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.
Biological Spatial Ontology
* BSPO:$sequence(7,0,999999999)$
spatial
based on FBql
2023-05-27
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
editor note
has ontology root term
Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
Nicolas Matentzoglu
has ontology root term
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Person:Alan Ruttenberg
Add as annotation triples in the granting ontology
term replaced by
term replaced by
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
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.
is a defining property chain axiom where second argument is reflexive
synonym typically used in the context of human anatomy
synonym typically used in the context of vertebrate anatomy
namespace-id-rule
synonym_type_property
database_cross_reference
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
has exact synonym
has_exact_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/20
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
https://github.com/information-artifact-ontology/ontology-metadata/issues/19
has narrow synonym
has_narrow_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/19
has_obo_format_version
has_obo_namespace
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
https://github.com/information-artifact-ontology/ontology-metadata/issues/21
has related synonym
has_related_synonym
https://github.com/information-artifact-ontology/ontology-metadata/issues/21
has_scope
has_synonym_type
shorthand
http://www.w3.org/2000/01/rdf-schema#seeAlso
spatial
seeAlso
true
seeAlso
see also
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
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.
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/
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'.
part_of
BFO:0000050
spatial
part_of
part_of
part of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
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.
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/
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'.
has_part
BFO:0000051
spatial
has_part
has_part
has part
has part
preceded by
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.
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.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
preceded by
precedes
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.
precedes
BSPO:0000095
spatial
anatomical_relation
anatomical_relation
anatomical relation
true
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.
BSPO:0000096
rostral_to
spatial
anterior_to
anterior_to
anterior to
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.
BSPO:cjm
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).
BSPO:0000097
spatial
distal_to
distal_to
distal to
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).
BSPO:cjm
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).
BSPO:0000098
spatial
dorsal_to
dorsal_to
dorsal to
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).
BSPO:cjm
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.
BSPO:0000099
caudal to
spatial
posterior_to
posterior_to
posterior to
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.
BSPO:cjm
caudal to
x proximal to y iff x is closer to the point of attachment with the body than y.
BSPO:0000100
NCIT:C25236
spatial
proximal_to
proximal_to
The elbow is proximal to the hand, but distal to the shoulder.
proximal to
x proximal to y iff x is closer to the point of attachment with the body than y.
BSPO:cjm
RO:0002221
BSPO:0000101
spatial
obsolete_surrounds
obsolete_surrounds
obsolete surrounds
true
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).
BSPO:0000102
spatial
ventral_to
ventral_to
ventral to
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).
BSPO:cjm
BSPO:0000103
spatial
vicinity_of
vicinity_of
vicinity of
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.
BSPO:0000104
spatial
approximately_perpendicular_to
approximately_perpendicular_to
approximately perpendicular to
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.
BSPO:cjm
On the same side as. For example, the left arm is ipsilateral to the left leg.
BSPO:0000105
spatial
ipsilateral_to
ipsilateral_to
ipsilateral to
On the same side as. For example, the left arm is ipsilateral to the left leg.
BSPO:cjm
On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg).
BSPO:0000106
spatial
contralateral_to
contralateral_to
contralateral to
On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg).
BSPO:cjm
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:0000107
spatial
deep_to
deep_to
deep to
Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.
BSPO:cjm
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:0000108
spatial
superficial_to
superficial_to
superficial to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:cjm
RO:0002219
BSPO:0000109
spatial
obsolete_surrounded_by
obsolete_surrounded_by
obsolete surrounded_by
true
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.
BSPO:0000110
spatial
left_of
left_of
left of
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.
BSPO:cjm
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.
BSPO:0000111
spatial
right_of
right_of
right of
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.
BSPO:cjm
Direcly opposite to. i.e. on the opposite side through the axis.
BSPO:0000113
spatial
opposite_to
opposite_to
opposite to
Direcly opposite to. i.e. on the opposite side through the axis.
BSPO:cjm
X lateral to y if x is further from the midsagittal plane than y.
Jennifer Girón
2021-04-21T01:01:01Z
lateral to
Jennifer Girón
2021-04-21T01:01:01Z
X medial to y if x is closer to the midsagittal plane than y.
medial to
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
BSPO:0000120
NCIT:C25229
spatial
in_left_side_of
in_left_side_of
in left side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion.
BSPO:PATO_mtg_2009
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
BSPO:0000121
NCIT:C25228
spatial
in_right_side_of
in_right_side_of
in right side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion.
BSPO:PATO_mtg_2009
X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
BSPO:0000122
spatial
in_posterior_side_of
in_posterior_side_of
in posterior side of
X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion.
BSPO:PATO_mtg_2009
X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
BSPO:0000123
spatial
in_anterior_side_of
in_anterior_side_of
in anterior side of
X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion.
BSPO:PATO_mtg_2009
x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
BSPO:0000124
spatial
in_proximal_side_of
in_proximal_side_of
in proximal side of
x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion.
BSPO:PATO_mtg_2009
x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
BSPO:0000125
spatial
in_distal_side_of
in_distal_side_of
in distal side of
x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion.
BSPO:PATO_mtg_2009
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
BSPO:0000126
spatial
in_lateral_side_of
in_lateral_side_of
in lateral side of
https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern
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
UBERON:cjm
X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the superficial portion.
BSPO:0001100
spatial
in_superficial_part_of
in_superficial_part_of
in superficial part of
X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the superficial portion.
BSPO:cjm
X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion.
BSPO:0001101
spatial
in_deep_part_of
in_deep_part_of
in deep part of
X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion.
BSPO:cjm
x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.
spatial
parallel_to
parallel to
x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross.
BSPO:curators
X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
BSPO:0001106
spatial
proximalmost_part_of
proximalmost_part_of
proximalmost part of
X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y
https://orcid.org/0000-0002-6601-2165
x immediately deep to y iff x deep_to y and x is contiguous with y.
BSPO:0001107
spatial
immediately_deep_to
immediately_deep_to
immediately deep to
x immediately deep to y iff x deep_to y and x is contiguous with y.
BSPO:curators
X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
BSPO:0001108
spatial
distalmost_part_of
distalmost_part_of
distalmost part of
X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y
https://orcid.org/0000-0002-6601-2165
BSPO:0001113
spatial
preaxialmost_part_of
preaxialmost_part_of
preaxialmost part of
x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side.
BSPO:0001114
spatial
posterior to (developmentally)
postaxial_to
postaxial_to
postaxial to
x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side.
http://medical-dictionary.thefreedictionary.com/postaxial
posterior to (developmentally)
MA:th
BSPO:0001115
spatial
postaxialmost_part_of
postaxialmost_part_of
postaxialmost part of
X intersects median plane of iff X crosses the midine plane of Y.
BSPO:0005001
spatial
intersects_midsagittal_plane_of
intersects_midsagittal_plane_of
intersects midsagittal plane of
BSPO:0015001
spatial
finishes_axis
finishes_axis
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
finishes axis
BSPO:0015002
spatial
follows_axis
follows_axis
follows axis
BSPO:0015003
spatial
has_axis
has_axis
has axis
A relation between an axis and a part of an organism, in which the part defines the initial point of the axis.
BSPO:0015004
spatial
has_end_point
has_end_point
Axes can be defined in a given species by subtyping the relevant axis type and stating a end and end point
has end point
A relation between an axis and a part of an organism, in which the part defines the initial point of the axis.
BSPO:cjm
crossing at right angles
BSPO:0015005
spatial
orthogonal_to
orthogonal_to
orthogonal to
crossing at right angles
BSPO:cjm
Intersects at two points.
BSPO:0015006
spatial
passes_through
passes_through
passes through
Intersects at two points.
BSPO:cjm
BSPO:0015007
spatial
starts_axis
starts_axis
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
starts axis
BSPO:0015008
spatial
surface_of
surface_of
placeholder. used for relation between anatomical surface and an anatomical side.
surface of
x immediately anterior to y iff x anterior to y and x is contiguous with y.
BSPO:0015009
spatial
immediately_anterior_to
immediately_anterior_to
immediately anterior to
x immediately anterior to y iff x anterior to y and x is contiguous with y.
BSPO:curators
x immediately distal to y iff x distal to y and x is contiguous with y.
BSPO:0015010
spatial
immediately_distal_to
immediately_distal_to
immediately distal to
x immediately distal to y iff x distal to y and x is contiguous with y.
BSPO:curators
x immediately dorsal to y iff x dorsal to y and x is contiguous with y.
BSPO:0015011
spatial
immediately_dorsal_to
immediately_dorsal_to
immediately dorsal to
x immediately dorsal to y iff x dorsal to y and x is contiguous with y.
BSPO:curators
x immediately posterior to y iff x posterior_to y and x is contiguous with y.
BSPO:0015012
spatial
immediately_posterior_to
immediately_posterior_to
immediately posterior to
x immediately posterior to y iff x posterior_to y and x is contiguous with y.
BSPO:curators
x immediately proximal to y iff x proximal to y and x is contiguous with y.
BSPO:0015013
spatial
immediately_proximal_to
immediately_proximal_to
immediately proximal to
x immediately proximal to y iff x proximal to y and x is contiguous with y.
BSPO:curators
x immediately superficial to y iff x superficial to y and x is contiguous with y.
BSPO:0015014
spatial
immediately_superficial_to
immediately_superficial_to
immediately superficial to
x immediately superficial to y iff x superficial to y and x is contiguous with y.
BSPO:curators
x immediately ventral to y iff x ventral to y and x is contiguous with y.
BSPO:0015015
spatial
immediately_ventral_to
immediately_ventral_to
immediately ventral to
x immediately ventral to y iff x ventral to y and x is contiguous with y.
BSPO:curators
x immediately left of y iff x left_of y and x is contiguous with y.
BSPO:0015016
spatial
immediately_left_of
immediately_left_of
immediately left of
x immediately left of y iff x left_of y and x is contiguous with y.
BSPO:curators
x immediately right of y iff x right of y and x is contiguous with y.
BSPO:0015017
spatial
immediately_right_of
immediately_right_of
immediately right of
x immediately right of y iff x right of y and x is contiguous with y.
BSPO:curators
X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion.
BSPO:0015101
spatial
in_dorsal_side_of
in_dorsal_side_of
in dorsal side of
X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion.
BSPO:cjm
X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion.
BSPO:0015102
spatial
in_ventral_side_of
in_ventral_side_of
in ventral side of
X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion.
BSPO:cjm
nearer to the oral opening of the organism, on the oral-aboral axis.
BSPO:0015201
spatial
oral_to
oral_to
oral to
nearer to the oral opening of the organism, on the oral-aboral axis.
BSPO:cjm
nearer to the aboral opening of the organism, on the oral-aboral axis.
BSPO:0015202
spatial
aboral_to
aboral_to
aboral to
nearer to the aboral opening of the organism, on the oral-aboral axis.
BSPO:cjm
X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
This was migrated from http://purl.obolibrary.org/obo/uberon/core#in_central_side_of in Uberon.
in central side of
X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.
BSPO:cjm
A relation between an axis and a part of an organism, in which the part defines the initial point of the axis.
This relationship was originally called http://purl.obolibrary.org/obo/#_has_start_point, but was renamed because of the non-standard IRI syntax.
:has_start_point
spatial
has_start_point
has_start_point
Axes can be defined in a given species by subtyping the relevant axis type and stating a start and end point.
has start point
A relation between an axis and a part of an organism, in which the part defines the initial point of the axis.
BSPO:cjm
x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y
BSPO:0030003
spatial
dorsalmost_part_of
dorsalmost_part_of
dorsalmost part of
x dorsalmost_part_of y iff x part_of y and there is no z which is part_of y and is more dorsal than x but not part_of x; x is adjacent to the dorsal boundary of y
https://orcid.org/0000-0003-2699-3066
x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y
BSPO:0030004
spatial
anteriormost_part_of
anteriormost_part_of
anteriormost part of
x anteriormost_part_of y iff x part_of y and there is no z which is part_of y and is more anterior than x but not part_of x; x is adjacent to the anterior boundary of y
https://orcid.org/0000-0003-2699-3066
x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y
BSPO:0030005
spatial
lateralmost_part_of
lateralmost_part_of
lateralmost part of
x lateralmost_part_of y iff x part_of y and there is no z which is part_of y and is more lateral than x but not part_of x; x is adjacent to the lateral boundary of y
https://orcid.org/0000-0003-2699-3066
X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion.
BSPO:0030006
spatial
in_medial_side_of
in_medial_side_of
in medial side of
X medial side of Y <=> if Y is subdivided into two medial and lateral portions, X is part of the medial portion.
https://orcid.org/0000-0003-2699-3066
x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y
BSPO:0030007
spatial
medialmost_part_of
medialmost_part_of
medialmost part of
x medialmost_part_of y iff x part_of y and there is no z which is part_of y and is more medial than x but not part_of x; x is adjacent to the medial boundary of y
https://orcid.org/0000-0003-2699-3066
x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the front.
BSPO:1000000
spatial
anterior to (developmentally)
lateral (radial) to
medial (tibial) to
preaxial_to
preaxial_to
preaxial to
x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the front.
http://medical-dictionary.thefreedictionary.com/preaxial
anterior to (developmentally)
MA:th
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
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.
inheres_in
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.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
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.
bearer_of
is bearer of
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
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.
function_of
is function of
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.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
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
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
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.
is role of
role_of
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
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
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.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
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.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
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.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
inverse of has disposition
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.
disposition of
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.
dos
2017-05-24T09:30:46Z
has regulatory component activity
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.
dos
2017-05-24T09:31:01Z
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 negative regulatory component activity
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.
dos
2017-05-24T09:31:17Z
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 positive regulatory component activity
dos
2017-05-24T09:44:33Z
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
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.
dos
2017-05-24T09:49:21Z
has component process
dos
2017-09-17T13:52:24Z
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.
directly regulated by
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.
GOC:dos
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.
dos
2017-09-17T13:52:38Z
directly negatively regulated by
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.
GOC:dos
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.
dos
2017-09-17T13:52:47Z
directly positively regulated by
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.
GOC:dos
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.
dos
2017-09-22T14:14:36Z
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
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.
GOC:dos
David Osumi-Sutherland
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
x overlaps y if and only if there exists some z such that x has part z and z part of y
x overlaps y iff they have some part in common.
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
spatial
overlaps
overlaps
"(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF []
overlaps
overlaps
true
x overlaps y iff they have some part in common.
BSPO:cjm
A is spatially_disjoint_from B if and only if they have no parts in common
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.
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
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
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.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
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.
has component
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
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.
has function realized in
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)".
capable of
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.
has function in
capable of part of
true
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.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
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.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
RO:0002220
spatial
adjacent_to
adjacent_to
adjacent to
adjacent to
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.
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.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
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.
consumes
has input
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.
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.
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
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.
affects
acts upstream of or within
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
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, positive effect
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
causally upstream of, negative effect
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.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
inheres in part of
characteristic of part of
true
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
catalyzes
executes
has
is catalyzing
is executing
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.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
false
part of structure that is capable of
true
c involved_in p if and only if c enables some process p', and p' is part of p
actively involved in
enables part of
involved in
inverse of enables
enabled by
inverse of regulates
regulated by (processual)
regulated by
inverse of negatively regulates
negatively regulated by
inverse of positively regulates
positively regulated by
inverse of has input
input of
inverse of upstream of
causally downstream of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly activates
indirectly positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly inhibits
indirectly negatively regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
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 yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
https://en.wikipedia.org/wiki/Causality
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
involved in negative regulation of
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
OWL does not allow defining object properties via a Union
involved in or reguates
involved in or involved in regulation of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
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.
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.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
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.
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
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.
molecularly controls
directly regulates activity of
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.
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
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.
directly activates
molecularly increases activity of
directly positively regulates activity of
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
is kinase activity
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
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 where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
depends on
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
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
causally influenced by (entity-centric)
causally influenced by
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
molecular interaction relation helper property
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).
causally influences (entity-centric)
causally influences
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
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
has part structure that is capable of
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.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
Inverse of 'causal agent in process'
process has causal agent
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
directly positively regulates
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
directly negatively regulates
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
2018-01-25T23:20:13Z
enables subfunction
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
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
2018-01-26T23:53:14Z
acts upstream of, positive effect
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
2018-01-26T23:53:22Z
acts upstream of, negative effect
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
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.
regulates activity of
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
pg
2022-09-26T06:07:17Z
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
pg
2022-09-26T06:08:01Z
indirectly regulates
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
negatively regulates characteristic
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.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
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.
realizable entity
quality
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.
specifically dependent continuant
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.
role
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
immaterial entity
The side of an organism that is left of the sagittal plane.
left
spatial
BSPO:0000000
left side
The side of an organism that is left of the sagittal plane.
BSPO:cjm
upper
spatial
BSPO:0000001
Consider merging with superior side.
upper side
lower
spatial
BSPO:0000002
Consider merging with inferior side.
lower side
BSPO:0000021
spatial
BSPO:00000021
was made obsolete because the ID had too many digits
deep-superficial gradient (obsolete)
true
deep
spatial
BSPO:0000003
deep side
superficial
spatial
BSPO:0000004
superficial side
A 2D surface of an anatomical continuant.
FMA:24137
surface
spatial
BSPO:0000005
to be merged into CARO
anatomical surface
A 2D surface of an anatomical continuant.
BSPO:cjm
Fiat anatomical region extending a short distance from the boundary of an object inwards.
edge
margin
spatial
BSPO:0000006
anatomical margin
Fiat anatomical region extending a short distance from the boundary of an object inwards.
BSPO:cjm
The side of an organism that is right of the sagittal plane.
right
spatial
BSPO:0000007
right side
The side of an organism that is right of the sagittal plane.
BSPO:cjm
BSPO:wd
Sagittal plane that divides a bilateral body into unequal left and right parts.
parasagittal section
spatial
BSPO:0000008
parasagittal plane
Sagittal plane that divides a bilateral body into unequal left and right parts.
BSPO:mah
Sagittal plane that divides bilateral body into equal left and right parts.
FMA:74563
median sagittal plane
midline plane
midsagittal section
spatial
median plane
BSPO:0000009
only in bilaterally symmetrical organisms
midsagittal plane
Sagittal plane that divides bilateral body into equal left and right parts.
BSPO:mah
median sagittal plane
FMA:74563
A straight line through space, intersecting an anatomical entity.
http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG
spatial
BSPO:0000010
Axis directions are defined in terms of axes.
anatomical axis
A straight line through space, intersecting an anatomical entity.
BSPO:cjm
An anatomical axis determined by gravity.
spatial
superior-inferior axis
BSPO:0000011
upper-lower axis
An anatomical axis determined by gravity.
BSPO:cjm
An axis that extends from an internal position to a more external position in the body or body part.
spatial
BSPO:0000012
Muscles are frequently categorized as 'deep', 'intermediate', and 'superficial'.
deep-superficial axis
An axis that extends from an internal position to a more external position in the body or body part.
BSPO:PM
An axis that extends through an organism from head end to opposite end of body or tail.
A-P axis
AP axis
anteroposterior axis
cephalocaudal axis
craniocaudal axis
rostral/caudal
rostrocaudal axis
spatial
longitudinal axis
BSPO:0000013
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]
anterior-posterior axis
An axis that extends through an organism from head end to opposite end of body or tail.
BSPO:cjm
cephalocaudal axis
http://en.wikipedia.org/wiki/Anatomical_terms_of_location
craniocaudal axis
rostral/caudal
rostrocaudal axis
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.
apical/basal
spatial
longitudinal axis
BSPO:0000014
apical-basal axis relative to substrate
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.
BSPO:mah
An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal).
proximal/distal
proximodistal
spatial
BSPO:0000015
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.
proximal-distal axis
An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal).
BSPO:curators
http://en.wikipedia.org/wiki/Anatomical_terms_of_location
An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body.
D-V axis
DV axis
dorsoventral axis
anterior-posterior axis
spatial
BSPO:0000016
dorsal-ventral axis
An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body.
BSPO:curators
anterior-posterior axis
An axis that bisects an organism from left to right sides of body, through a sagittal plane.
L-R axis
LR axis
R-L axis
RL axis
dextro-sinister axis
left to right axis
right to left axis
right-left axis
spatial
BSPO:0000017
left-right axis
An axis that bisects an organism from left to right sides of body, through a sagittal plane.
BSPO:cjm
Anatomical plane that divides body into anterior and posterior parts.
FMA:12247
axial plane
axial section
transverse section
spatial
cross-section
BSPO:0000018
transverse plane
Anatomical plane that divides body into anterior and posterior parts.
BSPO:mah
Anatomical plane that divides bilateral body into dorsal and ventral parts.
FMA:52810
frontal plane
horizontal anatomical plane
horizontal section
spatial
coronal section
frontal section
BSPO:0000019
horizontal plane
Anatomical plane that divides bilateral body into dorsal and ventral parts.
BSPO:mah
horizontal anatomical plane
FMA:52810
Anatomical gradient that is distributed along the upper-lower axis.
spatial
BSPO:0000020
upper-lower gradient
Anatomical gradient that is distributed along the upper-lower axis.
BSPO:wd
Anatomical gradient that is distributed along the deep-superficial axis.
spatial
BSPO:0000021
deep-superficial gradient
Anatomical gradient that is distributed along the deep-superficial axis.
BSPO:wd
The side that is higher relative to the substrate.
superior
spatial
cranial
BSPO:0000022
superior side
The side that is higher relative to the substrate.
BSPO:curators
Anatomical gradient that is distributed along the apical-basal axis.
spatial
BSPO:0000023
apical-basal gradient
Anatomical gradient that is distributed along the apical-basal axis.
BSPO:wd
Anatomical gradient that is distributed along the proximal-distal axis.
spatial
BSPO:0000024
proximal-distal gradient
Anatomical gradient that is distributed along the proximal-distal axis.
BSPO:wd
The side that is lower relative to the substrate.
inferior
spatial
caudal
BSPO:0000025
inferior side
The side that is lower relative to the substrate.
BSPO:curators
Anatomical region that overlaps the anterior and dorsal regions of a body or body part.
Melissa Haendel
2009-06-15T01:01:38Z
anterodorsal region
spatial
BSPO:0000026
antero-dorsal region
Anatomical region that overlaps the anterior and dorsal regions of a body or body part.
BSPO:wd
Anatomical region that overlaps the anterior and ventral regions of a body or body part.
Melissa Haendel
2009-06-15T01:04:59Z
anteroventral region
spatial
BSPO:0000027
antero-ventral region
Anatomical region that overlaps the anterior and ventral regions of a body or body part.
BSPO:wd
Anatomical region that overlaps the posterior and lateral regions of the body or body part.
Melissa Haendel
2009-06-15T01:06:01Z
posterolateral region
spatial
BSPO:0000028
postero-lateral region
Anatomical region that overlaps the posterior and lateral regions of the body or body part.
BSPO:wd
Anatomical region that overlaps the anterior and lateral regions of a body or body part.
Melissa Haendel
2009-06-15T01:07:18Z
anterolateral region
spatial
BSPO:0000029
antero-lateral region
Anatomical region that overlaps the anterior and lateral regions of a body or body part.
BSPO:wd
Anatomical region that overlaps the posterior and dorsal regions of the body or body part.
Melissa Haendel
2009-06-15T01:08:13Z
posterodorsal region
spatial
BSPO:0000030
postero-dorsal region
Anatomical region that overlaps the posterior and dorsal regions of the body or body part.
BSPO:wd
spatial
BSPO:0000031
upper region
spatial
BSPO:0000032
lower region
Anatomical region located deep within an organism or structure.
spatial
BSPO:0000033
deep region
Anatomical region located deep within an organism or structure.
BSPO:wd
Anatomical region superficially located on the body or body part.
spatial
BSPO:0000034
superficial region
Anatomical region superficially located on the body or body part.
BSPO:wd
Anatomical region that overlaps the posterior and ventral regions of a body or body part.
Melissa Haendel
2009-06-15T01:08:38Z
posteroventral region
spatial
BSPO:0000035
postero-ventral region
Anatomical region that overlaps the posterior and ventral regions of a body or body part.
BSPO:wd
Melissa Haendel
2009-06-16T08:49:03Z
anterior-most
anteriormost
spatial
BSPO:0000036
anterior-most region
Melissa Haendel
2009-06-16T08:49:50Z
posterior-most
posteriormost
spatial
BSPO:0000037
posterior-most region
Melissa Haendel
2009-06-16T08:50:26Z
dorsal-most
dorsalmost
spatial
BSPO:0000038
dorsal-most region
Melissa Haendel
2009-06-16T08:51:07Z
ventral-most
ventralmost
spatial
BSPO:0000039
ventral-most region
spatial
BSPO:0000040
upper/lower compartment boundary
spatial
BSPO:0000041
deep/superficial compartment boundary
Anatomical margin that is located on the antero-medial region of the body or body part.
Melissa Haendel
2009-09-10T08:49:57Z
anteromedial margin
spatial
BSPO:0000042
antero-medial margin
Anatomical margin that is located on the antero-medial region of the body or body part.
BSPO:wd
spatial
BSPO:0000043
apical/basal compartment boundary
spatial
BSPO:0000044
proximal/distal compartment boundary
Anatomical margin that is located on the antero-lateral region of the body or body part.
Melissa Haendel
2009-09-10T08:50:37Z
anterolateral margin
spatial
BSPO:0000045
antero-lateral margin
Anatomical margin that is located on the antero-lateral region of the body or body part.
BSPO:wd
Anatomical margin that is located on the postero-medial region of the body or body part.
Melissa Haendel
2009-09-10T08:51:07Z
posteromedial margin
spatial
BSPO:0000046
postero-medial margin
Anatomical margin that is located on the postero-medial region of the body or body part.
BSPO:wd
Anatomical margin that is located on the postero-lateral region of the body or body part.
Melissa Haendel
2009-09-10T08:51:42Z
posterolateral margin
spatial
BSPO:0000047
postero-lateral margin
Anatomical margin that is located on the postero-lateral region of the body or body part.
BSPO:wd
Anatomical margin that is located on the dorso-medial region of the body or body part.
Melissa Haendel
2009-09-10T08:52:04Z
dorso-medial margin
spatial
BSPO:0000048
dorso-medial margin
Anatomical margin that is located on the dorso-medial region of the body or body part.
BSPO:wd
Anatomical margin that is located on the ventro-medial region of the body or body part.
Melissa Haendel
2009-09-10T08:52:48Z
ventromedial margin
spatial
BSPO:0000049
ventro-medial margin
Anatomical margin that is located on the ventro-medial region of the body or body part.
BSPO:wd
Anatomical region that overlaps the anterior and medial regions of the body or body part.
Melissa Haendel
2009-09-10T08:55:32Z
anteromedial region
spatial
BSPO:0000050
antero-medial region
Anatomical region that overlaps the anterior and medial regions of the body or body part.
BSPO:wd
Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis.
FBql:00005254
spatial
BSPO:0000051
anatomical gradient
Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis.
BSPO:cjm
Anatomical gradient that is distributed along the anterior-posterior axis.
FBcv:0000142
FBql:00005256
spatial
BSPO:0000052
anterior-posterior gradient
Anatomical gradient that is distributed along the anterior-posterior axis.
BSPO:wd
Anatomical gradient that is distributed along the dorsal-ventral axis.
FBcv:0000143
FBql:00005255
spatial
BSPO:0000053
dorsal-ventral gradient
Anatomical gradient that is distributed along the dorsal-ventral axis.
BSPO:wd
An anatomical region bounded by a plane perpendicular to an axis through the middle.
FBql:00005841
spatial
BSPO:0000054
anatomical side
An anatomical region bounded by a plane perpendicular to an axis through the middle.
BSPO:cjm
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.
FBcv:0000053
FBql:00005848
anterior
rostral
spatial
BSPO:0000055
anterior side
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.
BSPO:RW
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.
FBcv:0000065
FBql:00005849
posterior
caudal
spatial
BSPO:0000056
posterior side
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.
BSPO:RW
BSPO:wd
caudal
Anatomical side that is located on the apical end of an organism or structure.
FBcv:0000054
FBql:00005854
apical
spatial
BSPO:0000057
apical side
Anatomical side that is located on the apical end of an organism or structure.
BSPO:wd
Anatomical side that is located on the basal end of an organism or structure.
FBcv:0000055
FBql:00005855
basal
spatial
BSPO:0000058
The part of the organism attached to a substrate. Axis of symmetry.
basal side
Anatomical side that is located on the basal end of an organism or structure.
BSPO:wd
Anatomical side that is centrally located on an organism or structure.
FBcv:0000056
FBql:00015851
central
spatial
BSPO:0000059
central is not an axis direction
central side
Anatomical side that is centrally located on an organism or structure.
BSPO:wd
On the opposite side.
FBcv:0000057
FBql:00005851
contralateral
spatial
BSPO:0000060
inherited from flybase cv. not clear how this would be used. Suggest we obsolete, and use the corresponding relation.
contralateral side
On the opposite side.
BSPO:cjm
FBcv:0000066
FBql:00005852
proximal
spatial
BSPO:0000061
proximal side
Anatomical side that is distally located on an organism or structure.
FBcv:0000058
FBql:00005853
distal
spatial
BSPO:0000062
distal side
Anatomical side that is distally located on an organism or structure.
BSPO:wd
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.
FBcv:0000059
FBql:00005842
dorsal
spatial
BSPO:0000063
dorsal side
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.
BSPO:wd
Anatomical region that overlaps the posterior and medial regions of the body or body part.
Melissa Haendel
2009-09-10T08:56:39Z
posteromedial region
spatial
BSPO:0000064
postero-medial region
Anatomical region that overlaps the posterior and medial regions of the body or body part.
BSPO:wd
On the same side
FBcv:0000062
FBql:00005850
ipsilateral
spatial
BSPO:0000065
inherited from flybase cv. not clear how this would be used. Suggest we obsolete, and use the corresponding relation.
ipsilateral side
On the same side
BSPO:cjm
FBcv:0000063
FBql:00005844
lateral
spatial
BSPO:0000066
lateral side
FBcv:0000064
FBql:00005847
medial
spatial
BSPO:0000067
a point in the centre of the organism (where the left-right axis intersects the midsagittal plane)
medial side
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.
FBcv:0000070
FBql:00005843
ventral
spatial
BSPO:0000068
ventral side
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.
BSPO:RW
BSPO:wd
Anatomical region that overlaps the dorsal and medial regions of the body or body part.
Melissa Haendel
2009-09-10T08:57:22Z
dorsomedial region
spatial
BSPO:0000069
dorso-medial region
Anatomical region that overlaps the dorsal and medial regions of the body or body part.
BSPO:wd
A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.
FBql:00005841
spatial
BSPO:0000070
to be merged into CARO
anatomical region
A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm.
BSPO:cjm
Anatomical region anteriorly located on the body or body part.
FBql:00005848
spatial
BSPO:0000071
anterior region
Anatomical region anteriorly located on the body or body part.
BSPO:wd
Anatomical region posteriorly located on the body or body part.
FBql:00005849
spatial
BSPO:0000072
posterior region
Anatomical region posteriorly located on the body or body part.
BSPO:wd
Anatomical region located on the apical end on the body or body part.
FBql:00005854
spatial
BSPO:0000073
apical region
Anatomical region located on the apical end on the body or body part.
BSPO:wd
Anatomical region located basally on the body or body part.
FBql:00005855
spatial
BSPO:0000074
basal region
Anatomical region located basally on the body or body part.
BSPO:wd
Anatomical region centrally located on the body or body part.
FBql:00015851
spatial
BSPO:0000075
central region
Anatomical region centrally located on the body or body part.
BSPO:wd
FBql:00005851
spatial
BSPO:0000076
inherited from flybase cv. not clear how this would be used
contralateral region
Anatomical region proximally located on the body or body part.
FBql:00005852
spatial
BSPO:0000077
proximal region
Anatomical region proximally located on the body or body part.
BSPO:wd
Anatomical region distally located on the body or body part.
FBql:00005853
spatial
BSPO:0000078
distal region
Anatomical region distally located on the body or body part.
BSPO:wd
Anatomical region dorsally located on the body or body part.
FBql:00005842
spatial
BSPO:0000079
dorsal region
Anatomical region dorsally located on the body or body part.
BSPO:wd
Anatomical region that overlaps the dorsal and lateral regions of a body or body part.
FBql:00005845
dorsolateral region
spatial
BSPO:0000080
dorso-lateral region
Anatomical region that overlaps the dorsal and lateral regions of a body or body part.
BSPO:wd
FBql:00005850
spatial
BSPO:0000081
ipsilateral region
Anatomical region laterally located on the body or body part.
FBql:00005844
spatial
BSPO:0000082
lateral region
Anatomical region laterally located on the body or body part.
BSPO:wd
Anatomical region medially located on the body or body part.
FBql:00005847
spatial
BSPO:0000083
medial region
Anatomical region medially located on the body or body part.
BSPO:wd
Anatomical region ventrally located on the body or body part.
FBql:00005843
spatial
BSPO:0000084
ventral region
Anatomical region ventrally located on the body or body part.
BSPO:wd
Anatomical region that overlaps the ventral and lateral regions of a body or body part.
FBql:00005846
ventrolateral region
spatial
BSPO:0000085
This is an example of a composition of two axis positions.
ventro-lateral region
Anatomical region that overlaps the ventral and lateral regions of a body or body part.
BSPO:wd
FBql:00005873
FMA:9647
spatial
BSPO:0000086
to be merged into CARO
anatomical compartment
FBcv:0000031
FBql:00005874
spatial
BSPO:0000087
anterior compartment
FBcv:0000032
FBql:00005878
spatial
BSPO:0000088
compartment boundary
FBcv:0000035
FBql:00005876
spatial
BSPO:0000089
dorsal compartment
FBcv:0000036
FBql:00005875
spatial
BSPO:0000090
posterior compartment
FBcv:0000037
FBql:00005877
spatial
BSPO:0000091
ventral compartment
FBql:00005881
spatial
BSPO:0000092
to be merged into CARO
anatomical compartment boundary
FBcv:0000033
FBql:00005880
spatial
BSPO:0000093
anterior/posterior compartment boundary
FBcv:0000034
FBql:00005879
spatial
BSPO:0000094
dorsal/ventral compartment boundary
The region corresponding to the ventral region of the entity, towards the midline.
Melissa Haendel
2009-09-10T08:57:54Z
medioventral region
ventromedial region
spatial
BSPO:0000112
ventro-medial region
The region corresponding to the ventral region of the entity, towards the midline.
BSPO:wd
Anatomical region peripherally located on the body or body part.
spatial
BSPO:0000127
peripheral region
Anatomical region peripherally located on the body or body part.
BSPO:wd
spatial
BSPO:0000128
axial region
spatial
BSPO:0000129
peripheral side
spatial
BSPO:0000130
axial side
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).
wasila.dahdul
2013-07-02T11:20:29Z
AA axis
spatial
dorsal-ventral axis
BSPO:0000195
adaxial-abaxial axis
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).
BSPO:RW
An anatomical axis that extends from the center of the body outwards or externally.
wasila.dahdul
2013-07-02T11:21:42Z
spatial
proximal-distal axis
BSPO:0000196
The medial-external axis could apply to a sphere-shaped body.
medial-external axis
An anatomical axis that extends from the center of the body outwards or externally.
BSPO:curators
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.
wasila.dahdul
2013-07-02T11:23:31Z
M-R axis
MR axis
spatial
BSPO:0000197
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.
medial-radial axis
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.
BSPO:curators
An axis that extends from the oral opening to the furthest point in an organism that is directly opposite.
wasila.dahdul
2013-07-02T11:29:33Z
spatial
BSPO:0000198
oral-aboral axis
An axis that extends from the oral opening to the furthest point in an organism that is directly opposite.
BSPO:PM
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).
wasila.dahdul
2013-07-02T11:30:13Z
A-V axis
AV axis
animal/vegetal axis
spatial
BSPO:0000199
animal-vegetal axis
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).
BSPO:PM
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.
spatial
BSPO:0000200
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.
apical-basal axis relative to direction of growth
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.
BSPO:RW
Anatomical plane that is perpendicular to a radial plane.
wasila.dahdul
2014-01-22T15:34:31Z
spatial
BSPO:0000201
Need to add logical definitions.
tangential plane
Anatomical plane that is perpendicular to a radial plane.
BSPO:wd
Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis.
wasila.dahdul
2014-01-22T15:34:02Z
spatial
BSPO:0000202
Need to add logical definitions.
radial plane
Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis.
BSPO:wd
Anatomical surface that is located on the anterior side of the body or body part.
FBql:00005848
spatial
BSPO:0000371
anterior surface
Anatomical surface that is located on the anterior side of the body or body part.
BSPO:wd
Anatomical surface that is located on the posterior side of the body or body part.
FBql:00005849
spatial
BSPO:0000372
posterior surface
Anatomical surface that is located on the posterior side of the body or body part.
BSPO:wd
Anatomical surface that is located on the apical side of the body or body part.
FBql:00005854
spatial
BSPO:0000373
apical surface
Anatomical surface that is located on the apical side of the body or body part.
BSPO:wd
Anatomical surface that is located on the basal side of the body or body part.
FBql:00005855
spatial
BSPO:0000374
basal surface
Anatomical surface that is located on the basal side of the body or body part.
BSPO:wd
FBql:00005851
spatial
BSPO:0000376
contralateral surface
Anatomical surface that is located on the proximal side of the body or body part.
FBql:00005852
spatial
BSPO:0000377
proximal surface
Anatomical surface that is located on the proximal side of the body or body part.
BSPO:wd
Anatomical surface that is located on the distal side of the body or body part.
FBql:00005853
spatial
BSPO:0000378
distal surface
Anatomical surface that is located on the distal side of the body or body part.
BSPO:wd
Anatomical surface that located on the dorsal side of the body or body part.
FBql:00005842
spatial
BSPO:0000379
dorsal surface
Anatomical surface that located on the dorsal side of the body or body part.
BSPO:wd
Anatomical surface that is located on the same side of an organism or structure.
FBql:00005850
spatial
BSPO:0000381
ipsilateral surface
Anatomical surface that is located on the same side of an organism or structure.
BSPO:wd
Anatomical surface that located on the lateral side of the body or body part.
FBql:00005844
spatial
BSPO:0000382
lateral surface
Anatomical surface that located on the lateral side of the body or body part.
BSPO:wd
Anatomical surface that located on the medial side of the body or body part.
FBql:00005847
spatial
BSPO:0000383
medial surface
Anatomical surface that located on the medial side of the body or body part.
BSPO:wd
Anatomical surface that is located on the ventral side of the body or body part.
FBql:00005843
spatial
BSPO:0000384
ventral surface
Anatomical surface that is located on the ventral side of the body or body part.
BSPO:wd
A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions.
FMA:242982
anatomical cross-section
anatomical section
plane
section
spatial
cross-section
BSPO:0000400
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.
anatomical plane
A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions.
BSPO:cjm
Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size.
FMA:11361
left/right plane
median plane
sagittal section
spatial
BSPO:0000417
sagittal plane
Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size.
BSPO:DOS
BSPO:cjm
BSPO:mah
Anatomical margin that is located on the anterior side of a body or body part.
spatial
BSPO:0000671
anterior margin
Anatomical margin that is located on the anterior side of a body or body part.
BSPO:wd
Anatomical margin that is located on the posterior side of the body or body part.
spatial
BSPO:0000672
posterior margin
Anatomical margin that is located on the posterior side of the body or body part.
BSPO:wd
Anatomical margin that is located on the apical side of the body or body part.
spatial
BSPO:0000673
apical margin
Anatomical margin that is located on the apical side of the body or body part.
BSPO:wd
Anatomical margin that is located on the basal side of the body or body part.
spatial
BSPO:0000674
basal margin
Anatomical margin that is located on the basal side of the body or body part.
BSPO:wd
Anatomical margin that is located on the proximal region of the body or body part.
spatial
BSPO:0000677
proximal margin
Anatomical margin that is located on the proximal region of the body or body part.
BSPO:wd
Anatomical margin that is located on the distal side of the body or body part.
spatial
BSPO:0000678
distal margin
Anatomical margin that is located on the distal side of the body or body part.
BSPO:wd
Anatomical margin that is located on the dorsal side of body or body part.
spatial
BSPO:0000679
dorsal margin
Anatomical margin that is located on the dorsal side of body or body part.
BSPO:wd
Anatomical margin that is located on the dorso-lateral region of the body or body part.
dorsolateral margin
spatial
BSPO:0000680
dorso-lateral margin
Anatomical margin that is located on the dorso-lateral region of the body or body part.
BSPO:wd
Anatomical margin that is located on the lateral side of the body or body part.
spatial
BSPO:0000682
lateral margin
Anatomical margin that is located on the lateral side of the body or body part.
BSPO:wd
Anatomical margin that is located on the medial side of the body or body part.
spatial
BSPO:0000683
medial margin
Anatomical margin that is located on the medial side of the body or body part.
BSPO:wd
Anatomical margin that is located on the ventral side of the body or body part.
spatial
BSPO:0000684
ventral margin
Anatomical margin that is located on the ventral side of the body or body part.
BSPO:wd
Anatomical margin that is located on the ventro-lateral region of the body or body part.
ventrolateral margin
spatial
BSPO:0000685
This is an example of a composition of two axis positions
ventro-lateral margin
Anatomical margin that is located on the ventro-lateral region of the body or body part.
BSPO:wd
Anatomical margin that is located on the antero-dorso region of the body or body part.
anterodorsal margin
spatial
BSPO:0000686
antero-dorsal margin
Anatomical margin that is located on the antero-dorso region of the body or body part.
BSPO:wd
Anatomical margin that is located on the postero-dorsal region of the body or body part.
posterodorsal margin
spatial
BSPO:0000687
postero-dorsal margin
Anatomical margin that is located on the postero-dorsal region of the body or body part.
BSPO:wd
Anatomical margin that is located on the antero-ventral region of the body or body part.
anteroventral margin
spatial
BSPO:0000688
antero-ventral margin
Anatomical margin that is located on the antero-ventral region of the body or body part.
BSPO:wd
Anatomical margin that is located on the postero-ventral region of the body or body part.
posteroventral margin
spatial
BSPO:0000689
postero-ventral margin
Anatomical margin that is located on the postero-ventral region of the body or body part.
BSPO:wd
An axis that extends from the center of organism to one or other side.
http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG
M-L axis
ML axis
medio-lateral axis
mediolateral axis
spatial
proximal-distal axis
BSPO:0001001
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.
medial-lateral axis
An axis that extends from the center of organism to one or other side.
BSPO:cjm
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
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.
spatial
CARO:0000000
Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.
anatomical entity
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
CAROC:Brownsville2014
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.
CARO:MAH
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
spatial
CARO:0000003
Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.
anatomical structure
connected anatomical structure
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CC:DOS
An anatomical entity that has mass.
spatial
CARO:0000006
material anatomical entity
An anatomical entity that has mass.
CC:DOS
An anatomical entity that has no mass.
Anatomical entity that has no mass.
spatial
CARO:0000007
immaterial anatomical entity
An anatomical entity that has no mass.
CC:DOS
A one dimensional, immaterial anatomical entity.
spatial
CARO:0000008
anatomical line
A one dimensional, immaterial anatomical entity.
CC:DOS
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
spatial
CARO:0000010
anatomical boundary
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
CC:DOS
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
molecular function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
GOC:pdt
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
jl
2012-09-19T15:05:24Z
Wikipedia:Biological_process
biological process
physiological process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
true
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
data item
data item
information content entity
information content entity
curation status specification
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.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
data about an ontology part
Data about an ontology part is a data item about a part of an ontology, for example a term
Person:Alan Ruttenberg
data about an ontology part
obsolescence reason specification
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.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
PERSON: Alan Ruttenberg
PERSON: Melanie Courtot
obsolescence reason specification
denotator type
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.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Alan Ruttenberg
Barry Smith, Werner Ceusters
denotator type
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
example to be eventually removed
example to be eventually removed
failed exploratory term
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
Person:Alan Ruttenberg
failed exploratory term
metadata complete
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.
metadata complete
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
ready for release
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."
ready for release
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
pending final vetting
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.
pending final vetting
placeholder removed
placeholder removed
terms merged
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
term imported
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 imported
term split
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.
term split
universal
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.
Alan Ruttenberg
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
defined class
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"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.
Alan Ruttenberg
defined class
named class expression
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
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
Alan Ruttenberg
named class expression
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
requires discussion
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.
Alan Ruttenberg
group:OBI
requires discussion
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
https://github.com/information-artifact-ontology/ontology-metadata/issues/77
https://orcid.org/0000-0001-5208-3432
out of scope
true
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
infer input from direct reg
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'
enabling an MF enables its parts
true
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'
involved in BP
This can't be added as a property chain because it causes a circularity violation for 'part of'.
This can't be added as a property chain because it causes a circularity violation for 'part of'.
This can't be added as a property chain because it causes a circularity violation for 'part of'.
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.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).