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Anatomy redesign statistics
Total rows in S-E-P table: 18,500 Total concepts in OWL : 37,003 (side,left,right) The “S” and “E” are there. The “P” are systematically excluded. SubClassOf axioms: 17,315 EquivalentClasses: 22,008 GCI (general concept inclusions) count: 1,227 Hidden GCI (general class axioms) count: 266 Sufficient definitions (EquivalentClass axioms) All “(S)” concepts = 18,500 Many “E” concepts: 22,008 – 18,500 = 3,508
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Top Level of Redesigned Anatomy (alpha)
(S) ‘structure of’ top level Stated, E ‘entire’ top level
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Anatomy logic definition patterns
Templates for defining concepts in groups Designed to depend on: Sufficient definitions to allow subsumption of subtypes General concept inclusions to entail subsumption under supertypes Role chaining to enable inferences across different object properties General class axioms for anonymous concepts where needed (e.g. laterality)
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Joint of <region> Joint of <region>
≡ joint part of <region> Demonstrates routine use of the general PartOf object property to create an EquivalentClass axiom E.g. ‘joint of upper limb’ = joint and PartOf some ‘upper limb’
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Hierarchy of object properties
allOrPartOf PartOf cPartOf aka constitutional rPartOf aka regional sPartOf aka systemic lateralHalfOf
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allOrPartOf A reflexive and transitive property
Used to define “(S)” concepts Means “the entire thing, or any part of it” An OWL EL workaround for what would be: X or (PartOf some X) Reflexive means each thing is allOrPartOf itself. Transitive means that X allOrPartOf Y, and Y allOrPartOf Z, implies X allOrPartOf Z.
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PartOf PartOf has the usual ‘proper part of’ meaning It is transitive
It subsumes cPartOf, rPartOf, sPartOf, and lateralHalfOf
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cPartOf cPartOf: C originally stood for ‘constitutional’ but might not fit completely with FMA ‘constitutional part of’ If “X” is non-countable stuff (skin, tissue, lumen), X cPartOf Y means all of the X that is in Y. A non-transitive object property, i.e. x cPartOf y, and y cPartOf z, does not automatically mean x cPartOf z.
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rPartOf rPartOf: r stands for ‘regional’ and is compatible with FMA ‘regional part of’ A transitive object property
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sPartOf sPartOf: s stands for ‘systemic’ and is mostly compatible with FMA ‘systematic part of’ A non-transitive object property Used to represent structures whose parts are related to each other by a system (e.g. musculoskeletal system), but not necessarily by direct contact or connection
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Use case: sites of fractures
A fracture is located in the (bone tissue of) a bone The set of possible sites for bone fractures Is exactly all the sub-regions of the bone tissue of all bones
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bone tissue of <bone organ>
≡ bone tissue constitutional part of <bone organ> cPartOf implies that this concept means “all of the bone tissue of this bone organ”.
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bone tissue of <region> bone tissue of <region>
≡ bone tissue part of <region> The grouper aggregates specific bits of bone tissue, so cPartOf is not necessary for the grouper concept, as long as the portions of bone to be subsumed use cPartOf BoneOrgan, and BoneOrgan is cPartOf region. Using partOf allows the transitive property to derive that the bone tissue concepts are properly subsumed.
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bone (organ, region, tissue) of <body region>
≡ bone (organ, region, tissue) part of <body region> Can’t be sure it is constitutional, since it may be a region of a constitutional part. So the most specific role is simply “Part Of”
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bone tissue of <zone of bone organ>
≡ bone tissue constitutional part of <zone of bone organ> ⊑ bone tissue regional part of bone tissue constitutional part of <bone organ> Employs a second clause that is SubClassOf, i.e. “also necessarily true” Note that the second clause is primitive, not sufficient, because the first clause references a primitive zone of bone organ. For example, the distal epiphysis is a zone of bone organ, but not all regional parts are distal epiphyses.
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Surface, skin, integument
Regions of the surface of the body, covered with integument Layers are: Surface Integument Skin Epidermis Dermis Subcutaneous tissue (superficial fascia)
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Skin of <region>
≡ region of skin constitutional part of <region> ≡ region of skin constitutional part of zone of integument constitutional part of <region> Illustrates how to infer that a layer is part of another layer of which it is a laminar part. In this case, a region of skin is a layer of a corresponding zone of integument.
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Skin of <region><side>
≡ region of skin constitutional part of <region> ≡ region of skin constitutional part of zone of integument constitutional part of <region> laterality <side>
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Inferring part-of musculoskeletal system of <x>
If we define “(S) musculoskeletal system of hand” allOrPartOf some ‘musculoskeletal system of hand’, And we define ‘musculoskeletal system of hand’ as ‘musculoskeletal system subdivision’ and PartOf some hand How will the system infer that the ligament of the distal interphalangeal joint of the left index finger is sPartOf the musculoskeletal system of the hand?
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‘part of musculoskeletal system of <region>’
Anonymous class, using general class axiom. Asserted for each region for which there is a musculoskeletal subdivision. Any musculoskeletal entity (which Inherits sPartOf = musculoskeletal system) that is part of some body region, (clause 1) will be inferred to be a systemic part of the ms subdivision of that region (clause 2) ≡ part of <region> systemic part of musculoskeletal system ≡ systemic part of musculoskeletal system subdivision constitutional part of <region>
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Laterality Assume that “laterality” is defined with respect to the mid-sagittal plane of the body. The left hand, and left side of the nose, are defined by (laterality some left) The left heart is not defined by (laterality some left). Role chain: PartOf ◦ laterality -> laterality (X PartOf Y), and (Y laterality R/L) implies (X laterality R/L) Any part of a structure lateral to the midline is also lateral to the midline
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Skin of <region>, <side>
skin of <side><region> <side> should be either “left” or “right”. <side of region> is an already lateralized structure, e.g. “left hand” or “left hemithorax” ≡ region of skin constitutional part of <sided region> e.g. “left hand” ≡ region of skin constitutional part of zone of integument e.g. “hand” constitutional part of <region> laterality L/R
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What about parts of midline entities?
Skin of nose: not lateral Skin of nostril: lateral Skin of lip: not lateral Skin of corner of lip: lateral Many others: occiput, sphenoid, vertebra, perineum, abdomen, thorax, back, neck, head
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‘lateral half of <midline entity>’
≡ lateral half of <midline entity> laterality <side> ‘lateralHalfOf’ is a special partof relationship. It distinguishes lateral half parts from regional parts. A lateral half is not a regional part. E.g. lateral half of nose = (‘lateral half of’ some nose) and (laterality some side)
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‘part of <L/R> lateral half of <midline entity>’
Anonymous classs, using general class axioms. ≡ part of <midline entity> laterality <side> ≡ all or part of lateral half of <midline entity> E.g. (part of ‘lower lip’) and (laterality side) = (allorpartof (lateralHalfOf ‘lower lip’). ≡ part of <lateral half of midline entity> laterality <L/R> ≡ part of <L/R> half of <midline entity> E.g. (part of ‘lateral half of trunk’) and (laterality left) = (part of ‘left half of trunk’).
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Surface of <region>
≡ subdivision of surface of body constitutional part of <region> ≡ subdivision of surface of body constitutional part of zone of integument constitutional part of <region>
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Subcutaneous tissue of <region>
≡ zone of superficial fascia constitutional part of <region> ≡ zone of superficial fascia constitutional part of zone of integument constitutional part of <region>
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Skin of part of <region>
≡ region of skin regional part of region of skin constitutional part of <region> ≡ region of skin constitutional part of regional part of <region> To ensure that “(S) skin of hand” subsumes the skin of regional parts of the hand
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<portion of tissue> of region of <entity>
≡ portion of <tissue> constitutional part of regional part of <entity> ≡ portion of <tissue> regional part of portion of <tissue> constitutional part of <entity>
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part of bone tissue of <bone, or complex of bones/bone parts>
≡ bone tissue constitutional part of regional part of <bone or complex> ≡ bone tissue regional part of bone tissue constitutional part of <bone or complex> e.g. part of bone tissue of skull, should subsume bone tissue of anterior fossa..
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part of space of <compartment or organ>
≡ space constitutional part of regional part of <compartment or organ> ≡ space regional part of space constitutional part of <compartment or organ> e.g. part of gastrointestinal lumen, should subsume gastric lumen..
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