1 / 32

A Preliminary Draft Ontology of Amphibian Morphology

A Preliminary Draft Ontology of Amphibian Morphology. AmphibiaTree 2006 Workshop Sunday 1 –1:15 A. Pugener. Building the Amphibian Ontology. Top-down Approach Based on anatomical systems Modeled after the ZFIN Zebrafish Anatomical Dictionary Bottom-up Approach

aquene
Download Presentation

A Preliminary Draft Ontology of Amphibian Morphology

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

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

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

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

  4. Elements of the Amphibian Ontology • Class • 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

  5. Elements of the Amphibian Ontology • Instance / Individual • Definition: “ground-level” components of an ontology

  6. Elements of the Amphibian Ontology • Attribute • Definition: property, feature, characteristic, or parameter that describes an instance

  7. Elements of the Amphibian Ontology • Attribute • Definition: property, feature, characteristic, or parameter that describes an instance

  8. Elements of the Amphibian Ontology • Relation • Definition: an attribute whose value is another instance in the ontology • KindsofRelations: • Object • Datatype • Annotation

  9. Elements of the Amphibian Ontology • Object Relation • Definition: binary relationship between two instances • Must have domain and range • KindsofObjectRelations: • Functional • Inverse_Functional • Symmetric • Transitive

  10. Elements of the Amphibian Ontology • Functional • Definition: relation that is limited to having a single value

  11. Elements of the Amphibian Ontology • ExampleofaFunctionalRelation: Optic_foramenis_bound_inBone

  12. Elements of the Amphibian Ontology • Inverse_Functional • Definition: relation that has an inverse

  13. Elements of the Amphibian Ontology • Example ofanInverse_FunctionalRelation: IF Inferior_perilymphatic_foramenis_lateral_toJugular_foramen THEN Jugular_foramenis_medial_toInferior_perilymphatic_foramen

  14. Elements of the Amphibian Ontology • Symmetric Relation • Definition: relation that is its own inverse

  15. Elements of the Amphibian Ontology • ExampleofaSymmetricProperty IF Zygomatic_ramus_of_squamosalarticulates_withDorsal_process_ of_ posterior_maxillary_process THEN Dorsal_process_of_posterior_maxillary_processarticulates_with Zygomatic_ramus_of_squamosal

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

  17. Elements of the Amphibian Ontology • ExampleofaTransitiveRelation IF Stylus_of_stapesis_part_ofPars_media_plectri AND Pars_media_plectriis_part_of Plectral_Apparatus THEN Stylus_of_stapesis_part_of Plectral_Apparatus

  18. 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 • QuantifierRestriction: describes the existence of relations to instances of a particular class • for some values of / some • for all values of / only • CardinalityRestriction: describes the set of instances that have a specified number of relations with other instances or datatype values • at least • at most • exactly • has_ValueRestriction: describes the set of instances that have at least one relations to a specific instance

  19. Elements of the Amphibian Ontology • QuantifierRestriction • Existential Restriction () Definition: specifies the existence of a relation to an instance that is a member of a specified class Example: Frontoparietal is_insome Adult 

  20. Elements of the Amphibian Ontology • QuantifierRestriction • 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_withonly (FrontalorParietal) 

  21. The Amphibian Ontology

  22. The Amphibian Ontology

  23. The Amphibian Ontology

  24. The Amphibian Ontology Partonomy

  25. Problematic Representations of Part_of • part_of means can_be_part_of, notis_always_a_part_of • Example: vomerine dentition is_a_part_of vomer • part_of / has_part; but if part_of means located_in, then • part_ofnot inverse ofhas_part • Example: occipital condyle is_part_of exoccipital • exoccipital has_part occipital condyle • jugular foramen is_part_of otic capsule • jugular foramen is_located_in otic capsule • otic capsule nothas_part jugular foramen

  26. The Alternative Is_a • 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 • Common Anatomy Reference Ontology (CARO) • Based on the Foundational Model of Anatomy • Top-level, structural is_a • Objectives • To facilitate queries within and between ontologies • To integrate anatomical terms

  27. CARO Amphibian Ontology

  28. CARO Amphibian Ontology

  29. CARO Amphibian Ontology

  30. CARO Amphibian Ontology

  31. CARO Amphibian Ontology

  32. CARO Amphibian Ontology

More Related