Transcript Dahdul-ROmeeting

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
•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.
Attached_to: bona fide boundary
• Examples:
– Muscle attached_to bone
– Tooth attached_to bone
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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
Attached_to: bona fide boundary
• Bone + bone attachment
• can also be called joint
Bona fide boundary example
• Tooth attached_to bone
Sire et al. 1998
Sire 2001
Spatial ontology
• Overview: top level divisions
• Examples of uses
• Spatial relations
Spatial ontology: top level
divisions
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anatomical axis
anatomical axis direction
anatomical compartment
anatomical compartment boundary
anatomical gradient
anatomical region
anatomical section
anatomical surface
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.
Phenoscape need for spatial terms
• Occurrences of quality (PATO) terms in 1,040
character descriptions
PATO term
posterior to
present
anterior to
absent
increased length
lateral to
dorsal to
ventral to
increased size
decreased length
shape
decreased height
concave
increased width
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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
Spatial relations
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anterior_to
distal_to
dorsal_to
posterior_to
proximal_to
surrounding
ventral_to
vicinity_of
Spatial relations and PATO
spatial relational qualities