Wikidata:WikiProject Anatomy/Ontology of Anatomy/draft

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Every anatomical item that isn't itself a metaclass should be instance of (P31) a first-order metaclass like cell type (Q189118) which in turn is instance of (P31) anatomical metaclass (Q94945104).

All entities that have a UBERON ID (P1554) are instances of a second-order class (Q24017414) edit

It's easy to model Albert Einstein's brain (Q2464312) instance of (P31) human brain (Q492038). However, deciding whether human brain (Q492038) instance of (P31) brain (Q1073) is wrong or not is harder. We decided against it and rather use subclass of (P279) to describe the relationship. It has the benefit of still being able to say Albert Einstein's brain (Q2464312) as an instance of (P31) human brain (Q492038) which we wouldn't be able if brain (Q1073) instance of (P31) second-order class (Q24017414). Being able to say Albert Einstein's brain (Q2464312) instance of (P31) organ (Q712378) is useful as well. Mapping the is_a used in BFO-derived ontologies like Uberon (Q7876491) as subclass of (P279) allows us to say that individual objects in reality like Albert Einstein's brain (Q2464312) as instances of any class above brain (Q1073) in the tree.

Uberon recently added adult brain (Q104055058) under the tree and we could also say Albert Einstein's brain (Q2464312) instance of (P31) adult brain (Q104055058). By our modeling adding finer classes like this doesn't change the order of any metaclass that we have. For contexts where a metaclass for organs that can be applied to brain (Q1073) is useful we have brain (Q1073) instance of (P31) organ type (Q103812529).

What's does it mean to be an anatomical metaclass? edit

Instance of an anatomical metaclass are supposed to be of the same nature. A key way of how that nature gets defined is via properties for this type (P1963). biceps brachii (Q201363), gracilis muscle (Q1428669) and orbitalis muscle (Q6592857) share a common nature that ocular muscle (Q103845612) doesn't share despite all four being subclass of (P279) muscle (Q7365). We model that shared nature by declaring that the first three are instance of (P31) muscle organ type (Q103813440) and declare

⟨ muscle organ type (Q103813440)  

 ⟩ properties for this type (P1963) ⟨ muscle origin (P3490) ⟩
has characteristic (P1552) ⟨ necessary in reality (Q103820223)  

 ⟩

Besides muscle origin (P3490) we specify other information about the metaclass as well that tell us about it's nature.

List of anatomical metaclasses edit

Metaclasses that have no direct instances edit

Manually update list

This list is periodically updated by a bot. Manual changes to the list will be removed on the next update!

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#	Metaclass	Description	Class	Class Description	Properties for this Type	Subclasses
1	anatomical entity type	metaclass for biological entities that are either member of a species or a unit of its structural organization	anatomical entity	biological entity that is either member of a species or a unit of its structural organization	UBERON ID Foundational Model of Anatomy ID	anatomical entity class type anatomical relation type physical anatomical entity type
2	anatomical structure type	metaclass for entities with a single connected inherent 3D shape that's created by coordinated expression of the organism's own DNA and that are located within the organism	anatomical structure	entity with a single connected inherent 3D shape that's created by coordinated expression of the organism's own DNA	anatomical location connects with part of has part(s) arterial supply venous drainage innervated by 3D model TA2 ID	anatomical system type developmental structure type anatomical junction type chiral anatomical structure type solitary anatomical structure type organ region type organism subdivision type lymph node type tissue type vein type cell type muscle organ type nerve type organ type
3	physical anatomical entity type	metaclass for units of member of a species's structural organization	physical anatomical entity	unit of member of a species's structural organization	found in taxon develops from	list of values as qualifiers
4	chiral anatomical structure type	anatomical structure that exists in a right-sided and left-sided solitary version	anatomical structure	entity with a single connected inherent 3D shape that's created by coordinated expression of the organism's own DNA	follows followed by	chiral bone type
5	solitary anatomical structure type	metaclass for an anatomical structure that exists once per organism (it's possible that certain individuals of the species don't have it)	anatomical structure	entity with a single connected inherent 3D shape that's created by coordinated expression of the organism's own DNA		solitary organ type solitary bone organ type solitary muscle organ type
6	solitary anatomical entity type	metaclass for an anatomical entity that exists once per organism (it's possible that certain individuals of the species don't have it)	anatomical entity	biological entity that is either member of a species or a unit of its structural organization		list of values as qualifiers
7	incidental anatomical entity type	anatomical entity that only appears in a special subset of the species
8	species anatomical structure type	version of an anatomical structure that applies to one species			found in taxon
9	sex-specific anatomical entity type
10	chiral anatomical entity type		anatomical entity	biological entity that is either member of a species or a unit of its structural organization

End of automatically generated list.

Metaclasses that have direct instances edit

Manually update list

This list is periodically updated by a bot. Manual changes to the list will be removed on the next update!

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#	Metaclass	Description	Class	Class Description	Properties for this Type	Model items
1	organ type	metaclass for collections of tissues joined as a structural unit that serves a common function	organ	collection of tissues with similar functions	segmental innervation	heart
2	nerve type	metaclass for enclosed, cable-like bundle of axons in the peripheral nervous system	nerve	enclosed, cable-like bundle of axons in the peripheral nervous system	innervates anatomical branch of has anatomical branch presynaptic connection postsynaptic connection	radial nerve
3	artery type	metaclass for blood vessels that carry blood away from the heart	artery	blood vessel that carries oxygenated blood away from the heart to other organs rather than lungs	anatomical branch of has anatomical branch	femoral artery
4	muscle organ type	metaclass for contractile soft tissue of mammals that has a muscle origin and muscle insertion	muscle	contractile soft tissue of animals	muscle origin muscle insertion muscle action antagonist muscle segmental innervation	deltoid muscle biceps brachii
5	vein type	metaclass for blood vessels that carry deoxygenated blood towards the heart, with the exception of the pulmonary vein	vein	blood vessel that carry deoxygenated blood towards the heart, with the exception of the pulmonary vein	anatomical branch of has anatomical branch	femoral vein
6	tissue type	metaclass for cellular organizational levels intermediate between cells and a complete organism; cells that are grouped together with a common function	tissue	cellular organizational level intermediate between cells and a complete organism; cells that are grouped together with a common function
7	lymph node type	metaclass for organs of the lymphatic system	lymph node	organ of the lymphatic system
8	organism subdivision type		organism subdivision
9	brain region type	metaclass for brain regions	brain region	some delineated part of the brain	anatomical location
10	bone organ type	metaclass for rigid organs that constitute part of the endoskeleton of vertebrates	bone	rigid organ that constitutes part of the endoskeleton of vertebrates		carpal bone proximal carpal bone rib
11	anatomical set type	metaclass for sets of discontinuous members of the same material anatomical entity within one organism	anatomical set	set of discontinuous members of the same material anatomical entity within one organism	has part(s) of the class	musculotendinous cuff
12	biogenic substance type	metaclass for substances produced by some anatomical structures or derived from some inhaled or ingested substances that have been modified by anatomical structures	biogenic substance	substance produced by life processes; it may be either constituents, or secretions, of plants or animals	produced by	urine Wharton's jelly amniotic fluid
13	anatomical relation type	metaclass for associations between two or more anatomical entities	anatomical relation	association between two or more anatomical entities		anatomical laterality
14	anatomical structure class type	class of anatomical structures that don't have direct instances	anatomical structure	entity with a single connected inherent 3D shape that's created by coordinated expression of the organism's own DNA		muscle cell
15	localized structure class type		anatomical structure	entity with a single connected inherent 3D shape that's created by coordinated expression of the organism's own DNA	anatomical location	muscle of anterior compartment of thigh
16	anatomical surface type	metaclass for 2-dimensional anatomical entities that are the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment	anatomical surface	2-dimensional anatomical entity that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment	connects with anatomical location area	iliac fossa
17	general anatomical term type	metaclass for anatomical terms that represents more than one entity	general anatomical term	anatomical term that represents more than one entity		fiber tract column
18	organ region type	metaclass for subdivisions of an organ	organ region	subdivision of an organ
19	chiral bone type		bone	rigid organ that constitutes part of the endoskeleton of vertebrates		first rib
20	solitary bone organ type	metaclass for rigid organs that constitute part of the endoskeleton of vertebrates that exists once per organism (it's possible that certain individuals of the species don't have it)	bone	rigid organ that constitutes part of the endoskeleton of vertebrates		left lunate right first rib sternum
21	solitary organ type		organ	collection of tissues with similar functions		right lung heart brain
22	solitary muscle organ type	metaclass for contractile soft tissue of mammals that has a muscle origin and muscle insertion that exists once per organism (it's possible that certain individuals of the species don't have it)	muscle	contractile soft tissue of animals		right biceps brachii thoracic diaphragm external anal sphincter
23	neural tree organ type		neural tree organ			cranial nervi autonomic nerve
24	anatomical entity class type		anatomical entity	biological entity that is either member of a species or a unit of its structural organization		anatomical structure physical anatomical entity biogenic substance
25	solitary anatomical set type	metaclass for sets of discontinuous members of the same material anatomical entity within one organism that exists once per organism (it's possible that certain individuals of the species don't have it)	anatomical set	set of discontinuous members of the same material anatomical entity within one organism		set of right rotator cuff muscles
26	solitary anatomical surface type	metaclass for 2-dimensional anatomical entities that are a boundary that exists once per organism (it's possible that certain individuals of the species don't have it)	anatomical surface	2-dimensional anatomical entity that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment		left iliac fossa
27	anatomical point type	metaclass for 0-dimensional non-material anatomical entities	anatomical point	0-dimensional non-material anatomical entity	anatomical location	apex of heart posterior inferior iliac spine (point)
28	solitary anatomical point type	metaclass for 0-dimensional non-material anatomical entities that exists once per organism (it's possible that certain individuals of the species don't have it)	anatomical point	0-dimensional non-material anatomical entity		left posterior inferior iliac spine (point)
29	anatomical line type	metaclass for 1-dimensional anatomical entities	anatomical line	1-dimensional anatomical entity	anatomical location length	pectinate line lateral margin of humerus
30	solitary anatomical line type	metaclass for 1-dimensional anatomical entities that exists once per organism (it's possible that certain individuals of the species don't have it)	anatomical line	1-dimensional anatomical entity		right radial border of forearm
31	anatomical junction type	metaclass for anatomical clusters in which parts of two or more anatomical structures establish physical continuity with one another or intermingle their component parts	anatomical junction	anatomical cluster in which parts of two or more anatomical structures establish physical continuity with one another or intermingle their component parts		lambda junction
32	developmental structure type	metaclass for an anatomical structure present before birth	developmental structure	anatomical structure present before birth
33	taxon body type	metaclass for the physical body of a specific taxon	body	physical structure of a living creature		human body brown rat body
34	sex-specific taxon body type	metaclass for the physical body of a specific taxon of a specific sex	body	physical structure of a living creature		female human body male human body female brown rat body
35	anatomical system type	metaclass for groups of organs that work together to perform one or more functions; collection of organs joined in structural unit to serve a common function	organ system	group of organs that work together to perform one or more functions; collection of organs joined in structural unit to serve a common function	development of anatomical structure	reproductive system nervous system circulatory system
36	taxon entity class type	metaclass for unit of an individual taxon's structural organization	physical anatomical entity	unit of member of a species's structural organization	found in taxon	fungal structure
37	biogenic substance type		biogenic substance	substance produced by life processes; it may be either constituents, or secretions, of plants or animals
38	gland type		gland	type of animal organ		exocrine gland
39	organ part type		organ part	anatomical structure, each instance of which has as its direct parts some instance of portions of two or more types of tissue and is continuous with some instance of one or more anatomical structures
40	solitary organ part type		organ part	anatomical structure, each instance of which has as its direct parts some instance of portions of two or more types of tissue and is continuous with some instance of one or more anatomical structures
41	artificial anatomical entity type	anatomical entity that's not naturally present but was added artificially, for example by an operation	artificial anatomical object	anatomical object that's not naturally present but was added artificially, for example by an operation
42	incidental bone organ type	bone that only appears in a special subset of the species	bone	rigid organ that constitutes part of the endoskeleton of vertebrates
43	anatomical cluster type		anatomical cluster
44	joint type		joint	location at which two or more bones make contact
45	ligament type		ligament organ
46	hair type		hair	protein filament that grows from follicles found in the dermis, or skin
47	species organ type		organ	collection of tissues with similar functions
48	tooth type		tooth	hard, calcified structure found in the jaws (or mouths) of many vertebrates and used to break down food
49	sex-specific organ type		organ	collection of tissues with similar functions
50	solitary sex-specific organ type		organ	collection of tissues with similar functions
51	sex-specific anatomical structure class type		anatomical structure	entity with a single connected inherent 3D shape that's created by coordinated expression of the organism's own DNA
52	chiral anatomical set type		anatomical set	set of discontinuous members of the same material anatomical entity within one organism
53	chiral anatomical surface type		anatomical surface	2-dimensional anatomical entity that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment
54	chiral anatomical point type		anatomical point	0-dimensional non-material anatomical entity
55	chiral anatomical line type		anatomical line	1-dimensional anatomical entity
56	chiral organ type		organ type	metaclass for collections of tissues joined as a structural unit that serves a common function
57	chiral anatomical class type	anatomical structure that exists in a right-sided and left-sided version but has no direct instances that are solitary versions	anatomical entity	biological entity that is either member of a species or a unit of its structural organization
58	chiral organ part type		organ part	anatomical structure, each instance of which has as its direct parts some instance of portions of two or more types of tissue and is continuous with some instance of one or more anatomical structures
59	chiral nerve type		nerve	enclosed, cable-like bundle of axons in the peripheral nervous system
60	serous sac type		serous sac	organ that contains a serous membrane and a serous cavity
61	chiral serous sac type		serous sac	organ that contains a serous membrane and a serous cavity
62	solitary serous sac type		serous sac	organ that contains a serous membrane and a serous cavity
63	muscle organ zone type		zone of muscle organ
64	species organism subdivision type		organism subdivision
65	chiral organism subdivision type		organism subdivision
66	solitary organism subdivision type		organism subdivision
67	skin type		skin	soft outer covering organ of vertebrates
68	species anatomical system type		organ system	group of organs that work together to perform one or more functions; collection of organs joined in structural unit to serve a common function		human circulatory system
69	anatomical space type	metaclass for 3-dimensional anatomical entities	anatomical space	3-dimensional immaterial anatomical entity
70	chiral anatomical space type		anatomical space	3-dimensional immaterial anatomical entity
71	solitary anatomical space type		anatomical space	3-dimensional immaterial anatomical entity
72	sex-specific organism subdivision type		organism subdivision
73	sex-specific anatomical structure type		anatomical structure	entity with a single connected inherent 3D shape that's created by coordinated expression of the organism's own DNA
74	sex-specific solitary organism subdivision type		organism subdivision
75	solitary ligament type		ligament	type of tissue that connects bones to other bones
76	chiral ligament type		ligament	type of tissue that connects bones to other bones
77	solitary anatomical cluster type		anatomical cluster
78	chiral anatomical cluster type		anatomical cluster
79	anatomical space class type		anatomical space	3-dimensional immaterial anatomical entity
80	sex-specific solitary anatomical space type		anatomical space	3-dimensional immaterial anatomical entity
81	sex-specific tissue type		tissue	cellular organizational level intermediate between cells and a complete organism; cells that are grouped together with a common function		urethral sponge
82	chiral joint type		joint	location at which two or more bones make contact
83	cell type	metaclass used to distinguish between morphologically or phenotypically distinct cell forms	cell	basic structural and functional unit of all organisms	Cell Ontology ID activating neurotransmitter Terminologia Histologica diameter has marker part of	red blood cell melanocyte neuron

End of automatically generated list.

Sets and classes edit

Whenever there are multiple instances of an anatomical structure A in the human body the individual instances subclass of (P279) A. Disjoint instances of A form together a anatomical set (Q27058130) B of which they are part of (Q66305721). Normally B has part(s) of the class (P2670) A.