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Phenotypes in Phenoscape

Phenotypes in Phenoscape. The current scenario. taxon. exhibits. inheres_in(quality, entity) ‏. Inheres in. Is a. entity. quality. An example. In Siluriformes , the shape of the dorsal surface of the basihyal bone is flat or convex - ”Albert, 2001”. Siluriiformes. exhibits.

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Phenotypes in Phenoscape

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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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