStylus_of_stapes is_part_of is_part_of Plectral_ApparatusPlectral_Apparatus


• Attributes

– Are used to describe and define classes by creating Are used to describe and define classes by creating restrictionsrestrictions that constrain the that constrain the instances of a particular that classinstances of a particular that class

• QuantifierQuantifier RestrictionRestriction: describes the existence of relations to instances of a particular : describes the existence of relations to instances of a particular classclass

– for some values of / somefor some values of / some– for all values of / onlyfor all values of / only

• CardinalityCardinality RestrictionRestriction: describes the set of instances that have a specified number of : describes the set of instances that have a specified number of relations with other instances or datatype values relations with other instances or datatype values

– at leastat least– at mostat most– exactlyexactly

• has_Valuehas_Value RestrictionRestriction: describes the set of instances that have at least one relations to : describes the set of instances that have at least one relations to a specific instancea specific instance


• Quantifier Restriction

– Existential Restriction (Existential Restriction ())

DefinitionDefinition: specifies the existence of a relation to an instance that is a member of : specifies the existence of a relation to an instance that is a member of a specified classa specified class

ExampleExample::

Frontoparietal Frontoparietal is_inis_in some some AdultAdult


• Quantifier Restriction

– Universal Restriction (Universal Restriction ())

DefinitionDefinition: specifies that the : specifies that the onlyonly relation that can exist must be to an instance that is a relation that can exist must be to an instance that is a member of a specified classmember of a specified class

ExampleExample::

Frontoparietal Frontoparietal is_partially_homologous_withis_partially_homologous_with only only (Frontal(Frontal oror Parietal) Parietal)

The Amphibian OntologyThe Amphibian Ontology

The Amphibian OntologyThe Amphibian OntologyPartonomyPartonomy

Problematic Representations of Part_ofProblematic Representations of Part_of

• part_ofpart_of means means can_be_part_ofcan_be_part_of, , notnot is_always_a_part_ofis_always_a_part_of

ExampleExample: vomerine dentition : vomerine dentition is_a_part_ofis_a_part_of vomer vomer

• part_ofpart_of / / has_parthas_part; but if ; but if part_ofpart_of means means located_inlocated_in, then , then part_ofpart_of not inverse ofnot inverse of has_parthas_part

ExampleExample: occipital condyle : occipital condyle is_part_ofis_part_of exoccipital exoccipital exoccipital exoccipital has_parthas_part occipital condyle occipital condyle

jugular foramen jugular foramen is_part_ofis_part_of otic capsule otic capsule jugular foramen jugular foramen is_located_inis_located_in otic capsule otic capsule otic capsule otic capsule notnot has_part has_part jugular foramen jugular foramen

The Alternative Is_aThe Alternative Is_a

• Represents relations between types that are universally Represents relations between types that are universally true (i.e., for all instancestrue (i.e., for all instances))

ExampleExample: jugular foramen : jugular foramen is_ais_a cranial conduit cranial conduit tooth tooth is_ais_a organ with organ cavity organ with organ cavity

• Common Anatomy Reference Ontology (CARO)Common Anatomy Reference Ontology (CARO)– Based on the Foundational Model of AnatomyBased on the Foundational Model of Anatomy– Top-level, structural Top-level, structural is_ais_a– ObjectivesObjectives

• To facilitate queries within and between ontologiesTo facilitate queries within and between ontologies• To integrate anatomical termsTo integrate anatomical terms

CARO Amphibian OntologyCARO Amphibian Ontology

a preliminary draft ontology of amphibian morphology amphibiatree 2006 workshop sunday 1–1:15 a....

Documents

ontology slide

amphibian ontology definition

amphibian ontology inverse

amphibian ontology example

inverse slide

foramen slide

instance slide

squamosal slide