Biological Spatial Ontology
type: Ontology
version IRI: bspo.owl
description: An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies.
license: https://creativecommons.org/licenses/by/3.0/
namespace-id-rule: * BSPO:$sequence(7,0,999999999)$
default-namespace: spatial
comment: based on FBql
version info: 2021-10-13

definition
type: AnnotationProperty
IAO_0000111: definition
IAO_0000114: ready for release
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
IAO_0000116: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
IAO_0000117: PERSON:Daniel Schober
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

term replaced by
type: AnnotationProperty
IAO_0000111: term replaced by
IAO_0000114: pending final vetting
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
IAO_0000117: Person:Alan Ruttenberg
IAO_0000119: Person:Alan Ruttenberg
comment: Add as annotation triples in the granting ontology

is a defining property chain axiom
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL

is a defining property chain axiom where second argument is reflexive
type: AnnotationProperty
definition: If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.

synonym typically used in the context of human anatomy
type: AnnotationProperty
has_scope: has_narrow_synonym
sub property of: synonym_type_property

synonym typically used in the context of vertebrate anatomy
type: AnnotationProperty
has_scope: has_narrow_synonym
sub property of: synonym_type_property

namespace-id-rule
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_scope
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

shorthand
type: AnnotationProperty

see also
type: AnnotationProperty
has_obo_namespace: spatial
id: seeAlso
is metadata tag: true
shorthand: seeAlso

part of
type: ObjectProperty
sub property of: overlaps
inverse of: has part
type: TransitiveProperty
IAO_0000111: is part of
IAO_0000112: my brain is part of my body (continuant parthood, two material entities)
IAO_0000112: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
IAO_0000112: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
IAO_0000116: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
IAO_0000118: part_of
RO_0001900: RO_0001901
RO_0040042: continuant
RO_0040042: occurrent
RO_0040042: independent continuant
RO_0040042: realizable entity
RO_0040042: quality
RO_0040042: specifically dependent continuant
RO_0040042: BFO_0000031
database_cross_reference: BFO:0000050
has_obo_namespace: spatial
id: part_of
in subset: valid for go annotation extension
in subset: valid for go gp2term
in subset: valid for go ontology
in subset: valid for gocam
shorthand: part_of

has part
type: ObjectProperty
sub property of: overlaps
type: TransitiveProperty
IAO_0000111: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
IAO_0000116: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
IAO_0000116: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
IAO_0000116: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
IAO_0000118: has_part
RO_0001900: RO_0001901
database_cross_reference: BFO:0000051
has_obo_namespace: spatial
id: has_part
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: has_part

preceded by
type: ObjectProperty
sub property of: ends after
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: preceded by
definition: x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
IAO_0000116: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
IAO_0000118: is preceded by
IAO_0000118: preceded_by
source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by
in subset: ro-eco

precedes
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
domain: occurrent
range: occurrent
property chain axiom: part of
IAO_0000111: precedes
definition: x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
in subset: ro-eco

anatomical relation
type: ObjectProperty
database_cross_reference: BSPO:0000095
has_obo_namespace: spatial
id: anatomical_relation
shorthand: anatomical_relation
deprecated: true

anterior to
type: ObjectProperty
inverse of: posterior to
type: TransitiveProperty
definition: x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
database_cross_reference: BSPO:0000096
has_exact_synonym: rostral_to
has_obo_namespace: spatial
id: anterior_to
shorthand: anterior_to

Axiom
annotated source: anterior to
annotated property: definition
annotated target: x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
database_cross_reference: BSPO:cjm

distal to
type: ObjectProperty
inverse of: proximal to
type: TransitiveProperty
definition: x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
database_cross_reference: BSPO:0000097
has_obo_namespace: spatial
id: distal_to
shorthand: distal_to

Axiom
annotated source: distal to
annotated property: definition
annotated target: x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
database_cross_reference: BSPO:cjm

dorsal to
type: ObjectProperty
inverse of: ventral to
type: TransitiveProperty
definition: x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
database_cross_reference: BSPO:0000098
has_obo_namespace: spatial
id: dorsal_to
shorthand: dorsal_to

Axiom
annotated source: dorsal to
annotated property: definition
annotated target: x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
database_cross_reference: BSPO:cjm

posterior to
type: ObjectProperty
type: TransitiveProperty
definition: x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
database_cross_reference: BSPO:0000099
has_narrow_synonym: caudal to
has_obo_namespace: spatial
id: posterior_to
shorthand: posterior_to

Axiom
annotated source: posterior to
annotated property: definition
annotated target: x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
database_cross_reference: BSPO:cjm

Axiom
annotated source: posterior to
annotated property: has_narrow_synonym
annotated target: caudal to
has_synonym_type: synonym typically used in the context of vertebrate anatomy

proximal to
type: ObjectProperty
type: TransitiveProperty
definition: x proximal to y iff x is closer to the point of attachment with the body than y.
database_cross_reference: BSPO:0000100
has_obo_namespace: spatial
id: proximal_to
shorthand: proximal_to
comment: The elbow is proximal to the hand, but distal to the shoulder.

Axiom
annotated source: proximal to
annotated property: definition
annotated target: x proximal to y iff x is closer to the point of attachment with the body than y.
database_cross_reference: BSPO:cjm

obsolete surrounds
type: ObjectProperty
term replaced by: RO:0002221
database_cross_reference: BSPO:0000101
has_obo_namespace: spatial
id: obsolete_surrounds
shorthand: obsolete_surrounds
deprecated: true

ventral to
type: ObjectProperty
type: TransitiveProperty
definition: x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
database_cross_reference: BSPO:0000102
has_obo_namespace: spatial
id: ventral_to
shorthand: ventral_to

Axiom
annotated source: ventral to
annotated property: definition
annotated target: x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
database_cross_reference: BSPO:cjm

vicinity of
type: ObjectProperty
database_cross_reference: BSPO:0000103
has_obo_namespace: spatial
id: vicinity_of
shorthand: vicinity_of

approximately perpendicular to
type: ObjectProperty
domain: anatomical axis
range: anatomical axis
definition: Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole.
database_cross_reference: BSPO:0000104
has_obo_namespace: spatial
id: approximately_perpendicular_to
shorthand: approximately_perpendicular_to

Axiom
annotated source: approximately perpendicular to
annotated property: definition
annotated target: Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole.
database_cross_reference: BSPO:cjm

ipsilateral to
type: ObjectProperty
type: SymmetricProperty
property disjoint with: contralateral to
definition: On the same side as. For example, the left arm is ipsilateral to the left leg.
database_cross_reference: BSPO:0000105
has_obo_namespace: spatial
id: ipsilateral_to
shorthand: ipsilateral_to

Axiom
annotated source: ipsilateral to
annotated property: definition
annotated target: On the same side as. For example, the left arm is ipsilateral to the left leg.
database_cross_reference: BSPO:cjm

contralateral to
type: ObjectProperty
sub property of: opposite to
type: SymmetricProperty
definition: On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg).
database_cross_reference: BSPO:0000106
has_obo_namespace: spatial
id: contralateral_to
shorthand: contralateral_to

Axiom
annotated source: contralateral to
annotated property: definition
annotated target: On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg).
database_cross_reference: BSPO:cjm

deep to
type: ObjectProperty
inverse of: superficial to
type: TransitiveProperty
definition: Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
database_cross_reference: BSPO:0000107
has_obo_namespace: spatial
id: deep_to
shorthand: deep_to

Axiom
annotated source: deep to
annotated property: definition
annotated target: Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
database_cross_reference: BSPO:cjm

superficial to
type: ObjectProperty
type: TransitiveProperty
definition: Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
database_cross_reference: BSPO:0000108
has_obo_namespace: spatial
id: superficial_to
shorthand: superficial_to

Axiom
annotated source: superficial to
annotated property: definition
annotated target: Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
database_cross_reference: BSPO:cjm

obsolete surrounded_by
type: ObjectProperty
term replaced by: RO:0002219
database_cross_reference: BSPO:0000109
has_obo_namespace: spatial
id: obsolete_surrounded_by
shorthand: obsolete_surrounded_by
deprecated: true

left of
type: ObjectProperty
inverse of: right of
type: TransitiveProperty
definition: Closer to the left side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is left of some instance y of Y, and there exists some organism o such that x part of o and y part of o.
database_cross_reference: BSPO:0000110
has_obo_namespace: spatial
id: left_of
shorthand: left_of

Axiom
annotated source: left of
annotated property: definition
annotated target: Closer to the left side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is left of some instance y of Y, and there exists some organism o such that x part of o and y part of o.
database_cross_reference: BSPO:cjm

right of
type: ObjectProperty
type: TransitiveProperty
definition: Closer to the right side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is right of some instance y of Y, and there exists some organism o such that x part of o and y part of o.
database_cross_reference: BSPO:0000111
has_obo_namespace: spatial
id: right_of
shorthand: right_of

Axiom
annotated source: right of
annotated property: definition
annotated target: Closer to the right side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is right of some instance y of Y, and there exists some organism o such that x part of o and y part of o.
database_cross_reference: BSPO:cjm

opposite to
type: ObjectProperty
definition: Direcly opposite to. i.e. on the opposite side through the axis.
database_cross_reference: BSPO:0000113
has_obo_namespace: spatial
id: opposite_to
shorthand: opposite_to

Axiom
annotated source: opposite to
annotated property: definition
annotated target: Direcly opposite to. i.e. on the opposite side through the axis.
database_cross_reference: BSPO:cjm

lateral to
type: ObjectProperty
inverse of: X medial to y if x is closer to the midsagittal plane than y.
type: TransitiveProperty
definition: X lateral to y if x is further from the midsagittal plane than y.
created by: Jennifer Girón
creation date: 2021-04-21T01:01:01Z

X medial to y if x is closer to the midsagittal plane than y.
type: ObjectProperty
type: TransitiveProperty
created by: Jennifer Girón
creation date: 2021-04-21T01:01:01Z
label: medial to

in left side of
type: ObjectProperty
sub property of: in lateral side of
property disjoint with: in right side of
definition: X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
database_cross_reference: BSPO:0000120
has_obo_namespace: spatial
id: in_left_side_of
shorthand: in_left_side_of

Axiom
annotated source: in left side of
annotated property: definition
annotated target: X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
database_cross_reference: BSPO:PATO_mtg_2009

in right side of
type: ObjectProperty
sub property of: in lateral side of
definition: X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
database_cross_reference: BSPO:0000121
has_obo_namespace: spatial
id: in_right_side_of
shorthand: in_right_side_of

Axiom
annotated source: in right side of
annotated property: definition
annotated target: X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
database_cross_reference: BSPO:PATO_mtg_2009

in posterior side of
type: ObjectProperty
sub property of: part of
definition: X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
database_cross_reference: BSPO:0000122
has_obo_namespace: spatial
id: in_posterior_side_of
shorthand: in_posterior_side_of

Axiom
annotated source: in posterior side of
annotated property: definition
annotated target: X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
database_cross_reference: BSPO:PATO_mtg_2009

in anterior side of
type: ObjectProperty
sub property of: part of
definition: X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
database_cross_reference: BSPO:0000123
has_obo_namespace: spatial
id: in_anterior_side_of
shorthand: in_anterior_side_of

Axiom
annotated source: in anterior side of
annotated property: definition
annotated target: X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
database_cross_reference: BSPO:PATO_mtg_2009

in proximal side of
type: ObjectProperty
sub property of: part of
definition: x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
database_cross_reference: BSPO:0000124
has_obo_namespace: spatial
id: in_proximal_side_of
shorthand: in_proximal_side_of

Axiom
annotated source: in proximal side of
annotated property: definition
annotated target: x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
database_cross_reference: BSPO:PATO_mtg_2009

in distal side of
type: ObjectProperty
sub property of: part of
definition: x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
database_cross_reference: BSPO:0000125
has_obo_namespace: spatial
id: in_distal_side_of
shorthand: in_distal_side_of

Axiom
annotated source: in distal side of
annotated property: definition
annotated target: x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
database_cross_reference: BSPO:PATO_mtg_2009

in lateral side of
type: ObjectProperty
sub property of: part of
definition: X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
database_cross_reference: BSPO:0000126
has_obo_namespace: spatial
id: in_lateral_side_of
shorthand: in_lateral_side_of

Axiom
annotated source: in lateral side of
annotated property: definition
annotated target: X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure
database_cross_reference: UBERON:cjm

in superficial part of
type: ObjectProperty
sub property of: part of
definition: X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the superficial portion.
database_cross_reference: BSPO:0001100
has_obo_namespace: spatial
id: in_superficial_part_of
shorthand: in_superficial_part_of

Axiom
annotated source: in superficial part of
annotated property: definition
annotated target: X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the superficial portion.
database_cross_reference: BSPO:cjm

in deep part of
type: ObjectProperty
sub property of: part of
definition: X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion.
database_cross_reference: BSPO:0001101
has_obo_namespace: spatial
id: in_deep_part_of
shorthand: in_deep_part_of

Axiom
annotated source: in deep part of
annotated property: definition
annotated target: X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion.
database_cross_reference: BSPO:cjm

proximalmost part of
type: ObjectProperty
sub property of: in proximal side of
definition: X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
database_cross_reference: BSPO:0001106
has_obo_namespace: spatial
id: proximalmost_part_of
shorthand: proximalmost_part_of

Axiom
annotated source: proximalmost part of
annotated property: definition
annotated target: X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
database_cross_reference: https://orcid.org/0000-0002-6601-2165

immediately deep to
type: ObjectProperty
sub property of: deep to
inverse of: immediately superficial to
definition: x immediately deep to y iff x deep_to y and x is contiguous with y.
database_cross_reference: BSPO:0001107
has_obo_namespace: spatial
id: immediately_deep_to
shorthand: immediately_deep_to

Axiom
annotated source: immediately deep to
annotated property: definition
annotated target: x immediately deep to y iff x deep_to y and x is contiguous with y.
database_cross_reference: BSPO:curators

distalmost part of
type: ObjectProperty
sub property of: in distal side of
definition: X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
database_cross_reference: BSPO:0001108
has_obo_namespace: spatial
id: distalmost_part_of
shorthand: distalmost_part_of

Axiom
annotated source: distalmost part of
annotated property: definition
annotated target: X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
database_cross_reference: https://orcid.org/0000-0002-6601-2165

preaxialmost part of
type: ObjectProperty
sub property of: part of
database_cross_reference: BSPO:0001113
has_obo_namespace: spatial
id: preaxialmost_part_of
shorthand: preaxialmost_part_of

postaxial to
type: ObjectProperty
type: TransitiveProperty
definition: x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side.
database_cross_reference: BSPO:0001114
has_obo_namespace: spatial
has_related_synonym: posterior to (developmentally)
id: postaxial_to
shorthand: postaxial_to

Axiom
annotated source: postaxial to
annotated property: definition
annotated target: x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side.
database_cross_reference: http://medical-dictionary.thefreedictionary.com/postaxial

Axiom
annotated source: postaxial to
annotated property: has_related_synonym
annotated target: posterior to (developmentally)
database_cross_reference: MA:th

postaxialmost part of
type: ObjectProperty
sub property of: part of
database_cross_reference: BSPO:0001115
has_obo_namespace: spatial
id: postaxialmost_part_of
shorthand: postaxialmost_part_of

intersects midsagittal plane of
type: ObjectProperty
sub property of: part of
definition: X intersects median plane of iff X crosses the midine plane of Y.
database_cross_reference: BSPO:0005001
has_obo_namespace: spatial
id: intersects_midsagittal_plane_of
shorthand: intersects_midsagittal_plane_of

finishes axis
type: ObjectProperty
domain: anatomical side
range: anatomical axis
database_cross_reference: BSPO:0015001
has_obo_namespace: spatial
id: finishes_axis
shorthand: finishes_axis
comment: A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. If s finishes axis x, and x has end point p, then x overlaps p

follows axis
type: ObjectProperty
range: anatomical axis
database_cross_reference: BSPO:0015002
has_obo_namespace: spatial
id: follows_axis
shorthand: follows_axis

has axis
type: ObjectProperty
database_cross_reference: BSPO:0015003
has_obo_namespace: spatial
id: has_axis
shorthand: has_axis

has end point
type: ObjectProperty
domain: anatomical axis
range: anatomical entity
definition: A relation between an axis and a part of an organism, in which the part defines the initial point of the axis.
database_cross_reference: BSPO:0015004
has_obo_namespace: spatial
id: has_end_point
shorthand: has_end_point
comment: Axes can be defined in a given species by subtyping the relevant axis type and stating a end and end point

Axiom
annotated source: has end point
annotated property: definition
annotated target: A relation between an axis and a part of an organism, in which the part defines the initial point of the axis.
database_cross_reference: BSPO:cjm

orthogonal to
type: ObjectProperty
domain: anatomical axis
range: anatomical plane
definition: crossing at right angles
database_cross_reference: BSPO:0015005
has_obo_namespace: spatial
id: orthogonal_to
shorthand: orthogonal_to

Axiom
annotated source: orthogonal to
annotated property: definition
annotated target: crossing at right angles
database_cross_reference: BSPO:cjm

passes through
type: ObjectProperty
domain: anatomical axis
definition: Intersects at two points.
database_cross_reference: BSPO:0015006
has_obo_namespace: spatial
id: passes_through
shorthand: passes_through

Axiom
annotated source: passes through
annotated property: definition
annotated target: Intersects at two points.
database_cross_reference: BSPO:cjm

starts axis
type: ObjectProperty
domain: anatomical side
range: anatomical axis
database_cross_reference: BSPO:0015007
has_obo_namespace: spatial
id: starts_axis
shorthand: starts_axis
comment: A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. . If s starts axis x, and x has start point p, then x overlaps p

surface of
type: ObjectProperty
domain: anatomical surface
database_cross_reference: BSPO:0015008
has_obo_namespace: spatial
id: surface_of
shorthand: surface_of
comment: placeholder. used for relation between anatomical surface and an anatomical side.

immediately anterior to
type: ObjectProperty
sub property of: anterior to
inverse of: immediately posterior to
definition: x immediately anterior to y iff x anterior to y and x is contiguous with y.
database_cross_reference: BSPO:0015009
has_obo_namespace: spatial
id: immediately_anterior_to
shorthand: immediately_anterior_to

Axiom
annotated source: immediately anterior to
annotated property: definition
annotated target: x immediately anterior to y iff x anterior to y and x is contiguous with y.
database_cross_reference: BSPO:curators

immediately distal to
type: ObjectProperty
sub property of: distal to
inverse of: immediately proximal to
definition: x immediately distal to y iff x distal to y and x is contiguous with y.
database_cross_reference: BSPO:0015010
has_obo_namespace: spatial
id: immediately_distal_to
shorthand: immediately_distal_to

Axiom
annotated source: immediately distal to
annotated property: definition
annotated target: x immediately distal to y iff x distal to y and x is contiguous with y.
database_cross_reference: BSPO:curators

immediately dorsal to
type: ObjectProperty
sub property of: dorsal to
inverse of: immediately ventral to
definition: x immediately dorsal to y iff x dorsal to y and x is contiguous with y.
database_cross_reference: BSPO:0015011
has_obo_namespace: spatial
id: immediately_dorsal_to
shorthand: immediately_dorsal_to

Axiom
annotated source: immediately dorsal to
annotated property: definition
annotated target: x immediately dorsal to y iff x dorsal to y and x is contiguous with y.
database_cross_reference: BSPO:curators

immediately posterior to
type: ObjectProperty
sub property of: posterior to
definition: x immediately posterior to y iff x posterior_to y and x is contiguous with y.
database_cross_reference: BSPO:0015012
has_obo_namespace: spatial
id: immediately_posterior_to
shorthand: immediately_posterior_to

Axiom
annotated source: immediately posterior to
annotated property: definition
annotated target: x immediately posterior to y iff x posterior_to y and x is contiguous with y.
database_cross_reference: BSPO:curators

immediately proximal to
type: ObjectProperty
sub property of: proximal to
definition: x immediately proximal to y iff x proximal to y and x is contiguous with y.
database_cross_reference: BSPO:0015013
has_obo_namespace: spatial
id: immediately_proximal_to
shorthand: immediately_proximal_to

Axiom
annotated source: immediately proximal to
annotated property: definition
annotated target: x immediately proximal to y iff x proximal to y and x is contiguous with y.
database_cross_reference: BSPO:curators

immediately superficial to
type: ObjectProperty
sub property of: superficial to
definition: x immediately superficial to y iff x superficial to y and x is contiguous with y.
database_cross_reference: BSPO:0015014
has_obo_namespace: spatial
id: immediately_superficial_to
shorthand: immediately_superficial_to

Axiom
annotated source: immediately superficial to
annotated property: definition
annotated target: x immediately superficial to y iff x superficial to y and x is contiguous with y.
database_cross_reference: BSPO:curators

immediately ventral to
type: ObjectProperty
sub property of: ventral to
definition: x immediately ventral to y iff x ventral to y and x is contiguous with y.
database_cross_reference: BSPO:0015015
has_obo_namespace: spatial
id: immediately_ventral_to
shorthand: immediately_ventral_to

Axiom
annotated source: immediately ventral to
annotated property: definition
annotated target: x immediately ventral to y iff x ventral to y and x is contiguous with y.
database_cross_reference: BSPO:curators

immediately left of
type: ObjectProperty
sub property of: left of
inverse of: immediately right of
definition: x immediately left of y iff x left_of y and x is contiguous with y.
database_cross_reference: BSPO:0015016
has_obo_namespace: spatial
id: immediately_left_of
shorthand: immediately_left_of

Axiom
annotated source: immediately left of
annotated property: definition
annotated target: x immediately left of y iff x left_of y and x is contiguous with y.
database_cross_reference: BSPO:curators

immediately right of
type: ObjectProperty
sub property of: right of
definition: x immediately right of y iff x right of y and x is contiguous with y.
database_cross_reference: BSPO:0015017
has_obo_namespace: spatial
id: immediately_right_of
shorthand: immediately_right_of

Axiom
annotated source: immediately right of
annotated property: definition
annotated target: x immediately right of y iff x right of y and x is contiguous with y.
database_cross_reference: BSPO:curators

in dorsal side of
type: ObjectProperty
sub property of: part of
definition: X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion.
database_cross_reference: BSPO:0015101
has_obo_namespace: spatial
id: in_dorsal_side_of
shorthand: in_dorsal_side_of

Axiom
annotated source: in dorsal side of
annotated property: definition
annotated target: X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion.
database_cross_reference: BSPO:cjm

in ventral side of
type: ObjectProperty
sub property of: part of
definition: X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion.
database_cross_reference: BSPO:0015102
has_obo_namespace: spatial
id: in_ventral_side_of
shorthand: in_ventral_side_of

Axiom
annotated source: in ventral side of
annotated property: definition
annotated target: X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion.
database_cross_reference: BSPO:cjm

oral to
type: ObjectProperty
type: TransitiveProperty
definition: nearer to the oral opening of the organism, on the oral-aboral axis.
database_cross_reference: BSPO:0015201
has_obo_namespace: spatial
id: oral_to
shorthand: oral_to

Axiom
annotated source: oral to
annotated property: definition
annotated target: nearer to the oral opening of the organism, on the oral-aboral axis.
database_cross_reference: BSPO:cjm

aboral to
type: ObjectProperty
type: TransitiveProperty
definition: nearer to the aboral opening of the organism, on the oral-aboral axis.
database_cross_reference: BSPO:0015202
has_obo_namespace: spatial
id: aboral_to
shorthand: aboral_to

Axiom
annotated source: aboral to
annotated property: definition
annotated target: nearer to the aboral opening of the organism, on the oral-aboral axis.
database_cross_reference: BSPO:cjm

preaxial to
type: ObjectProperty
type: TransitiveProperty
definition: x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the front.
database_cross_reference: BSPO:1000000
has_obo_namespace: spatial
has_related_synonym: anterior to (developmentally)
has_related_synonym: lateral (radial) to
has_related_synonym: medial (tibial) to
id: preaxial_to
shorthand: preaxial_to

Axiom
annotated source: preaxial to
annotated property: definition
annotated target: x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the front.
database_cross_reference: http://medical-dictionary.thefreedictionary.com/preaxial

Axiom
annotated source: preaxial to
annotated property: has_related_synonym
annotated target: anterior to (developmentally)
database_cross_reference: MA:th

characteristic of
type: ObjectProperty
sub property of: characteristic of part of
inverse of: has characteristic
type: FunctionalProperty
IAO_0000111: inheres in
IAO_0000112: this fragility is a characteristic of this vase
IAO_0000112: this red color is a characteristic of this apple
definition: a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
IAO_0000118: inheres_in
RO_0001900: RO_0001901
comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.

has characteristic
type: ObjectProperty
type: InverseFunctionalProperty
range: specifically dependent continuant
IAO_0000111: bearer of
IAO_0000112: this apple is bearer of this red color
IAO_0000112: this vase is bearer of this fragility
definition: Inverse of characteristic_of
IAO_0000116: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
IAO_0000118: bearer_of
IAO_0000118: is bearer of
RO_0001900: RO_0001901

participates in
type: ObjectProperty
inverse of: has participant
domain: continuant
range: occurrent
IAO_0000111: participates in
IAO_0000112: this blood clot participates in this blood coagulation
IAO_0000112: this input material (or this output material) participates in this process
IAO_0000112: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
IAO_0000118: participates_in

has participant
type: ObjectProperty
domain: occurrent
range: continuant
property chain axiom: has part
IAO_0000111: has participant
IAO_0000112: this blood coagulation has participant this blood clot
IAO_0000112: this investigation has participant this investigator
IAO_0000112: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
IAO_0000116: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
IAO_0000118: has_participant
source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

function of
type: ObjectProperty
sub property of: characteristic of
inverse of: has function
domain: function
IAO_0000112: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
IAO_0000116: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
IAO_0000118: function_of
IAO_0000118: is function of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

quality of
type: ObjectProperty
sub property of: characteristic of
inverse of: has quality
IAO_0000112: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
IAO_0000116: A quality inheres in its bearer at all times for which the quality exists.
IAO_0000118: is quality of
IAO_0000118: quality_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

role of
type: ObjectProperty
sub property of: characteristic of
inverse of: has role
IAO_0000112: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
IAO_0000116: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
IAO_0000118: is role of
IAO_0000118: role_of
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has function
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: function
IAO_0000112: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
IAO_0000118: has_function

has quality
type: ObjectProperty
sub property of: has characteristic
range: quality
IAO_0000112: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
IAO_0000118: has_quality

has role
type: ObjectProperty
sub property of: has characteristic
domain: independent continuant
range: role
IAO_0000112: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
IAO_0000116: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
IAO_0000118: has_role

has disposition
type: ObjectProperty
sub property of: has characteristic
inverse of: disposition of
domain: independent continuant
range: disposition
definition: a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence

disposition of
type: ObjectProperty
sub property of: characteristic of
definition: inverse of has disposition
in subset: RO_0002259
comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.

has regulatory component activity
type: ObjectProperty
sub property of: has component activity
sub property of: regulated by
definition: A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
created by: dos
creation date: 2017-05-24T09:30:46Z

has negative regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: negatively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:01Z
comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.

has positive regulatory component activity
type: ObjectProperty
sub property of: has regulatory component activity
sub property of: positively regulated by
definition: A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
created by: dos
creation date: 2017-05-24T09:31:17Z
comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.

has component activity
type: ObjectProperty
sub property of: has component process
created by: dos
creation date: 2017-05-24T09:44:33Z
comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.

has component process
type: ObjectProperty
sub property of: has component
domain: process
range: process
definition: w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
created by: dos
creation date: 2017-05-24T09:49:21Z

directly regulated by
type: ObjectProperty
sub property of: regulated by
inverse of: directly regulates
created by: dos
creation date: 2017-09-17T13:52:24Z
comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.

Axiom
annotated source: directly regulated by
annotated property: comment
annotated target: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
database_cross_reference: GOC:dos

directly negatively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly negatively regulates
definition: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:38Z

Axiom
annotated source: directly negatively regulated by
annotated property: definition
annotated target: Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
database_cross_reference: GOC:dos

directly positively regulated by
type: ObjectProperty
sub property of: directly regulated by
inverse of: directly positively regulates
definition: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
created by: dos
creation date: 2017-09-17T13:52:47Z

Axiom
annotated source: directly positively regulated by
annotated property: definition
annotated target: Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
database_cross_reference: GOC:dos

has effector activity
type: ObjectProperty
sub property of: has component activity
type: FunctionalProperty
definition: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
created by: dos
creation date: 2017-09-22T14:14:36Z
comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.

Axiom
annotated source: has effector activity
annotated property: definition
annotated target: A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
database_cross_reference: GOC:dos

ends after
type: ObjectProperty
sub property of: temporally related to
type: TransitiveProperty
IAO_0000117: David Osumi-Sutherland
in subset: ro-eco
comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)

immediately preceded by
type: ObjectProperty
sub property of: preceded by
inverse of: immediately precedes
IAO_0000117: David Osumi-Sutherland
IAO_0000118: starts_at_end_of
comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)

immediately precedes
type: ObjectProperty
sub property of: precedes
IAO_0000117: David Osumi-Sutherland
IAO_0000118: ends_at_start_of
IAO_0000118: meets
RO_0002575: precedes
in subset: ro-eco
comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)

overlaps
type: ObjectProperty
sub property of: mereotopologically related to
property chain axiom: part of
property chain axiom: has part
IAO_0000114: pending final vetting
definition: x overlaps y if and only if there exists some z such that x has part z and z part of y
definition: x overlaps y iff they have some part in common.
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO_0001900: RO_0001901
database_cross_reference: RO:0002131
has_obo_namespace: spatial
id: overlaps
in subset: valid for go annotation extension
in subset: valid for gocam
in subset: ro-eco
shorthand: overlaps
comment: "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []

Axiom
annotated source: overlaps
annotated property: propertyChainAxiom
annotated target: has part
annotated target: part of
RO_0002582: true

Axiom
annotated source: overlaps
annotated property: definition
annotated target: x overlaps y iff they have some part in common.
database_cross_reference: BSPO:cjm

spatially disjoint from
type: ObjectProperty
sub property of: mereotopologically related to
IAO_0000114: pending final vetting
definition: A is spatially_disjoint_from B if and only if they have no parts in common
IAO_0000116: There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
IAO_0000117: Chris Mungall
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/22293552
IAO_0000232: Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
RO_0001900: RO_0001901
in subset: ro-eco

has component
type: ObjectProperty
sub property of: has part
IAO_0000114: pending final vetting
definition: w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
IAO_0000116: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
IAO_0000232: For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO_0001900: RO_0001901
in subset: ro-eco

regulates
type: ObjectProperty
sub property of: causally upstream of
inverse of: regulated by
type: TransitiveProperty
domain: process
range: process
property chain axiom: has effector activity
property chain axiom: directly regulates
IAO_0000114: pending final vetting
definition: process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
IAO_0000116: We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
IAO_0000117: Chris Mungall
IAO_0000117: David Hill
IAO_0000117: Tanya Berardini
IAO_0000119: causal-relations
IAO_0000119: GO
IAO_0000232: Regulation precludes parthood; the regulatory process may not be within the regulated process.
IAO_0000589: regulates (processual)
IAO_0000600: false
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

negatively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, negative effect
inverse of: negatively regulated by
definition: Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: negatively regulates (process to process)
RO_0004050: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

positively regulates
type: ObjectProperty
sub property of: regulates
sub property of: causally upstream of, positive effect
inverse of: positively regulated by
type: TransitiveProperty
property chain axiom: negatively regulates
definition: Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: positively regulates (process to process)
RO_0004049: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

capable of
type: ObjectProperty
sub property of: capable of part of
domain: independent continuant
range: process
IAO_0000112: mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
IAO_0000112: osteoclast SubClassOf 'capable of' some 'bone resorption'
definition: A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
IAO_0000117: Chris Mungall
IAO_0000118: has function realized in
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20123131
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/21208450
IAO_0000232: For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
in subset: ro-eco

capable of part of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: part of
definition: c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
IAO_0000117: Chris Mungall
IAO_0000118: has function in

Axiom
annotated source: capable of part of
annotated property: propertyChainAxiom
annotated target: capable of
annotated target: part of
RO_0002582: true

adjacent to
type: ObjectProperty
sub property of: spatially disjoint from
type: SymmetricProperty
domain: independent continuant
range: independent continuant
IAO_0000112: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
IAO_0000112: The epidermis layer of a vertebrate is adjacent to the dermis.
IAO_0000112: The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
IAO_0000112: The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
IAO_0000114: pending final vetting
definition: x adjacent to y if and only if x and y share a boundary.
IAO_0000116: This relation acts as a join point with BSPO
IAO_0000117: Chris Mungall
RO_0001900: RO_0001901
database_cross_reference: RO:0002220
has_obo_namespace: spatial
id: adjacent_to
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
shorthand: adjacent_to

Axiom
annotated source: adjacent to
annotated property: IAO_0000112
annotated target: A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.

temporally related to
type: ObjectProperty
domain: occurrent
range: occurrent
IAO_0000114: pending final vetting
IAO_0000117: Chris Mungall
IAO_0000119: Allen's interval algebra
IAO_0000232: Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
source: https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit
in subset: ro-eco
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

has input
type: ObjectProperty
sub property of: has participant
inverse of: input of
domain: process
IAO_0000114: pending final vetting
definition: p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
IAO_0000117: Chris Mungall
IAO_0000118: consumes
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam
in subset: ro-eco

acts upstream of
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of
IAO_0000112: A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
definition: c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
in subset: valid for go gp2term

acts upstream of or within
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: enables
property chain axiom: causally upstream of or within
IAO_0000112: A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
definition: c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
has_related_synonym: affects
in subset: valid for go gp2term

causally upstream of, positive effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, positive effect
RO_0004049: causally upstream of
creator: cjm
in subset: valid for go annotation extension
in subset: valid for gocam
comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y

causally upstream of, negative effect
type: ObjectProperty
sub property of: causally upstream of
sub property of: causally upstream of or within, negative effect
RO_0004050: causally upstream of
creator: cjm
comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y

characteristic of part of
type: ObjectProperty
sub property of: depends on
property chain axiom: characteristic of
property chain axiom: part of
definition: q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
IAO_0000116: Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
IAO_0000117: Chris Mungall
IAO_0000118: inheres in part of
IAO_0000119: http://www.ncbi.nlm.nih.gov/pubmed/20064205
RO_0001900: RO_0001901

Axiom
annotated source: characteristic of part of
annotated property: propertyChainAxiom
annotated target: characteristic of
annotated target: part of
RO_0002582: true

mereotopologically related to
type: ObjectProperty
definition: A mereological relationship or a topological relationship
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO_0001900: RO_0001901

enables
type: ObjectProperty
sub property of: capable of
inverse of: enabled by
property chain axiom: has part
property chain axiom: has component activity
IAO_0000112: a particular instances of akt-2 enables some instance of protein kinase activity
IAO_0000117: Chris Mungall
IAO_0000118: catalyzes
IAO_0000118: executes
IAO_0000118: has
IAO_0000118: is catalyzing
IAO_0000118: is executing
IAO_0000232: This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
IAO_0000232: This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
in subset: valid for go gp2term

functionally related to
type: ObjectProperty
definition: A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
IAO_0000117: Chris Mungall
IAO_0000232: This is a grouping relation that collects relations used for the purpose of connecting structure and function

part of structure that is capable of
type: ObjectProperty
sub property of: functionally related to
property chain axiom: part of
property chain axiom: capable of
definition: this relation holds between c and p when c is part of some c', and c' is capable of p.
IAO_0000117: Chris Mungall
IAO_0000118: false

Axiom
annotated source: part of structure that is capable of
annotated property: propertyChainAxiom
annotated target: part of
annotated target: capable of
is a defining property chain axiom: true

involved in
type: ObjectProperty
sub property of: participates in
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: part of
definition: c involved_in p if and only if c enables some process p', and p' is part of p
IAO_0000117: Chris Mungall
IAO_0000118: actively involved in
IAO_0000118: enables part of

enabled by
type: ObjectProperty
sub property of: has participant
sub property of: functionally related to
definition: inverse of enables
IAO_0000117: Chris Mungall
in subset: valid for gocam

regulated by
type: ObjectProperty
sub property of: causally downstream of or within
type: TransitiveProperty
domain: process
range: process
definition: inverse of regulates
IAO_0000117: Chris Mungall
IAO_0000589: regulated by (processual)
in subset: RO_0002259

negatively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of negatively regulates
IAO_0000117: Chris Mungall
in subset: RO_0002259

positively regulated by
type: ObjectProperty
sub property of: regulated by
definition: inverse of positively regulates
IAO_0000117: Chris Mungall
in subset: RO_0002259

input of
type: ObjectProperty
sub property of: participates in
sub property of: functionally related to
definition: inverse of has input
IAO_0000117: Chris Mungall
in subset: RO_0002259
in subset: ro-eco

causally downstream of
type: ObjectProperty
sub property of: preceded by
sub property of: causally downstream of or within
inverse of: causally upstream of
IAO_0000114: requires discussion
definition: inverse of upstream of
IAO_0000117: Chris Mungall

immediately causally downstream of
type: ObjectProperty
sub property of: immediately preceded by
sub property of: causally downstream of
inverse of: immediately causally upstream of
IAO_0000114: requires discussion
IAO_0000117: Chris Mungall

causally related to
type: ObjectProperty
IAO_0000114: requires discussion
definition: This relation groups causal relations between material entities and causal relations between processes
IAO_0000116: This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yiel…
IAO_0000117: Chris Mungall
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally upstream of
type: ObjectProperty
sub property of: precedes
sub property of: causally upstream of or within
type: TransitiveProperty
IAO_0000114: requires discussion
definition: p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
IAO_0000117: Chris Mungall
in subset: valid for go annotation extension
in subset: valid for gocam

immediately causally upstream of
type: ObjectProperty
sub property of: immediately precedes
sub property of: causally upstream of
IAO_0000114: requires discussion
definition: p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
IAO_0000117: Chris Mungall
RO_0002575: causally upstream of

causally upstream of or within
type: ObjectProperty
sub property of: causal relation between processes
inverse of: causally downstream of or within
type: TransitiveProperty
definition: p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
IAO_0000116: We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
IAO_0000117: Chris Mungall
IAO_0000118: influences (processual)
has_related_synonym: affects

causally downstream of or within
type: ObjectProperty
sub property of: causal relation between processes
type: TransitiveProperty
definition: inverse of causally upstream of or within
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
in subset: RO_0002259

involved in regulation of
type: ObjectProperty
sub property of: acts upstream of
sub property of: involved in or involved in regulation of
property chain axiom: enables
property chain axiom: regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' regulates some p
IAO_0000117: Chris Mungall

involved in positive regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: positively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' positively regulates some p
IAO_0000117: Chris Mungall
RO_0004049: involved in regulation of

involved in negative regulation of
type: ObjectProperty
sub property of: involved in regulation of
property chain axiom: enables
property chain axiom: negatively regulates
property chain axiom: involved in
definition: c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
IAO_0000117: Chris Mungall
RO_0004050: involved in regulation of

involved in or involved in regulation of
type: ObjectProperty
sub property of: acts upstream of or within
sub property of: functionally related to
sub property of: causal agent in process
definition: c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
IAO_0000116: OWL does not allow defining object properties via a Union
IAO_0000117: Chris Mungall
IAO_0000118: involved in or reguates

interacts with
type: ObjectProperty
type: SymmetricProperty
domain: material entity
range: material entity
definition: A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
IAO_0000116: Considering relabeling as 'pairwise interacts with'
IAO_0000116: This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
IAO_0000117: Chris Mungall
IAO_0000232: Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
has_exact_synonym: in pairwise interaction with
in subset: ro-eco

molecularly interacts with
type: ObjectProperty
sub property of: interacts with
type: SymmetricProperty
definition: An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
IAO_0000117: Chris Mungall
IAO_0000118: binds
IAO_0000118: molecularly binds with

phosphorylates
type: ObjectProperty
sub property of: molecularly interacts with
IAO_0000116: Axiomatization to GO to be added later
IAO_0000117: Chris Mungall
IAO_0000118: An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.

directly regulates activity of
type: ObjectProperty
sub property of: molecularly interacts with
sub property of: regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
has_exact_synonym: molecularly controls

directly negatively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly negatively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly inhibits
has_exact_synonym: molecularly decreases activity of

directly positively regulates activity of
type: ObjectProperty
sub property of: directly regulates activity of
domain: material entity
range: material entity
property chain axiom: enables
property chain axiom: directly positively regulates
property chain axiom: enabled by
definition: The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000118: directly activates
has_exact_synonym: molecularly increases activity of

helper property (not for use in curation)
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000232: This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.

is kinase activity
type: ObjectProperty
sub property of: molecular interaction relation helper property
IAO_0000117: Chris Mungall

causal agent in process
type: ObjectProperty
sub property of: causal relation between material entity and a process
inverse of: process has causal agent
definition: A relationship between a material entity and a process where the material entity has some causal role that influences the process
IAO_0000119: causal-relations

causal relation between processes
type: ObjectProperty
sub property of: causally related to
domain: occurrent
range: occurrent
definition: p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

depends on
type: ObjectProperty
IAO_0000117: Chris Mungall

causal relation between entities
type: ObjectProperty
sub property of: causally related to
domain: continuant
range: continuant
IAO_0000116: The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

causally influenced by
type: ObjectProperty
sub property of: causal relation between entities
inverse of: causally influences
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: causally influenced by (entity-centric)

interaction relation helper property
type: ObjectProperty
sub property of: helper property (not for use in curation)
IAO_0000117: Chris Mungall

molecular interaction relation helper property
type: ObjectProperty
sub property of: interaction relation helper property
IAO_0000117: Chris Mungall

causally influences
type: ObjectProperty
sub property of: causal relation between entities
domain: continuant
range: continuant
property chain axiom: enables
property chain axiom: causally upstream of
property chain axiom: has input
property chain axiom: enabled by
definition: The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
IAO_0000117: Chris Mungall
IAO_0000117: Vasundra Touré
IAO_0000119: causal-relations
IAO_0000589: causally influences (entity-centric)

directly regulates
type: ObjectProperty
sub property of: regulates
sub property of: immediately causally upstream of
definition: Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations
IAO_0000589: directly regulates (processual)
RO_0002575: regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

has part structure that is capable of
type: ObjectProperty
sub property of: functionally related to
sub property of: causal relation between material entity and a process
property chain axiom: has part
property chain axiom: capable of
IAO_0000112: gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
definition: s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
IAO_0000117: Chris Mungall

causal relation between material entity and a process
type: ObjectProperty
sub property of: causally related to
domain: material entity
range: process
definition: A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
IAO_0000116: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
IAO_0000117: Chris Mungall
IAO_0000119: causal-relations

capable of regulating
type: ObjectProperty
sub property of: causal agent in process
property chain axiom: capable of
property chain axiom: regulates
IAO_0000112: pyrethroid -> growth
definition: Holds between c and p if and only if c is capable of some activity a, and a regulates p.
IAO_0000119: causal-relations

capable of negatively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: negatively regulates
definition: Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
IAO_0000119: causal-relations

capable of positively regulating
type: ObjectProperty
sub property of: capable of regulating
property chain axiom: capable of
property chain axiom: positively regulates
IAO_0000112: renin -> arteriolar smooth muscle contraction
definition: Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
IAO_0000119: causal-relations

process has causal agent
type: ObjectProperty
sub property of: causally related to
definition: Inverse of 'causal agent in process'
IAO_0000119: causal-relations

directly positively regulates
type: ObjectProperty
sub property of: positively regulates
sub property of: directly regulates
definition: Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
IAO_0000119: causal-relations
IAO_0000589: directly positively regulates (process to process)
RO_0004049: directly regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

directly negatively regulates
type: ObjectProperty
sub property of: negatively regulates
sub property of: directly regulates
definition: Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
IAO_0000119: causal-relations
IAO_0000589: directly negatively regulates (process to process)
RO_0004050: directly regulates
in subset: valid for go annotation extension
in subset: valid for go ontology
in subset: valid for gocam

enables subfunction
type: ObjectProperty
sub property of: functionally related to
property chain axiom: enables
property chain axiom: has part
definition: Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
created by: cjm
creation date: 2018-01-25T23:20:13Z

acts upstream of or within, positive effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, positive effect
RO_0004049: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:30Z
in subset: valid for go gp2term

acts upstream of or within, negative effect
type: ObjectProperty
sub property of: acts upstream of or within
property chain axiom: enables
property chain axiom: causally upstream of or within, negative effect
RO_0004050: acts upstream of or within
created by: cjm
creation date: 2018-01-26T23:49:51Z
in subset: valid for go gp2term

acts upstream of, positive effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, positive effect
property chain axiom: enables
property chain axiom: causally upstream of, positive effect
definition: c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
RO_0004049: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:14Z
in subset: valid for go gp2term

acts upstream of, negative effect
type: ObjectProperty
sub property of: acts upstream of
sub property of: acts upstream of or within, negative effect
property chain axiom: enables
property chain axiom: causally upstream of, negative effect
definition: c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
RO_0004050: acts upstream of
created by: cjm
creation date: 2018-01-26T23:53:22Z
in subset: valid for go gp2term

causally upstream of or within, negative effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004050: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:05Z

causally upstream of or within, positive effect
type: ObjectProperty
sub property of: causally upstream of or within
RO_0004049: causally upstream of or within
created by: cjm
creation date: 2018-03-13T23:55:19Z

regulates activity of
type: ObjectProperty
sub property of: causally influences
domain: material entity
range: material entity
definition: The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
IAO_0000117: Vasundra Touré

has start point
type: ObjectProperty
domain: anatomical axis
range: anatomical entity
definition: A relation between an axis and a part of an organism, in which the part defines the initial point of the axis.
database_cross_reference: :has_start_point
has_obo_namespace: spatial
id: has_start_point
shorthand: has_start_point
comment: Axes can be defined in a given species by subtyping the relevant axis type and stating a start and end point.

Axiom
annotated source: has start point
annotated property: definition
annotated target: A relation between an axis and a part of an organism, in which the part defines the initial point of the axis.
database_cross_reference: BSPO:cjm

parallel to
type: ObjectProperty
definition: x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.
has_obo_namespace: spatial
id: parallel_to

Axiom
annotated source: parallel to
annotated property: definition
annotated target: x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.
database_cross_reference: BSPO:curators

continuant
type: Class
subclass of: Restriction
  on property: part of
  all values from: continuant
disjoint with: occurrent
disjoint with: Restriction
  on property: part of
  some values from: occurrent
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.

occurrent
type: Class
subclass of: Restriction
  on property: part of
  all values from: occurrent
disjoint with: Restriction
  on property: part of
  some values from: continuant
definition: An entity that has temporal parts and that happens, unfolds or develops through time.

independent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: independent continuant
disjoint with: specifically dependent continuant
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.

process
type: Class
subclass of: occurrent
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.

disposition
type: Class
subclass of: realizable entity
disjoint with: role

realizable entity
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: realizable entity
disjoint with: quality
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.

quality
type: Class
subclass of: specifically dependent continuant
subclass of: Restriction
  on property: part of
  all values from: quality

specifically dependent continuant
type: Class
subclass of: continuant
subclass of: Restriction
  on property: part of
  all values from: specifically dependent continuant
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.

role
type: Class
subclass of: realizable entity
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.

function
type: Class
subclass of: disposition

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
disjoint with: Restriction
  on property: part of
  some values from: immaterial entity
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

immaterial entity
type: Class
subclass of: independent continuant
disjoint with: Restriction
  on property: has part
  some values from: material entity

left side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: left of
  some values from: right side
subclass of: Restriction
  on property: starts axis
  some values from: left-right axis
definition: The side of an organism that is left of the sagittal plane.
has_exact_synonym: left
has_obo_namespace: spatial
id: BSPO:0000000

Axiom
annotated source: left side
annotated property: definition
annotated target: The side of an organism that is left of the sagittal plane.
database_cross_reference: BSPO:cjm

upper side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: starts axis
  some values from: upper-lower axis
has_exact_synonym: upper
has_obo_namespace: spatial
id: BSPO:0000001
comment: Consider merging with superior side.

lower side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: finishes axis
  some values from: upper-lower axis
has_exact_synonym: lower
has_obo_namespace: spatial
id: BSPO:0000002
comment: Consider merging with inferior side.

deep-superficial gradient (obsolete)
type: Class
term replaced by: BSPO:0000021
has_obo_namespace: spatial
id: BSPO:00000021
comment: was made obsolete because the ID had too many digits
deprecated: true

deep side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: deep to
  some values from: superficial side
subclass of: Restriction
  on property: starts axis
  some values from: deep-superficial axis
has_exact_synonym: deep
has_obo_namespace: spatial
id: BSPO:0000003

superficial side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: finishes axis
  some values from: deep-superficial axis
has_exact_synonym: superficial
has_obo_namespace: spatial
id: BSPO:0000004

anatomical surface
type: Class
subclass of: anatomical boundary
definition: A 2D surface of an anatomical continuant.
database_cross_reference: FMA:24137
has_exact_synonym: surface
has_obo_namespace: spatial
id: BSPO:0000005
comment: to be merged into CARO

Axiom
annotated source: anatomical surface
annotated property: definition
annotated target: A 2D surface of an anatomical continuant.
database_cross_reference: BSPO:cjm

anatomical margin
type: Class
subclass of: anatomical region
definition: Fiat anatomical region extending a short distance from the boundary of an object inwards.
has_exact_synonym: edge
has_exact_synonym: margin
has_obo_namespace: spatial
id: BSPO:0000006

Axiom
annotated source: anatomical margin
annotated property: definition
annotated target: Fiat anatomical region extending a short distance from the boundary of an object inwards.
database_cross_reference: BSPO:cjm

right side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: finishes axis
  some values from: left-right axis
definition: The side of an organism that is right of the sagittal plane.
has_exact_synonym: right
has_obo_namespace: spatial
id: BSPO:0000007

Axiom
annotated source: right side
annotated property: definition
annotated target: The side of an organism that is right of the sagittal plane.
database_cross_reference: BSPO:cjm
database_cross_reference: BSPO:wd

parasagittal plane
type: Class
subclass of: sagittal plane
definition: Sagittal plane that divides a bilateral body into unequal left and right parts.
has_exact_synonym: parasagittal section
has_obo_namespace: spatial
id: BSPO:0000008

Axiom
annotated source: parasagittal plane
annotated property: definition
annotated target: Sagittal plane that divides a bilateral body into unequal left and right parts.
database_cross_reference: BSPO:mah

midsagittal plane
type: Class
subclass of: sagittal plane
definition: Sagittal plane that divides bilateral body into equal left and right parts.
database_cross_reference: FMA:74563
has_exact_synonym: median sagittal plane
has_exact_synonym: midline plane
has_exact_synonym: midsagittal section
has_obo_namespace: spatial
has_related_synonym: median plane
id: BSPO:0000009
comment: only in bilaterally symmetrical organisms

Axiom
annotated source: midsagittal plane
annotated property: definition
annotated target: Sagittal plane that divides bilateral body into equal left and right parts.
database_cross_reference: BSPO:mah

Axiom
annotated source: midsagittal plane
annotated property: has_exact_synonym
annotated target: median sagittal plane
database_cross_reference: FMA:74563

anatomical axis
type: Class
subclass of: anatomical line
subclass of: Restriction
  on property: passes through
  some values from: anatomical entity
definition: A straight line through space, intersecting an anatomical entity.
has_obo_namespace: spatial
id: BSPO:0000010
comment: Axis directions are defined in terms of axes.

Axiom
annotated source: anatomical axis
annotated property: definition
annotated target: A straight line through space, intersecting an anatomical entity.
database_cross_reference: BSPO:cjm

upper-lower axis
type: Class
subclass of: anatomical axis
definition: An anatomical axis determined by gravity.
has_obo_namespace: spatial
has_related_synonym: superior-inferior axis
id: BSPO:0000011

Axiom
annotated source: upper-lower axis
annotated property: definition
annotated target: An anatomical axis determined by gravity.
database_cross_reference: BSPO:cjm

deep-superficial axis
type: Class
subclass of: anatomical axis
definition: An axis that extends from an internal position to a more external position in the body or body part.
has_obo_namespace: spatial
id: BSPO:0000012
comment: Muscles are frequently categorized as 'deep', 'intermediate', and 'superficial'.

Axiom
annotated source: deep-superficial axis
annotated property: definition
annotated target: An axis that extends from an internal position to a more external position in the body or body part.
database_cross_reference: BSPO:PM

anterior-posterior axis
type: Class
equivalent class: Class
  intersection of: anatomical axis
  intersection of: Restriction
    on property: orthogonal to
    some values from: transverse plane
subclass of: anatomical axis
subclass of: Restriction
  on property: approximately perpendicular to
  some values from: dorsal-ventral axis
subclass of: Restriction
  on property: orthogonal to
  some values from: transverse plane
definition: An axis that extends through an organism from head end to opposite end of body or tail.
has_exact_synonym: A-P axis
has_exact_synonym: AP axis
has_exact_synonym: anteroposterior axis
has_narrow_synonym: cephalocaudal axis
has_narrow_synonym: craniocaudal axis
has_narrow_synonym: rostral/caudal
has_narrow_synonym: rostrocaudal axis
has_obo_namespace: spatial
has_related_synonym: longitudinal axis
id: BSPO:0000013
comment: In sponges, AP is used to indicate the direction of movement [in larval stage] (as it is in other metazoans that move, e.g., the basal bilaterians). [PM]

Axiom
annotated source: anterior-posterior axis
annotated property: definition
annotated target: An axis that extends through an organism from head end to opposite end of body or tail.
database_cross_reference: BSPO:cjm

Axiom
annotated source: anterior-posterior axis
annotated property: has_narrow_synonym
annotated target: cephalocaudal axis
database_cross_reference: http://en.wikipedia.org/wiki/Anatomical_terms_of_location

Axiom
annotated source: anterior-posterior axis
annotated property: has_narrow_synonym
annotated target: craniocaudal axis
has_synonym_type: synonym typically used in the context of vertebrate anatomy

Axiom
annotated source: anterior-posterior axis
annotated property: has_narrow_synonym
annotated target: rostral/caudal
has_synonym_type: synonym typically used in the context of vertebrate anatomy

Axiom
annotated source: anterior-posterior axis
annotated property: has_narrow_synonym
annotated target: rostrocaudal axis
has_synonym_type: synonym typically used in the context of vertebrate anatomy

apical-basal axis relative to substrate
type: Class
subclass of: anatomical axis
definition: An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure.
has_exact_synonym: apical/basal
has_obo_namespace: spatial
has_related_synonym: longitudinal axis
id: BSPO:0000014

Axiom
annotated source: apical-basal axis relative to substrate
annotated property: definition
annotated target: An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure.
database_cross_reference: BSPO:mah

proximal-distal axis
type: Class
subclass of: anatomical axis
definition: An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal).
has_exact_synonym: proximal/distal
has_exact_synonym: proximodistal
has_obo_namespace: spatial
id: BSPO:0000015
comment: In some communities, proximal and distal are used when specifying the position of parts of elements that are contained within the body, such as gill arches or vertebral spines. In these cases, use of the classes medial-lateral axis or medial-external axis are more appropriate.

Axiom
annotated source: proximal-distal axis
annotated property: definition
annotated target: An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal).
database_cross_reference: BSPO:curators
database_cross_reference: http://en.wikipedia.org/wiki/Anatomical_terms_of_location

dorsal-ventral axis
type: Class
equivalent class: Class
  intersection of: anatomical axis
  intersection of: Restriction
    on property: orthogonal to
    some values from: horizontal plane
subclass of: anatomical axis
subclass of: Restriction
  on property: orthogonal to
  some values from: horizontal plane
definition: An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body.
has_exact_synonym: D-V axis
has_exact_synonym: DV axis
has_exact_synonym: dorsoventral axis
has_narrow_synonym: anterior-posterior axis
has_obo_namespace: spatial
id: BSPO:0000016

Axiom
annotated source: dorsal-ventral axis
annotated property: definition
annotated target: An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body.
database_cross_reference: BSPO:curators

Axiom
annotated source: dorsal-ventral axis
annotated property: has_narrow_synonym
annotated target: anterior-posterior axis
has_synonym_type: synonym typically used in the context of human anatomy

left-right axis
type: Class
equivalent class: Class
  intersection of: anatomical axis
  intersection of: Restriction
    on property: orthogonal to
    some values from: sagittal plane
subclass of: anatomical axis
subclass of: Restriction
  on property: orthogonal to
  some values from: sagittal plane
definition: An axis that bisects an organism from left to right sides of body, through a sagittal plane.
has_exact_synonym: L-R axis
has_exact_synonym: LR axis
has_exact_synonym: R-L axis
has_exact_synonym: RL axis
has_exact_synonym: dextro-sinister axis
has_exact_synonym: left to right axis
has_exact_synonym: right to left axis
has_exact_synonym: right-left axis
has_obo_namespace: spatial
id: BSPO:0000017

Axiom
annotated source: left-right axis
annotated property: definition
annotated target: An axis that bisects an organism from left to right sides of body, through a sagittal plane.
database_cross_reference: BSPO:cjm

transverse plane
type: Class
subclass of: anatomical plane
definition: Anatomical plane that divides body into anterior and posterior parts.
database_cross_reference: FMA:12247
has_exact_synonym: axial plane
has_exact_synonym: axial section
has_exact_synonym: transverse section
has_obo_namespace: spatial
has_related_synonym: cross-section
id: BSPO:0000018

Axiom
annotated source: transverse plane
annotated property: definition
annotated target: Anatomical plane that divides body into anterior and posterior parts.
database_cross_reference: BSPO:mah

horizontal plane
type: Class
subclass of: anatomical plane
definition: Anatomical plane that divides bilateral body into dorsal and ventral parts.
database_cross_reference: FMA:52810
has_exact_synonym: frontal plane
has_exact_synonym: horizontal anatomical plane
has_exact_synonym: horizontal section
has_obo_namespace: spatial
has_related_synonym: coronal section
has_related_synonym: frontal section
id: BSPO:0000019

Axiom
annotated source: horizontal plane
annotated property: definition
annotated target: Anatomical plane that divides bilateral body into dorsal and ventral parts.
database_cross_reference: BSPO:mah

Axiom
annotated source: horizontal plane
annotated property: has_exact_synonym
annotated target: horizontal anatomical plane
database_cross_reference: FMA:52810

upper-lower gradient
type: Class
equivalent class: Class
  intersection of: anatomical gradient
  intersection of: Restriction
    on property: follows axis
    some values from: upper-lower axis
subclass of: anatomical gradient
subclass of: Restriction
  on property: follows axis
  some values from: upper-lower axis
definition: Anatomical gradient that is distributed along the upper-lower axis.
has_obo_namespace: spatial
id: BSPO:0000020

Axiom
annotated source: upper-lower gradient
annotated property: definition
annotated target: Anatomical gradient that is distributed along the upper-lower axis.
database_cross_reference: BSPO:wd

deep-superficial gradient
type: Class
equivalent class: Class
  intersection of: anatomical gradient
  intersection of: Restriction
    on property: follows axis
    some values from: deep-superficial axis
subclass of: anatomical gradient
subclass of: Restriction
  on property: follows axis
  some values from: deep-superficial axis
definition: Anatomical gradient that is distributed along the deep-superficial axis.
has_obo_namespace: spatial
id: BSPO:0000021

Axiom
annotated source: deep-superficial gradient
annotated property: definition
annotated target: Anatomical gradient that is distributed along the deep-superficial axis.
database_cross_reference: BSPO:wd

superior side
type: Class
subclass of: anatomical side
definition: The side that is higher relative to the substrate.
has_exact_synonym: superior
has_obo_namespace: spatial
has_related_synonym: cranial
id: BSPO:0000022

Axiom
annotated source: superior side
annotated property: definition
annotated target: The side that is higher relative to the substrate.
database_cross_reference: BSPO:curators

apical-basal gradient
type: Class
equivalent class: Class
  intersection of: anatomical gradient
  intersection of: Restriction
    on property: follows axis
    some values from: apical-basal axis relative to substrate
subclass of: anatomical gradient
subclass of: Restriction
  on property: follows axis
  some values from: apical-basal axis relative to substrate
definition: Anatomical gradient that is distributed along the apical-basal axis.
has_obo_namespace: spatial
id: BSPO:0000023

Axiom
annotated source: apical-basal gradient
annotated property: definition
annotated target: Anatomical gradient that is distributed along the apical-basal axis.
database_cross_reference: BSPO:wd

proximal-distal gradient
type: Class
equivalent class: Class
  intersection of: anatomical gradient
  intersection of: Restriction
    on property: follows axis
    some values from: proximal-distal axis
subclass of: anatomical gradient
subclass of: Restriction
  on property: follows axis
  some values from: proximal-distal axis
definition: Anatomical gradient that is distributed along the proximal-distal axis.
has_obo_namespace: spatial
id: BSPO:0000024

Axiom
annotated source: proximal-distal gradient
annotated property: definition
annotated target: Anatomical gradient that is distributed along the proximal-distal axis.
database_cross_reference: BSPO:wd

inferior side
type: Class
subclass of: anatomical side
definition: The side that is lower relative to the substrate.
has_exact_synonym: inferior
has_obo_namespace: spatial
has_related_synonym: caudal
id: BSPO:0000025

Axiom
annotated source: inferior side
annotated property: definition
annotated target: The side that is lower relative to the substrate.
database_cross_reference: BSPO:curators

antero-dorsal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
subclass of: anterior region
subclass of: dorsal region
definition: Anatomical region that overlaps the anterior and dorsal regions of a body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:01:38Z
has_exact_synonym: anterodorsal region
has_obo_namespace: spatial
id: BSPO:0000026

Axiom
annotated source: antero-dorsal region
annotated property: definition
annotated target: Anatomical region that overlaps the anterior and dorsal regions of a body or body part.
database_cross_reference: BSPO:wd

antero-ventral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: anterior region
subclass of: ventral region
definition: Anatomical region that overlaps the anterior and ventral regions of a body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:04:59Z
has_exact_synonym: anteroventral region
has_obo_namespace: spatial
id: BSPO:0000027

Axiom
annotated source: antero-ventral region
annotated property: definition
annotated target: Anatomical region that overlaps the anterior and ventral regions of a body or body part.
database_cross_reference: BSPO:wd

postero-lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: posterior region
subclass of: lateral region
definition: Anatomical region that overlaps the posterior and lateral regions of the body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:06:01Z
has_exact_synonym: posterolateral region
has_obo_namespace: spatial
id: BSPO:0000028

Axiom
annotated source: postero-lateral region
annotated property: definition
annotated target: Anatomical region that overlaps the posterior and lateral regions of the body or body part.
database_cross_reference: BSPO:wd

antero-lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: anterior region
subclass of: lateral region
definition: Anatomical region that overlaps the anterior and lateral regions of a body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:07:18Z
has_exact_synonym: anterolateral region
has_obo_namespace: spatial
id: BSPO:0000029

Axiom
annotated source: antero-lateral region
annotated property: definition
annotated target: Anatomical region that overlaps the anterior and lateral regions of a body or body part.
database_cross_reference: BSPO:wd

postero-dorsal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
subclass of: posterior region
subclass of: dorsal region
definition: Anatomical region that overlaps the posterior and dorsal regions of the body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:08:13Z
has_exact_synonym: posterodorsal region
has_obo_namespace: spatial
id: BSPO:0000030

Axiom
annotated source: postero-dorsal region
annotated property: definition
annotated target: Anatomical region that overlaps the posterior and dorsal regions of the body or body part.
database_cross_reference: BSPO:wd

upper region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: upper side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: upper side
has_obo_namespace: spatial
id: BSPO:0000031

lower region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: lower side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: lower side
has_obo_namespace: spatial
id: BSPO:0000032

deep region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: deep side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: deep side
definition: Anatomical region located deep within an organism or structure.
has_obo_namespace: spatial
id: BSPO:0000033

Axiom
annotated source: deep region
annotated property: definition
annotated target: Anatomical region located deep within an organism or structure.
database_cross_reference: BSPO:wd

superficial region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: superficial side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: superficial side
definition: Anatomical region superficially located on the body or body part.
has_obo_namespace: spatial
id: BSPO:0000034

Axiom
annotated source: superficial region
annotated property: definition
annotated target: Anatomical region superficially located on the body or body part.
database_cross_reference: BSPO:wd

postero-ventral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: posterior region
subclass of: ventral region
definition: Anatomical region that overlaps the posterior and ventral regions of a body or body part.
created by: Melissa Haendel
creation date: 2009-06-15T01:08:38Z
has_exact_synonym: posteroventral region
has_obo_namespace: spatial
id: BSPO:0000035

Axiom
annotated source: postero-ventral region
annotated property: definition
annotated target: Anatomical region that overlaps the posterior and ventral regions of a body or body part.
database_cross_reference: BSPO:wd

anterior-most region
type: Class
subclass of: anterior region
created by: Melissa Haendel
creation date: 2009-06-16T08:49:03Z
has_exact_synonym: anterior-most
has_exact_synonym: anteriormost
has_obo_namespace: spatial
id: BSPO:0000036

posterior-most region
type: Class
subclass of: posterior region
created by: Melissa Haendel
creation date: 2009-06-16T08:49:50Z
has_exact_synonym: posterior-most
has_exact_synonym: posteriormost
has_obo_namespace: spatial
id: BSPO:0000037

dorsal-most region
type: Class
subclass of: dorsal region
created by: Melissa Haendel
creation date: 2009-06-16T08:50:26Z
has_exact_synonym: dorsal-most
has_exact_synonym: dorsalmost
has_obo_namespace: spatial
id: BSPO:0000038

ventral-most region
type: Class
subclass of: ventral region
created by: Melissa Haendel
creation date: 2009-06-16T08:51:07Z
has_exact_synonym: ventral-most
has_exact_synonym: ventralmost
has_obo_namespace: spatial
id: BSPO:0000039

upper/lower compartment boundary
type: Class
equivalent class: Class
  intersection of: anatomical compartment boundary
  intersection of: Restriction
    on property: has axis
    some values from: upper-lower axis
subclass of: anatomical compartment boundary
subclass of: Restriction
  on property: has axis
  some values from: upper-lower axis
has_obo_namespace: spatial
id: BSPO:0000040

deep/superficial compartment boundary
type: Class
equivalent class: Class
  intersection of: anatomical compartment boundary
  intersection of: Restriction
    on property: has axis
    some values from: deep-superficial axis
subclass of: anatomical compartment boundary
subclass of: Restriction
  on property: has axis
  some values from: deep-superficial axis
has_obo_namespace: spatial
id: BSPO:0000041

antero-medial margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
subclass of: antero-medial region
subclass of: anterior margin
subclass of: medial margin
definition: Anatomical margin that is located on the antero-medial region of the body or body part.
created by: Melissa Haendel
creation date: 2009-09-10T08:49:57Z
has_exact_synonym: anteromedial margin
has_obo_namespace: spatial
id: BSPO:0000042

Axiom
annotated source: antero-medial margin
annotated property: definition
annotated target: Anatomical margin that is located on the antero-medial region of the body or body part.
database_cross_reference: BSPO:wd

apical/basal compartment boundary
type: Class
equivalent class: Class
  intersection of: anatomical compartment boundary
  intersection of: Restriction
    on property: has axis
    some values from: apical-basal axis relative to substrate
subclass of: anatomical compartment boundary
subclass of: Restriction
  on property: has axis
  some values from: apical-basal axis relative to substrate
has_obo_namespace: spatial
id: BSPO:0000043

proximal/distal compartment boundary
type: Class
equivalent class: Class
  intersection of: anatomical compartment boundary
  intersection of: Restriction
    on property: has axis
    some values from: proximal-distal axis
subclass of: anatomical compartment boundary
subclass of: Restriction
  on property: has axis
  some values from: proximal-distal axis
has_obo_namespace: spatial
id: BSPO:0000044

antero-lateral margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: antero-lateral region
subclass of: anterior margin
subclass of: lateral margin
definition: Anatomical margin that is located on the antero-lateral region of the body or body part.
created by: Melissa Haendel
creation date: 2009-09-10T08:50:37Z
has_exact_synonym: anterolateral margin
has_obo_namespace: spatial
id: BSPO:0000045

Axiom
annotated source: antero-lateral margin
annotated property: definition
annotated target: Anatomical margin that is located on the antero-lateral region of the body or body part.
database_cross_reference: BSPO:wd

postero-medial margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
subclass of: postero-medial region
subclass of: posterior margin
subclass of: medial margin
definition: Anatomical margin that is located on the postero-medial region of the body or body part.
created by: Melissa Haendel
creation date: 2009-09-10T08:51:07Z
has_exact_synonym: posteromedial margin
has_obo_namespace: spatial
id: BSPO:0000046

Axiom
annotated source: postero-medial margin
annotated property: definition
annotated target: Anatomical margin that is located on the postero-medial region of the body or body part.
database_cross_reference: BSPO:wd

postero-lateral margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: postero-lateral region
subclass of: posterior margin
subclass of: lateral margin
definition: Anatomical margin that is located on the postero-lateral region of the body or body part.
created by: Melissa Haendel
creation date: 2009-09-10T08:51:42Z
has_exact_synonym: posterolateral margin
has_obo_namespace: spatial
id: BSPO:0000047

Axiom
annotated source: postero-lateral margin
annotated property: definition
annotated target: Anatomical margin that is located on the postero-lateral region of the body or body part.
database_cross_reference: BSPO:wd

dorso-medial margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
subclass of: dorso-medial region
subclass of: dorsal margin
subclass of: medial margin
definition: Anatomical margin that is located on the dorso-medial region of the body or body part.
created by: Melissa Haendel
creation date: 2009-09-10T08:52:04Z
has_exact_synonym: dorso-medial margin
has_obo_namespace: spatial
id: BSPO:0000048

Axiom
annotated source: dorso-medial margin
annotated property: definition
annotated target: Anatomical margin that is located on the dorso-medial region of the body or body part.
database_cross_reference: BSPO:wd

ventro-medial margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: ventro-medial region
subclass of: medial margin
subclass of: ventral margin
definition: Anatomical margin that is located on the ventro-medial region of the body or body part.
created by: Melissa Haendel
creation date: 2009-09-10T08:52:48Z
has_exact_synonym: ventromedial margin
has_obo_namespace: spatial
id: BSPO:0000049

Axiom
annotated source: ventro-medial margin
annotated property: definition
annotated target: Anatomical margin that is located on the ventro-medial region of the body or body part.
database_cross_reference: BSPO:wd

antero-medial region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
subclass of: anterior region
subclass of: medial region
definition: Anatomical region that overlaps the anterior and medial regions of the body or body part.
created by: Melissa Haendel
creation date: 2009-09-10T08:55:32Z
has_exact_synonym: anteromedial region
has_obo_namespace: spatial
id: BSPO:0000050

Axiom
annotated source: antero-medial region
annotated property: definition
annotated target: Anatomical region that overlaps the anterior and medial regions of the body or body part.
database_cross_reference: BSPO:wd

anatomical gradient
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis.
database_cross_reference: FBql:00005254
has_obo_namespace: spatial
id: BSPO:0000051

Axiom
annotated source: anatomical gradient
annotated property: definition
annotated target: Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis.
database_cross_reference: BSPO:cjm

anterior-posterior gradient
type: Class
equivalent class: Class
  intersection of: anatomical gradient
  intersection of: Restriction
    on property: has axis
    some values from: anterior-posterior axis
subclass of: anatomical gradient
subclass of: Restriction
  on property: has axis
  some values from: anterior-posterior axis
definition: Anatomical gradient that is distributed along the anterior-posterior axis.
database_cross_reference: FBcv:0000142
database_cross_reference: FBql:00005256
has_obo_namespace: spatial
id: BSPO:0000052

Axiom
annotated source: anterior-posterior gradient
annotated property: definition
annotated target: Anatomical gradient that is distributed along the anterior-posterior axis.
database_cross_reference: BSPO:wd

dorsal-ventral gradient
type: Class
equivalent class: Class
  intersection of: anatomical gradient
  intersection of: Restriction
    on property: has axis
    some values from: dorsal-ventral axis
subclass of: anatomical gradient
subclass of: Restriction
  on property: has axis
  some values from: dorsal-ventral axis
definition: Anatomical gradient that is distributed along the dorsal-ventral axis.
database_cross_reference: FBcv:0000143
database_cross_reference: FBql:00005255
has_obo_namespace: spatial
id: BSPO:0000053

Axiom
annotated source: dorsal-ventral gradient
annotated property: definition
annotated target: Anatomical gradient that is distributed along the dorsal-ventral axis.
database_cross_reference: BSPO:wd

anatomical side
type: Class
subclass of: anatomical region
definition: An anatomical region bounded by a plane perpendicular to an axis through the middle.
database_cross_reference: FBql:00005841
has_obo_namespace: spatial
id: BSPO:0000054

Axiom
annotated source: anatomical side
annotated property: definition
annotated target: An anatomical region bounded by a plane perpendicular to an axis through the middle.
database_cross_reference: BSPO:cjm

anterior side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: anterior to
  some values from: posterior side
subclass of: Restriction
  on property: opposite to
  some values from: posterior side
subclass of: Restriction
  on property: starts axis
  some values from: anterior-posterior axis
definition: An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane.
database_cross_reference: FBcv:0000053
database_cross_reference: FBql:00005848
has_exact_synonym: anterior
has_exact_synonym: rostral
has_obo_namespace: spatial
id: BSPO:0000055

Axiom
annotated source: anterior side
annotated property: definition
annotated target: An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane.
database_cross_reference: BSPO:RW

posterior side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: posterior to
  some values from: anterior side
subclass of: Restriction
  on property: finishes axis
  some values from: anterior-posterior axis
definition: An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane.
database_cross_reference: FBcv:0000065
database_cross_reference: FBql:00005849
has_exact_synonym: posterior
has_narrow_synonym: caudal
has_obo_namespace: spatial
id: BSPO:0000056

Axiom
annotated source: posterior side
annotated property: definition
annotated target: An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane.
database_cross_reference: BSPO:RW
database_cross_reference: BSPO:wd

Axiom
annotated source: posterior side
annotated property: has_narrow_synonym
annotated target: caudal
has_synonym_type: synonym typically used in the context of vertebrate anatomy

apical side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: opposite to
  some values from: basal side
subclass of: Restriction
  on property: starts axis
  some values from: apical-basal axis relative to substrate
definition: Anatomical side that is located on the apical end of an organism or structure.
database_cross_reference: FBcv:0000054
database_cross_reference: FBql:00005854
has_exact_synonym: apical
has_obo_namespace: spatial
id: BSPO:0000057

Axiom
annotated source: apical side
annotated property: definition
annotated target: Anatomical side that is located on the apical end of an organism or structure.
database_cross_reference: BSPO:wd

basal side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: finishes axis
  some values from: apical-basal axis relative to substrate
definition: Anatomical side that is located on the basal end of an organism or structure.
database_cross_reference: FBcv:0000055
database_cross_reference: FBql:00005855
has_exact_synonym: basal
has_obo_namespace: spatial
id: BSPO:0000058
comment: The part of the organism attached to a substrate. Axis of symmetry.

Axiom
annotated source: basal side
annotated property: definition
annotated target: Anatomical side that is located on the basal end of an organism or structure.
database_cross_reference: BSPO:wd

central side
type: Class
subclass of: anatomical side
definition: Anatomical side that is centrally located on an organism or structure.
database_cross_reference: FBcv:0000056
database_cross_reference: FBql:00015851
has_exact_synonym: central
has_obo_namespace: spatial
id: BSPO:0000059
comment: central is not an axis direction

Axiom
annotated source: central side
annotated property: definition
annotated target: Anatomical side that is centrally located on an organism or structure.
database_cross_reference: BSPO:wd

contralateral side
type: Class
subclass of: anatomical side
definition: On the opposite side.
database_cross_reference: FBcv:0000057
database_cross_reference: FBql:00005851
has_exact_synonym: contralateral
has_obo_namespace: spatial
id: BSPO:0000060
comment: inherited from flybase cv. not clear how this would be used. Suggest we obsolete, and use the corresponding relation.

Axiom
annotated source: contralateral side
annotated property: definition
annotated target: On the opposite side.
database_cross_reference: BSPO:cjm

proximal side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: opposite to
  some values from: distal side
subclass of: Restriction
  on property: starts axis
  some values from: proximal-distal axis
database_cross_reference: FBcv:0000066
database_cross_reference: FBql:00005852
has_exact_synonym: proximal
has_obo_namespace: spatial
id: BSPO:0000061

distal side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: distal to
  some values from: proximal side
subclass of: Restriction
  on property: finishes axis
  some values from: proximal-distal axis
definition: Anatomical side that is distally located on an organism or structure.
database_cross_reference: FBcv:0000058
database_cross_reference: FBql:00005853
has_exact_synonym: distal
has_obo_namespace: spatial
id: BSPO:0000062

Axiom
annotated source: distal side
annotated property: definition
annotated target: Anatomical side that is distally located on an organism or structure.
database_cross_reference: BSPO:wd

dorsal side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: dorsal to
  some values from: lateral side
subclass of: Restriction
  on property: opposite to
  some values from: ventral side
subclass of: Restriction
  on property: starts axis
  some values from: dorsal-ventral axis
definition: An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane.
database_cross_reference: FBcv:0000059
database_cross_reference: FBql:00005842
has_exact_synonym: dorsal
has_obo_namespace: spatial
id: BSPO:0000063

Axiom
annotated source: dorsal side
annotated property: definition
annotated target: An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane.
database_cross_reference: BSPO:wd

postero-medial region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
subclass of: posterior region
subclass of: medial region
definition: Anatomical region that overlaps the posterior and medial regions of the body or body part.
created by: Melissa Haendel
creation date: 2009-09-10T08:56:39Z
has_exact_synonym: posteromedial region
has_obo_namespace: spatial
id: BSPO:0000064

Axiom
annotated source: postero-medial region
annotated property: definition
annotated target: Anatomical region that overlaps the posterior and medial regions of the body or body part.
database_cross_reference: BSPO:wd

ipsilateral side
type: Class
subclass of: anatomical side
definition: On the same side
database_cross_reference: FBcv:0000062
database_cross_reference: FBql:00005850
has_exact_synonym: ipsilateral
has_obo_namespace: spatial
id: BSPO:0000065
comment: inherited from flybase cv. not clear how this would be used. Suggest we obsolete, and use the corresponding relation.

Axiom
annotated source: ipsilateral side
annotated property: definition
annotated target: On the same side
database_cross_reference: BSPO:cjm

lateral side
type: Class
subclass of: anatomical side
database_cross_reference: FBcv:0000063
database_cross_reference: FBql:00005844
has_exact_synonym: lateral
has_obo_namespace: spatial
id: BSPO:0000066

medial side
type: Class
subclass of: anatomical side
database_cross_reference: FBcv:0000064
database_cross_reference: FBql:00005847
has_exact_synonym: medial
has_obo_namespace: spatial
id: BSPO:0000067
comment: a point in the centre of the organism (where the left-right axis intersects the midsagittal plane)

ventral side
type: Class
subclass of: anatomical side
subclass of: Restriction
  on property: finishes axis
  some values from: dorsal-ventral axis
definition: An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane.
database_cross_reference: FBcv:0000070
database_cross_reference: FBql:00005843
has_exact_synonym: ventral
has_obo_namespace: spatial
id: BSPO:0000068

Axiom
annotated source: ventral side
annotated property: definition
annotated target: An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane.
database_cross_reference: BSPO:RW
database_cross_reference: BSPO:wd

dorso-medial region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
subclass of: dorsal region
subclass of: medial region
definition: Anatomical region that overlaps the dorsal and medial regions of the body or body part.
created by: Melissa Haendel
creation date: 2009-09-10T08:57:22Z
has_exact_synonym: dorsomedial region
has_obo_namespace: spatial
id: BSPO:0000069

Axiom
annotated source: dorso-medial region
annotated property: definition
annotated target: Anatomical region that overlaps the dorsal and medial regions of the body or body part.
database_cross_reference: BSPO:wd

anatomical region
type: Class
subclass of: anatomical structure
definition: A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.
database_cross_reference: FBql:00005841
has_obo_namespace: spatial
id: BSPO:0000070
comment: to be merged into CARO

Axiom
annotated source: anatomical region
annotated property: definition
annotated target: A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.
database_cross_reference: BSPO:cjm

anterior region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: anterior side
definition: Anatomical region anteriorly located on the body or body part.
database_cross_reference: FBql:00005848
has_obo_namespace: spatial
id: BSPO:0000071

Axiom
annotated source: anterior region
annotated property: definition
annotated target: Anatomical region anteriorly located on the body or body part.
database_cross_reference: BSPO:wd

posterior region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: posterior side
definition: Anatomical region posteriorly located on the body or body part.
database_cross_reference: FBql:00005849
has_obo_namespace: spatial
id: BSPO:0000072

Axiom
annotated source: posterior region
annotated property: definition
annotated target: Anatomical region posteriorly located on the body or body part.
database_cross_reference: BSPO:wd

apical region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: apical side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: apical side
definition: Anatomical region located on the apical end on the body or body part.
database_cross_reference: FBql:00005854
has_obo_namespace: spatial
id: BSPO:0000073

Axiom
annotated source: apical region
annotated property: definition
annotated target: Anatomical region located on the apical end on the body or body part.
database_cross_reference: BSPO:wd

basal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: basal side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: basal side
definition: Anatomical region located basally on the body or body part.
database_cross_reference: FBql:00005855
has_obo_namespace: spatial
id: BSPO:0000074

Axiom
annotated source: basal region
annotated property: definition
annotated target: Anatomical region located basally on the body or body part.
database_cross_reference: BSPO:wd

central region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: central side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: central side
definition: Anatomical region centrally located on the body or body part.
database_cross_reference: FBql:00015851
has_obo_namespace: spatial
id: BSPO:0000075

Axiom
annotated source: central region
annotated property: definition
annotated target: Anatomical region centrally located on the body or body part.
database_cross_reference: BSPO:wd

contralateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: contralateral side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: contralateral side
database_cross_reference: FBql:00005851
has_obo_namespace: spatial
id: BSPO:0000076
comment: inherited from flybase cv. not clear how this would be used

proximal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: proximal side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: proximal side
definition: Anatomical region proximally located on the body or body part.
database_cross_reference: FBql:00005852
has_obo_namespace: spatial
id: BSPO:0000077

Axiom
annotated source: proximal region
annotated property: definition
annotated target: Anatomical region proximally located on the body or body part.
database_cross_reference: BSPO:wd

distal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: distal side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: distal side
definition: Anatomical region distally located on the body or body part.
database_cross_reference: FBql:00005853
has_obo_namespace: spatial
id: BSPO:0000078

Axiom
annotated source: distal region
annotated property: definition
annotated target: Anatomical region distally located on the body or body part.
database_cross_reference: BSPO:wd

dorsal region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: dorsal side
definition: Anatomical region dorsally located on the body or body part.
database_cross_reference: FBql:00005842
has_obo_namespace: spatial
id: BSPO:0000079

Axiom
annotated source: dorsal region
annotated property: definition
annotated target: Anatomical region dorsally located on the body or body part.
database_cross_reference: BSPO:wd

dorso-lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: dorsal region
subclass of: lateral region
definition: Anatomical region that overlaps the dorsal and lateral regions of a body or body part.
database_cross_reference: FBql:00005845
has_exact_synonym: dorsolateral region
has_obo_namespace: spatial
id: BSPO:0000080

Axiom
annotated source: dorso-lateral region
annotated property: definition
annotated target: Anatomical region that overlaps the dorsal and lateral regions of a body or body part.
database_cross_reference: BSPO:wd

ipsilateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: ipsilateral side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: ipsilateral side
database_cross_reference: FBql:00005850
has_obo_namespace: spatial
id: BSPO:0000081

lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: lateral side
definition: Anatomical region laterally located on the body or body part.
database_cross_reference: FBql:00005844
has_obo_namespace: spatial
id: BSPO:0000082

Axiom
annotated source: lateral region
annotated property: definition
annotated target: Anatomical region laterally located on the body or body part.
database_cross_reference: BSPO:wd

medial region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: medial side
definition: Anatomical region medially located on the body or body part.
database_cross_reference: FBql:00005847
has_obo_namespace: spatial
id: BSPO:0000083

Axiom
annotated source: medial region
annotated property: definition
annotated target: Anatomical region medially located on the body or body part.
database_cross_reference: BSPO:wd

ventral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: ventral side
definition: Anatomical region ventrally located on the body or body part.
database_cross_reference: FBql:00005843
has_obo_namespace: spatial
id: BSPO:0000084

Axiom
annotated source: ventral region
annotated property: definition
annotated target: Anatomical region ventrally located on the body or body part.
database_cross_reference: BSPO:wd

ventro-lateral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: lateral region
subclass of: ventral region
definition: Anatomical region that overlaps the ventral and lateral regions of a body or body part.
database_cross_reference: FBql:00005846
has_exact_synonym: ventrolateral region
has_obo_namespace: spatial
id: BSPO:0000085
comment: This is an example of a composition of two axis positions.

Axiom
annotated source: ventro-lateral region
annotated property: definition
annotated target: Anatomical region that overlaps the ventral and lateral regions of a body or body part.
database_cross_reference: BSPO:wd

anatomical compartment
type: Class
subclass of: anatomical structure
database_cross_reference: FBql:00005873
database_cross_reference: FMA:9647
has_obo_namespace: spatial
id: BSPO:0000086
comment: to be merged into CARO

anterior compartment
type: Class
subclass of: anatomical compartment
database_cross_reference: FBcv:0000031
database_cross_reference: FBql:00005874
has_obo_namespace: spatial
id: BSPO:0000087

compartment boundary
type: Class
subclass of: anatomical compartment
database_cross_reference: FBcv:0000032
database_cross_reference: FBql:00005878
has_obo_namespace: spatial
id: BSPO:0000088

dorsal compartment
type: Class
subclass of: anatomical compartment
database_cross_reference: FBcv:0000035
database_cross_reference: FBql:00005876
has_obo_namespace: spatial
id: BSPO:0000089

posterior compartment
type: Class
subclass of: anatomical compartment
database_cross_reference: FBcv:0000036
database_cross_reference: FBql:00005875
has_obo_namespace: spatial
id: BSPO:0000090

ventral compartment
type: Class
subclass of: anatomical compartment
database_cross_reference: FBcv:0000037
database_cross_reference: FBql:00005877
has_obo_namespace: spatial
id: BSPO:0000091

anatomical compartment boundary
type: Class
subclass of: anatomical boundary
database_cross_reference: FBql:00005881
has_obo_namespace: spatial
id: BSPO:0000092
comment: to be merged into CARO

anterior/posterior compartment boundary
type: Class
subclass of: anatomical compartment boundary
database_cross_reference: FBcv:0000033
database_cross_reference: FBql:00005880
has_obo_namespace: spatial
id: BSPO:0000093

dorsal/ventral compartment boundary
type: Class
subclass of: anatomical compartment boundary
database_cross_reference: FBcv:0000034
database_cross_reference: FBql:00005879
has_obo_namespace: spatial
id: BSPO:0000094

ventro-medial region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: medial region
subclass of: ventral region
definition: The region corresponding to the ventral region of the entity, towards the midline.
created by: Melissa Haendel
creation date: 2009-09-10T08:57:54Z
has_exact_synonym: medioventral region
has_exact_synonym: ventromedial region
has_obo_namespace: spatial
id: BSPO:0000112

Axiom
annotated source: ventro-medial region
annotated property: definition
annotated target: The region corresponding to the ventral region of the entity, towards the midline.
database_cross_reference: BSPO:wd

peripheral region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: peripheral side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: peripheral side
definition: Anatomical region peripherally located on the body or body part.
has_obo_namespace: spatial
id: BSPO:0000127

Axiom
annotated source: peripheral region
annotated property: definition
annotated target: Anatomical region peripherally located on the body or body part.
database_cross_reference: BSPO:wd

axial region
type: Class
equivalent class: Class
  intersection of: anatomical region
  intersection of: Restriction
    on property: overlaps
    some values from: axial side
subclass of: anatomical region
subclass of: Restriction
  on property: overlaps
  some values from: axial side
has_obo_namespace: spatial
id: BSPO:0000128

peripheral side
type: Class
subclass of: anatomical side
has_obo_namespace: spatial
id: BSPO:0000129

axial side
type: Class
subclass of: anatomical side
has_obo_namespace: spatial
id: BSPO:0000130

adaxial-abaxial axis
type: Class
subclass of: anatomical axis
definition: An anatomical axis that extends from the side of the anatomical entity that is closer to an axis (adaxial) to the side that is further from the same axis (abaxial).
created by: wasila.dahdul
creation date: 2013-07-02T11:20:29Z
has_exact_synonym: AA axis
has_obo_namespace: spatial
has_related_synonym: dorsal-ventral axis
id: BSPO:0000195

Axiom
annotated source: adaxial-abaxial axis
annotated property: definition
annotated target: An anatomical axis that extends from the side of the anatomical entity that is closer to an axis (adaxial) to the side that is further from the same axis (abaxial).
database_cross_reference: BSPO:RW

medial-external axis
type: Class
subclass of: anatomical axis
definition: An anatomical axis that extends from the center of the body outwards or externally.
created by: wasila.dahdul
creation date: 2013-07-02T11:21:42Z
has_obo_namespace: spatial
has_related_synonym: proximal-distal axis
id: BSPO:0000196
comment: The medial-external axis could apply to a sphere-shaped body.

Axiom
annotated source: medial-external axis
annotated property: definition
annotated target: An anatomical axis that extends from the center of the body outwards or externally.
database_cross_reference: BSPO:curators

medial-radial axis
type: Class
subclass of: medial-external axis
definition: An anatomical axis that is perpendicular to an apical/basal axis or proximal/distal axis and extends from the center of an axis (shoot axis or root in the case of plants) to any point on the exterior of the axis.
created by: wasila.dahdul
creation date: 2013-07-02T11:23:31Z
has_exact_synonym: M-R axis
has_exact_synonym: MR axis
has_obo_namespace: spatial
id: BSPO:0000197
comment: In plants, lateral growth (http://purl.obolibrary.org/obo/GO_0080190) run is along the medial/radial axis (from medial to radial) [RW]. Also applies to radially symmetrical animals such as sea urchins, cnidarians [PM] or applies to more-or-less cylindrical body parts in animals, like limbs.

Axiom
annotated source: medial-radial axis
annotated property: definition
annotated target: An anatomical axis that is perpendicular to an apical/basal axis or proximal/distal axis and extends from the center of an axis (shoot axis or root in the case of plants) to any point on the exterior of the axis.
database_cross_reference: BSPO:curators

oral-aboral axis
type: Class
subclass of: anatomical axis
definition: An axis that extends from the oral opening to the furthest point in an organism that is directly opposite.
created by: wasila.dahdul
creation date: 2013-07-02T11:29:33Z
has_obo_namespace: spatial
id: BSPO:0000198

Axiom
annotated source: oral-aboral axis
annotated property: definition
annotated target: An axis that extends from the oral opening to the furthest point in an organism that is directly opposite.
database_cross_reference: BSPO:PM

animal-vegetal axis
type: Class
subclass of: anatomical axis
definition: An axis that extends from the animal end of an egg or early embryo to the opposite, vegetal end. In animals with yolk-bearing eggs, the vegetal end is the yolk bearing pole. (pertains to animals only - both vertebrate and invertebrate embryos).
created by: wasila.dahdul
creation date: 2013-07-02T11:30:13Z
has_exact_synonym: A-V axis
has_exact_synonym: AV axis
has_exact_synonym: animal/vegetal axis
has_obo_namespace: spatial
id: BSPO:0000199

Axiom
annotated source: animal-vegetal axis
annotated property: definition
annotated target: An axis that extends from the animal end of an egg or early embryo to the opposite, vegetal end. In animals with yolk-bearing eggs, the vegetal end is the yolk bearing pole. (pertains to animals only - both vertebrate and invertebrate embryos).
database_cross_reference: BSPO:PM

apical-basal axis relative to direction of growth
type: Class
subclass of: anatomical axis
definition: An axis of a plant structure that is determined by the direction of apical growth, either by an apical meristem or an apical cell. Apical is toward the direction of apical growth: toward the tip of a growing shoot axis, root, thallus, or non-vascular leaf. Basal is away from the direction of apical growth: toward the root-shoot junction in the case of the primary root or stem, toward the primary root or stem for higher order roots or branches, toward the point of attachment for non-vascular leaves, and toward the original point of growth (as determined in the embryo) for thalli.
has_obo_namespace: spatial
id: BSPO:0000200
comment: Plant structures that do not grow from an apical meristem, such as vascular leaves or petals, should be described using the proximal-distal axis. The proximal-distal axis may also be used for branches or lateral roots, and, in those cases, is concordant with the apical-basal axis.

Axiom
annotated source: apical-basal axis relative to direction of growth
annotated property: definition
annotated target: An axis of a plant structure that is determined by the direction of apical growth, either by an apical meristem or an apical cell. Apical is toward the direction of apical growth: toward the tip of a growing shoot axis, root, thallus, or non-vascular leaf. Basal is away from the direction of apical growth: toward the root-shoot junction in the case of the primary root or stem, toward the primary root or stem for higher order roots or branches, toward the point of attachment for non-vascular leaves, and toward the original point of growth (as determined in the embryo) for thalli.
database_cross_reference: BSPO:RW

tangential plane
type: Class
subclass of: anatomical plane
definition: Anatomical plane that is perpendicular to a radial plane.
created by: wasila.dahdul
creation date: 2014-01-22T15:34:31Z
has_obo_namespace: spatial
id: BSPO:0000201
comment: Need to add logical definitions.

Axiom
annotated source: tangential plane
annotated property: definition
annotated target: Anatomical plane that is perpendicular to a radial plane.
database_cross_reference: BSPO:wd

radial plane
type: Class
subclass of: anatomical plane
definition: Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis.
created by: wasila.dahdul
creation date: 2014-01-22T15:34:02Z
has_obo_namespace: spatial
id: BSPO:0000202
comment: Need to add logical definitions.

Axiom
annotated source: radial plane
annotated property: definition
annotated target: Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis.
database_cross_reference: BSPO:wd

anterior surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: anterior side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: anterior side
definition: Anatomical surface that is located on the anterior side of the body or body part.
database_cross_reference: FBql:00005848
has_obo_namespace: spatial
id: BSPO:0000371

Axiom
annotated source: anterior surface
annotated property: definition
annotated target: Anatomical surface that is located on the anterior side of the body or body part.
database_cross_reference: BSPO:wd

posterior surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: posterior side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: posterior side
definition: Anatomical surface that is located on the posterior side of the body or body part.
database_cross_reference: FBql:00005849
has_obo_namespace: spatial
id: BSPO:0000372

Axiom
annotated source: posterior surface
annotated property: definition
annotated target: Anatomical surface that is located on the posterior side of the body or body part.
database_cross_reference: BSPO:wd

apical surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: apical side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: apical side
definition: Anatomical surface that is located on the apical side of the body or body part.
database_cross_reference: FBql:00005854
has_obo_namespace: spatial
id: BSPO:0000373

Axiom
annotated source: apical surface
annotated property: definition
annotated target: Anatomical surface that is located on the apical side of the body or body part.
database_cross_reference: BSPO:wd

basal surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: basal side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: basal side
definition: Anatomical surface that is located on the basal side of the body or body part.
database_cross_reference: FBql:00005855
has_obo_namespace: spatial
id: BSPO:0000374

Axiom
annotated source: basal surface
annotated property: definition
annotated target: Anatomical surface that is located on the basal side of the body or body part.
database_cross_reference: BSPO:wd

contralateral surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: contralateral side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: contralateral side
database_cross_reference: FBql:00005851
has_obo_namespace: spatial
id: BSPO:0000376

proximal surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: proximal side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: proximal side
definition: Anatomical surface that is located on the proximal side of the body or body part.
database_cross_reference: FBql:00005852
has_obo_namespace: spatial
id: BSPO:0000377

Axiom
annotated source: proximal surface
annotated property: definition
annotated target: Anatomical surface that is located on the proximal side of the body or body part.
database_cross_reference: BSPO:wd

distal surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: distal side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: distal side
definition: Anatomical surface that is located on the distal side of the body or body part.
database_cross_reference: FBql:00005853
has_obo_namespace: spatial
id: BSPO:0000378

Axiom
annotated source: distal surface
annotated property: definition
annotated target: Anatomical surface that is located on the distal side of the body or body part.
database_cross_reference: BSPO:wd

dorsal surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: dorsal side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: dorsal side
definition: Anatomical surface that located on the dorsal side of the body or body part.
database_cross_reference: FBql:00005842
has_obo_namespace: spatial
id: BSPO:0000379

Axiom
annotated source: dorsal surface
annotated property: definition
annotated target: Anatomical surface that located on the dorsal side of the body or body part.
database_cross_reference: BSPO:wd

ipsilateral surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: ipsilateral side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: ipsilateral side
definition: Anatomical surface that is located on the same side of an organism or structure.
database_cross_reference: FBql:00005850
has_obo_namespace: spatial
id: BSPO:0000381

Axiom
annotated source: ipsilateral surface
annotated property: definition
annotated target: Anatomical surface that is located on the same side of an organism or structure.
database_cross_reference: BSPO:wd

lateral surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: lateral side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: lateral side
definition: Anatomical surface that located on the lateral side of the body or body part.
database_cross_reference: FBql:00005844
has_obo_namespace: spatial
id: BSPO:0000382

Axiom
annotated source: lateral surface
annotated property: definition
annotated target: Anatomical surface that located on the lateral side of the body or body part.
database_cross_reference: BSPO:wd

medial surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: medial side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: medial side
definition: Anatomical surface that located on the medial side of the body or body part.
database_cross_reference: FBql:00005847
has_obo_namespace: spatial
id: BSPO:0000383

Axiom
annotated source: medial surface
annotated property: definition
annotated target: Anatomical surface that located on the medial side of the body or body part.
database_cross_reference: BSPO:wd

ventral surface
type: Class
equivalent class: Class
  intersection of: anatomical surface
  intersection of: Restriction
    on property: surface of
    some values from: ventral side
subclass of: anatomical surface
subclass of: Restriction
  on property: surface of
  some values from: ventral side
definition: Anatomical surface that is located on the ventral side of the body or body part.
database_cross_reference: FBql:00005843
has_obo_namespace: spatial
id: BSPO:0000384

Axiom
annotated source: ventral surface
annotated property: definition
annotated target: Anatomical surface that is located on the ventral side of the body or body part.
database_cross_reference: BSPO:wd

anatomical plane
type: Class
subclass of: anatomical boundary
definition: A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions.
database_cross_reference: FMA:242982
has_exact_synonym: anatomical cross-section
has_exact_synonym: anatomical section
has_exact_synonym: plane
has_exact_synonym: section
has_obo_namespace: spatial
has_related_synonym: cross-section
id: BSPO:0000400
comment: These anatomical sections are applicable to most bilaterally symmetrical animals, but bipedal animals such as humans have more complex usage of these terms. For example, in post-embryonic humans a coronal plane is vertical and a transverse plane is horizontal, but for embryos and quadrupeds a coronal plane is horizontal and a transverse plane is vertical.

Axiom
annotated source: anatomical plane
annotated property: definition
annotated target: A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions.
database_cross_reference: BSPO:cjm

sagittal plane
type: Class
equivalent class: Class
  intersection of: anatomical plane
  intersection of: Restriction
    on property: orthogonal to
    some values from: left-right axis
  intersection of: Restriction
    on property: parallel to
    some values from: anterior-posterior axis
  intersection of: Restriction
    on property: parallel to
    some values from: dorsal-ventral axis
subclass of: anatomical axis
subclass of: anatomical plane
subclass of: Restriction
  on property: orthogonal to
  some values from: left-right axis
subclass of: Restriction
  on property: parallel to
  some values from: anterior-posterior axis
subclass of: Restriction
  on property: parallel to
  some values from: dorsal-ventral axis
definition: Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size.
database_cross_reference: FMA:11361
has_exact_synonym: left/right plane
has_exact_synonym: median plane
has_exact_synonym: sagittal section
has_obo_namespace: spatial
id: BSPO:0000417

Axiom
annotated source: sagittal plane
annotated property: definition
annotated target: Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size.
database_cross_reference: BSPO:DOS
database_cross_reference: BSPO:cjm
database_cross_reference: BSPO:mah

anterior margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
subclass of: anatomical margin
subclass of: anterior region
definition: Anatomical margin that is located on the anterior side of a body or body part.
has_obo_namespace: spatial
id: BSPO:0000671

Axiom
annotated source: anterior margin
annotated property: definition
annotated target: Anatomical margin that is located on the anterior side of a body or body part.
database_cross_reference: BSPO:wd

posterior margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
subclass of: anatomical margin
subclass of: posterior region
definition: Anatomical margin that is located on the posterior side of the body or body part.
has_obo_namespace: spatial
id: BSPO:0000672

Axiom
annotated source: posterior margin
annotated property: definition
annotated target: Anatomical margin that is located on the posterior side of the body or body part.
database_cross_reference: BSPO:wd

apical margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: apical side
subclass of: anatomical margin
subclass of: apical region
definition: Anatomical margin that is located on the apical side of the body or body part.
has_obo_namespace: spatial
id: BSPO:0000673

Axiom
annotated source: apical margin
annotated property: definition
annotated target: Anatomical margin that is located on the apical side of the body or body part.
database_cross_reference: BSPO:wd

basal margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: basal side
subclass of: anatomical margin
subclass of: basal region
definition: Anatomical margin that is located on the basal side of the body or body part.
has_obo_namespace: spatial
id: BSPO:0000674

Axiom
annotated source: basal margin
annotated property: definition
annotated target: Anatomical margin that is located on the basal side of the body or body part.
database_cross_reference: BSPO:wd

proximal margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: proximal side
subclass of: anatomical margin
subclass of: proximal region
definition: Anatomical margin that is located on the proximal region of the body or body part.
has_obo_namespace: spatial
id: BSPO:0000677

Axiom
annotated source: proximal margin
annotated property: definition
annotated target: Anatomical margin that is located on the proximal region of the body or body part.
database_cross_reference: BSPO:wd

distal margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: distal side
subclass of: anatomical margin
subclass of: distal region
definition: Anatomical margin that is located on the distal side of the body or body part.
has_obo_namespace: spatial
id: BSPO:0000678

Axiom
annotated source: distal margin
annotated property: definition
annotated target: Anatomical margin that is located on the distal side of the body or body part.
database_cross_reference: BSPO:wd

dorsal margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
subclass of: anatomical margin
subclass of: dorsal region
definition: Anatomical margin that is located on the dorsal side of body or body part.
has_obo_namespace: spatial
id: BSPO:0000679

Axiom
annotated source: dorsal margin
annotated property: definition
annotated target: Anatomical margin that is located on the dorsal side of body or body part.
database_cross_reference: BSPO:wd

dorso-lateral margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: dorso-lateral region
subclass of: dorsal margin
subclass of: lateral margin
definition: Anatomical margin that is located on the dorso-lateral region of the body or body part.
has_exact_synonym: dorsolateral margin
has_obo_namespace: spatial
id: BSPO:0000680

Axiom
annotated source: dorso-lateral margin
annotated property: definition
annotated target: Anatomical margin that is located on the dorso-lateral region of the body or body part.
database_cross_reference: BSPO:wd

lateral margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
subclass of: anatomical margin
subclass of: lateral region
definition: Anatomical margin that is located on the lateral side of the body or body part.
has_obo_namespace: spatial
id: BSPO:0000682

Axiom
annotated source: lateral margin
annotated property: definition
annotated target: Anatomical margin that is located on the lateral side of the body or body part.
database_cross_reference: BSPO:wd

medial margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: medial side
subclass of: anatomical margin
subclass of: medial region
definition: Anatomical margin that is located on the medial side of the body or body part.
has_obo_namespace: spatial
id: BSPO:0000683

Axiom
annotated source: medial margin
annotated property: definition
annotated target: Anatomical margin that is located on the medial side of the body or body part.
database_cross_reference: BSPO:wd

ventral margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: anatomical margin
subclass of: ventral region
definition: Anatomical margin that is located on the ventral side of the body or body part.
has_obo_namespace: spatial
id: BSPO:0000684

Axiom
annotated source: ventral margin
annotated property: definition
annotated target: Anatomical margin that is located on the ventral side of the body or body part.
database_cross_reference: BSPO:wd

ventro-lateral margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: lateral side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: ventro-lateral region
subclass of: lateral margin
subclass of: ventral margin
definition: Anatomical margin that is located on the ventro-lateral region of the body or body part.
has_exact_synonym: ventrolateral margin
has_obo_namespace: spatial
id: BSPO:0000685
comment: This is an example of a composition of two axis positions

Axiom
annotated source: ventro-lateral margin
annotated property: definition
annotated target: Anatomical margin that is located on the ventro-lateral region of the body or body part.
database_cross_reference: BSPO:wd

antero-dorsal margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
subclass of: antero-dorsal region
subclass of: anterior margin
subclass of: dorsal margin
definition: Anatomical margin that is located on the antero-dorso region of the body or body part.
has_exact_synonym: anterodorsal margin
has_obo_namespace: spatial
id: BSPO:0000686

Axiom
annotated source: antero-dorsal margin
annotated property: definition
annotated target: Anatomical margin that is located on the antero-dorso region of the body or body part.
database_cross_reference: BSPO:wd

postero-dorsal margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: dorsal side
subclass of: postero-dorsal region
subclass of: posterior margin
subclass of: dorsal margin
definition: Anatomical margin that is located on the postero-dorsal region of the body or body part.
has_exact_synonym: posterodorsal margin
has_obo_namespace: spatial
id: BSPO:0000687

Axiom
annotated source: postero-dorsal margin
annotated property: definition
annotated target: Anatomical margin that is located on the postero-dorsal region of the body or body part.
database_cross_reference: BSPO:wd

antero-ventral margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: anterior side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: antero-ventral region
subclass of: anterior margin
subclass of: ventral margin
definition: Anatomical margin that is located on the antero-ventral region of the body or body part.
has_exact_synonym: anteroventral margin
has_obo_namespace: spatial
id: BSPO:0000688

Axiom
annotated source: antero-ventral margin
annotated property: definition
annotated target: Anatomical margin that is located on the antero-ventral region of the body or body part.
database_cross_reference: BSPO:wd

postero-ventral margin
type: Class
equivalent class: Class
  intersection of: anatomical margin
  intersection of: Restriction
    on property: overlaps
    some values from: posterior side
  intersection of: Restriction
    on property: overlaps
    some values from: ventral side
subclass of: postero-ventral region
subclass of: posterior margin
subclass of: ventral margin
definition: Anatomical margin that is located on the postero-ventral region of the body or body part.
has_exact_synonym: posteroventral margin
has_obo_namespace: spatial
id: BSPO:0000689

Axiom
annotated source: postero-ventral margin
annotated property: definition
annotated target: Anatomical margin that is located on the postero-ventral region of the body or body part.
database_cross_reference: BSPO:wd

medial-lateral axis
type: Class
subclass of: medial-external axis
definition: An axis that extends from the center of organism to one or other side.
has_exact_synonym: M-L axis
has_exact_synonym: ML axis
has_exact_synonym: medio-lateral axis
has_exact_synonym: mediolateral axis
has_obo_namespace: spatial
has_related_synonym: proximal-distal axis
id: BSPO:0001001
comment: Properly, the ML axis is a half axis; practically, its usage is less clumsy and less linguistically biased than "left-right". The terms may still be used relatively to describe locations along the LR axis. The gills are medial to the operculum, but lateral to the heart.

Axiom
annotated source: medial-lateral axis
annotated property: definition
annotated target: An axis that extends from the center of organism to one or other side.
database_cross_reference: BSPO:cjm

anatomical entity
type: Class
subclass of: biological entity
definition: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
IAO_0000412: caro.owl
has_obo_namespace: spatial
id: CARO:0000000

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
database_cross_reference: CARO:MAH

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
IAO_0000412: caro.owl
has_obo_namespace: spatial
id: CARO:0000003
label: connected anatomical structure

Axiom
annotated source: anatomical structure
annotated property: definition
annotated target: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
database_cross_reference: CC:DOS

material anatomical entity
type: Class
subclass of: material entity
subclass of: anatomical entity
definition: An anatomical entity that has mass.
IAO_0000412: caro.owl
has_obo_namespace: spatial
id: CARO:0000006

Axiom
annotated source: material anatomical entity
annotated property: definition
annotated target: An anatomical entity that has mass.
database_cross_reference: CC:DOS

immaterial anatomical entity
type: Class
subclass of: immaterial entity
subclass of: anatomical entity
definition: An anatomical entity that has no mass.
has_obo_namespace: spatial
id: CARO:0000007

Axiom
annotated source: immaterial anatomical entity
annotated property: definition
annotated target: An anatomical entity that has no mass.
database_cross_reference: CC:DOS

anatomical line
type: Class
subclass of: immaterial anatomical entity
definition: A one dimensional, immaterial anatomical entity.
has_obo_namespace: spatial
id: CARO:0000008

Axiom
annotated source: anatomical line
annotated property: definition
annotated target: A one dimensional, immaterial anatomical entity.
database_cross_reference: CC:DOS

anatomical boundary
type: Class
subclass of: immaterial anatomical entity
definition: A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
has_obo_namespace: spatial
id: CARO:0000010

Axiom
annotated source: anatomical boundary
annotated property: definition
annotated target: A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
database_cross_reference: CC:DOS

biological entity
type: Class
subclass of: independent continuant

molecular_function
type: Class
subclass of: process
IAO_0000589: molecular process

catalytic activity
type: Class
subclass of: molecular_function

biological_process
type: Class
subclass of: process

kinase activity
type: Class
subclass of: transferase activity, transferring phosphorus-containing groups
subclass of: Restriction
  on property: is kinase activity
  has self: true

transferase activity
type: Class
subclass of: catalytic activity

transferase activity, transferring phosphorus-containing groups
type: Class
subclass of: transferase activity

data item
type: Class
subclass of: information content entity
IAO_0000111: data item

information content entity
type: Class
subclass of: BFO_0000031
IAO_0000111: information content entity

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
IAO_0000111: curation status specification
IAO_0000114: pending final vetting
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
IAO_0000116: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
IAO_0000117: PERSON:Bill Bug
IAO_0000119: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO_0000119: OBI_0000266

data about an ontology part
type: Class
subclass of: data item
IAO_0000111: data about an ontology part
definition: Data about an ontology part is a data item about a part of an ontology, for example a term
IAO_0000117: Person:Alan Ruttenberg

obsolescence reason specification
type: Class
equivalent class: Class
  one of: failed exploratory term
  one of: placeholder removed
  one of: terms merged
  one of: term imported
  one of: term split
subclass of: data about an ontology part
IAO_0000111: obsolescence reason specification
IAO_0000114: pending final vetting
definition: The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
IAO_0000116: The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Melanie Courtot

denotator type
type: Class
equivalent class: Class
  one of: universal
  one of: defined class
  one of: named class expression
subclass of: data about an ontology part
IAO_0000111: denotator type
IAO_0000112: The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
definition: A denotator type indicates how a term should be interpreted from an ontological perspective.
IAO_0000117: Alan Ruttenberg
IAO_0000119: Barry Smith, Werner Ceusters

example to be eventually removed
type: NamedIndividual
type: curation status specification
IAO_0000111: example to be eventually removed

failed exploratory term
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: failed exploratory term
definition: The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
IAO_0000117: Person:Alan Ruttenberg

metadata complete
type: NamedIndividual
type: curation status specification
IAO_0000111: metadata complete
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: NamedIndividual
type: curation status specification
IAO_0000111: organizational term
definition: Term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: NamedIndividual
type: curation status specification
IAO_0000111: ready for release
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: NamedIndividual
type: curation status specification
IAO_0000111: metadata incomplete
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: NamedIndividual
type: curation status specification
IAO_0000111: uncurated
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: NamedIndividual
type: curation status specification
IAO_0000111: pending final vetting
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

placeholder removed
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: placeholder removed

terms merged
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: terms merged
IAO_0000116: An editor note should explain what were the merged terms and the reason for the merge.

term imported
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: term imported
IAO_0000116: This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.

term split
type: NamedIndividual
type: obsolescence reason specification
IAO_0000111: term split
IAO_0000116: This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.

universal
type: NamedIndividual
type: denotator type
IAO_0000111: universal
IAO_0000116: Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
IAO_0000117: Alan Ruttenberg
IAO_0000119: A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf

defined class
type: NamedIndividual
type: denotator type
IAO_0000111: defined class
definition: A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
IAO_0000116: "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
IAO_0000117: Alan Ruttenberg

named class expression
type: NamedIndividual
type: denotator type
IAO_0000111: named class expression
definition: A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
IAO_0000116: named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
IAO_0000117: Alan Ruttenberg

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
IAO_0000111: to be replaced with external ontology term
definition: Terms with this status should eventually replaced with a term from another ontology.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
IAO_0000111: requires discussion
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
IAO_0000117: Alan Ruttenberg
IAO_0000119: group:OBI

infer input from direct reg
is rule enabled: true
comment: MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
type: Imp
body: IndividualPropertyAtom
  property predicate: enables
  argument1: http://purl.obolibrary.org/obo/ro.owl#z
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#y
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
body: ClassAtom
  class predicate: molecular_function
  argument1: http://purl.obolibrary.org/obo/ro.owl#y
head: IndividualPropertyAtom
  property predicate: has input
  argument1: http://purl.obolibrary.org/obo/ro.owl#x
  argument2: http://purl.obolibrary.org/obo/ro.owl#z

enabling an MF enables its parts
comment: GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
type: Imp
body: ClassAtom
  class predicate: molecular_function
  argument1: y
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: has part
  argument1: y
  argument2: z
head: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: z

involved in BP
is rule enabled: true
comment: GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
type: Imp
body: ClassAtom
  class predicate: biological_process
  argument1: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: enables
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: involved in
  argument1: x
  argument2: z

Imp
comment: This can't be added as a property chain because it causes a circularity violation for 'part of'.
body: IndividualPropertyAtom
  property predicate: in left side of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: in left side of
  argument1: x
  argument2: z

Imp
comment: This can't be added as a property chain because it causes a circularity violation for 'part of'.
body: IndividualPropertyAtom
  property predicate: in right side of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: in right side of
  argument1: x
  argument2: z

Imp
comment: This can't be added as a property chain because it causes a circularity violation for 'part of'.
body: IndividualPropertyAtom
  property predicate: in lateral side of
  argument1: y
  argument2: z
body: IndividualPropertyAtom
  property predicate: part of
  argument1: x
  argument2: y
head: IndividualPropertyAtom
  property predicate: in lateral side of
  argument1: x
  argument2: z

inferring direct reg edge from input to regulatory subfunction
comment: If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: A
  argument2: D

inferring direct neg reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has negative regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: A
  argument2: D

inferring direct positive reg edge from input to regulatory subfunction
type: Imp
body: IndividualPropertyAtom
  property predicate: input of
  argument1: B
  argument2: C
body: IndividualPropertyAtom
  property predicate: enabled by
  argument1: A
  argument2: B
body: IndividualPropertyAtom
  property predicate: has positive regulatory component activity
  argument1: D
  argument2: C
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: A
  argument2: D

effector input is compound function input
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in

Input of effector is input of its parent MF
type: Imp
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: has input
  argument1: mf
  argument2: in
head: IndividualPropertyAtom
  property predicate: has input
  argument1: eff
  argument2: in

Imp
comment: if effector directly regulates X, its parent MF directly regulates X
body: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly regulates
  argument1: eff
  argument2: mf2

Imp
comment: if effector directly positively regulates X, its parent MF directly positively regulates X
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
body: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: mf
  argument2: mf2
head: IndividualPropertyAtom
  property predicate: directly positively regulates
  argument1: eff
  argument2: mf2

if effector directly negatively regulates X, its parent MF directly negatively regulates X
type: Imp
body: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: mf
  argument2: mf2
body: IndividualPropertyAtom
  property predicate: has effector activity
  argument1: mf
  argument2: eff
head: IndividualPropertyAtom
  property predicate: directly negatively regulates
  argument1: eff
  argument2: mf2

'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally downstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x

'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
type: Imp
body: IndividualPropertyAtom
  property predicate: overlaps
  argument1: x
  argument2: y
body: IndividualPropertyAtom
  property predicate: causally upstream of
  argument1: x
  argument2: y
head: ClassAtom
  class predicate: Nothing
  argument1: y
head: ClassAtom
  class predicate: Nothing
  argument1: x