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Connected_to and attached_to

Connected_to and attached_to. Shared boundary between objects Bona fide vs. fiat - when does it matter?. Connected_to: fiat boundary. Example: axon tract connected_to neuropil.

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Connected_to and attached_to

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  1. Connected_to and attached_to • Shared boundary between objects • Bona fide vs. fiat - when does it matter?

  2. Connected_to: fiat boundary Example: axon tract connected_to neuropil • FMA definition:Structural anatomical relation which holds between each anatomical structure of type A and some anatomical structure of type B such that each structure shares some part of its bona fide anatomical surface with that of the other. • Barry’s definition (from obo-discuss): x is connected_to y if x and y share a fiat boundary.

  3. Attached_to: bona fide boundary • Examples: • Muscle attached_to bone • Tooth attached_to bone • FMA definition: Connected_to relation which holds between each anatomical entity of type A and some anatomical entity of type B such that there is no bona fide boundary between their contiguous constitutional parts. Sire et al. 1998 Sire et al. 1998

  4. Attached_to: bona fide boundary • Bone + bone attachment • can also be called joint

  5. Bona fide boundary example • Tooth attached_to bone Sire et al. 1998 Sire 2001

  6. Spatial ontology • Overview: top level divisions • Examples of uses • Spatial relations

  7. Spatial ontology: top level divisions • anatomical axis • anatomical axis direction • anatomical compartment • anatomical compartment boundary • anatomical gradient • anatomical region • anatomical section • anatomical surface

  8. Phenoscape need for spatial terms • Occurrences of quality (PATO) terms in 1,040 character descriptions • Sample character: Posterior margin of lateral ethmoid: (0) straight, parallel to anterior edge of orbitosphenoid & abruptly angled at midline; (1) broadly curved in ventral view, forming convex arc.

  9. Phenoscape need for spatial terms • Occurrences of quality (PATO) terms in 1,040 character descriptions

  10. Examples • Spatial terms as anatomical qualifiers: • “anterior margin of supraorbital bone” • BSPO:anterior margin part_of TAO:supraorbital bone • Spatial terms as modifiers for quality terms: • “frontal bone laterally compressed” • E: frontal; • PATO:compressed has_axis BSPO:left/right axis

  11. Spatial relations • anterior_to • distal_to • dorsal_to • posterior_to • proximal_to • surrounding • ventral_to • vicinity_of Spatial relations and PATO spatial relational qualities

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