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Understanding Phenotypes in Phenoscape: Ontological Relationships Explored

Explore the complex relationships between phenotypes, entities, and qualities in the context of Siluriformes. Investigate how absence or lack of processes in basihyal bones can impact taxon characteristics. Contribution to inferencing presented. Understand the implications for new representations in the field.

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Understanding Phenotypes in Phenoscape: Ontological Relationships Explored

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  1. Phenotypes in Phenoscape

  2. The current scenario taxon exhibits inheres_in(quality, entity)‏ Inheres in Is a entity quality

  3. An example In Siluriformes, the shape of the dorsal surface of the basihyal bone is flat or convex - ”Albert, 2001” Siluriiformes exhibits inheres_in(flat, bas. bone)‏ Is a Inheres in flat basihyal bone

  4. The problem ”process of posterior margin of basihyal bone absent in Luxilus cornutus” - Coburn and Cavender, 1992 L. cornutus exhibits inheres_in(absent, proc. of basi. bone)‏ Is a Inheres in absent process of basihyal bone Absence inheres in something??

  5. A solution ”process of posterior margin of basihyal bone absent in Luxilus cornutus” - Coburn and Cavender, 1992 L. cornutus exhibits lacks_part(proc. of basi. bone)‏ Is a Lacks part absent process of basihyal bone

  6. Implications to inferencing At present Luxilus exhibits Inheres in part of basihyal bone Is a L. cornutus exhibits inheres_in(absent, proc. of basi. bone)‏ Part of Is a absent Inheres in Inheres in process of basihyal bone process Is a

  7. Inferences in the new representation Luxilus exhibits ?? basihyal bone Is a L. cornutus exhibits lacks_part(proc. of basi. bone)‏ Part of Is a Lacks part absent ?? process of basihyal bone process Is a

  8. Filling in the ontological blanks exhibits exhibits PHENOSCAPE:exhibits Is a OBO_REL:is_a OBO_REL:part_of Part of Inheres in OBO_REL:inheres_in Lacks part OBO_REL:lacks_part Inheres in part of OBO_REL:inheres_in_part_of ?? ???? ???? ??

  9. Use cases in the new scenario • ”Absence of process of basihyal bone in L. Cornutus” must be found when searching for • Process • Bashiyal bone • Luxilus cornutus* * trivial

  10. Semantically speaking... • If a fish is missing a process of a basihyal bone • Is it missing the basihyal bone? • This is the role composition represented by the dashed violet arrow • Does it exhibit any process of any kind? • This is the role composition represented by the dashed gray arrow • The answers can never be yes at all times, nor can they be no

  11. What do we call the new relations then? ?? • Lacks_part(Phenotype, Entity1) ^ part_of(Entity1, Entity2) => ??(Phenotype, Entity2)‏ • Lacks_part(Phenotype, Entity1) ^ is_a(Entity1, Entity2) => ??(Phenotype, Entity2)‏ ??

  12. To be continued • Send your thoughts to cartik.kothari@duke.edu • Implementation details will be taken up later • Thanks for your attention!

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