An ontology of human and animal behaviours.
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
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
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
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.
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
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
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.
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
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
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
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
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
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
disposition of
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
location_of
location of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning: domain: material entity range: spatial region or site (immaterial continuant)
contained_in
contains
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
surface of
2D boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
has boundary
has_2D_boundary
has 2D boundary
innervated_by
X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer 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.
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.
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.
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
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
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.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
Primitive instance level timing relation between events
before or simultaneous with
t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)
simultaneous with
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
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
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
<http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
innervates
X continuous_with Y if and only if X and Y share a fiat boundary.
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
continuous with
lactation SubClassOf 'only in taxon' some 'Mammalia'
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Connects a biological entity to its taxon of origin.
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
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
connects
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attached to part of (anatomical structure to anatomical structure)
attached to part of
Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure
supplies
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
drains
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
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
This is the transitive form of the develops from relation
develops from
develops into
Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y.
directly develops from
directly develops into
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.
Regulation precludes parthood; the regulatory process may not be within the regulated process.
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.
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.
capable of part of
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
surrounded by
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
adjacent to
surrounds
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.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
starts
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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.
starts with
x develops from part of y if and only if there exists some z such that x develops from z and z is part of y
develops from part of
x develops_in y if x is located in y whilst x is developing
develops in
ends
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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.
ends with
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
has end location
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.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
has output
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
has developmental contribution from
inverse of has developmental contribution from
developmentally contributes to
t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T
Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]
developmentally induced by
Inverse of developmentally induced by
developmentally induces
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
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.
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.
x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else
This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage
developmentally replaces
developmentally succeeded by
'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue
part of developmental precursor of
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
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.
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
characteristic of part of
A relationship that holds via some environmental process
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
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 relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally 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.
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.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
output of
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
attached to (anatomical structure to anatomical structure)
attached to
m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
has muscle origin
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
has muscle insertion
A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships
This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)
in branching relationship with
Deschutes River tributary_of Columbia River
inferior epigastric vein tributary_of external iliac vein
x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.
tributary of
x spatially_coextensive_with y if and inly if x and y have the same location
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S
x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y
branching part of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
has potential to developmentally contribute to
x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y
has potential to developmentally induce
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
has potential to directly develop into
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 positively regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly negatively regulates
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
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
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
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 involved in regulation of
A protein that enables activity in a cytosol.
p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
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.
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.
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
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.
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 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 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)
'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'
x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
relation between physical entity and a process or stage
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).
x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships
x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
A relationship between a material entity and a process where the material entity has some causal role that influences the 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.
q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2
This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C.
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
Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'
A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.
The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell).
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).
A relation that holds between elements of a musculoskeletal system or its analogs.
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.
x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.
This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.
x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.
s is luminal space of x iff s is lumen_of x and s is an immaterial entity
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
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
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.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
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.
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
produced by
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
acts upstream of or within, positive effect
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
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
causally upstream of or within, negative effect
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.
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.
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
indirectly regulates
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.
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
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.
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.
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.
by_means
has-input
in_response_to
is_about
qualifier
has number of atomic nuclei
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
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.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable
realizable entity
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
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.
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.
electron
Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium.
A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens.
dicarboxylic acids and O-substituted derivatives
A carbohydrate acid derivative anion obtained by deprotonation of the carboxy groups of hyaluronic acid; major species at pH 7.3.
Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa.
An organic cation obtained by protonation of the amino group of any tertiary amino compound.
An N-alkylpyrrolidine that consists of N-methylpyrrolidine bearing a pyridin-3-yl substituent at position 2.
A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water.
Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa).
An antigenic epitope recognized by an anti-bilirubin monoclonal antibody designated 24G7. A substructure of bilirubin IXalpha, it is the region containing the oxo group at C-1, the methyl group at C-2, C-(4, 5, 6, 9), and N-21 and -22.
A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity.
An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms
A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it.
A peptide containing ten or more amino acid residues.
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms.
A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid.
A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group.
A mucopolysaccharide composed of N-acetylglucosamine and glucuronic acid subunits. It is found in the connective tissues of vertebrates. A principal constituent of the extracellular matrix (ECM), it mediates the growth and metastasis of tumour cells.
A naturally occurring polypeptide synthesized at the ribosome.
Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001.
A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin.
A compound in which a carbohydrate component is covalently bound to a protein component.
A morphinane alkaloid that is a highly potent opiate analgesic psychoactive drug. Morphine acts directly on the central nervous system (CNS) to relieve pain but has a high potential for addiction, with tolerance and both physical and psychological dependence developing rapidly. Morphine is the most abundant opiate found in Papaver somniferum (the opium poppy).
Any compound that supports healthy aging, slows the biological aging process, or extends lifespan.
A 3-(1-methylpyrrolidin-2-yl)pyridine in which the chiral centre has S-configuration. The naturally occurring and most active enantiomer of nicotine, isolated from Nicotiana tabacum.
The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group.
A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity.
'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
Any polysaccharide containing a substantial proportion of aminomonosaccharide residues.
A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.
A racemate composed of equimolar amounts of (R)- and (S)-nicotine.
An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids.
Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids.
A monoatomic or polyatomic species having one or more elementary charges of the electron.
A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides.
A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base).
Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives.
Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group.
A sodium salt of the conjugate of any bile acid with either glycine or taurine.
An insecticide compound naturally occurring in plants.
The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid.
An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group).
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.
A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.
Any primary alcohol based on an ethanol skeleton.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A role played by the molecular entity or part thereof within a biological context.
A defined linked collection of atoms or a single atom within a molecular entity.
A cyclic compound having as ring members atoms of carbon and at least of one other element.
Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).
A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons).
A molecular entity that contains no carbon.
Strictly, a substance intended to kill members of the class Insecta. In common usage, any substance used for preventing, destroying, repelling or controlling insects.
A salt is an assembly of cations and anions.
A molecular entity having a net electric charge.
Any alkaloid that has a structure based on an isoquinoline nucleus. They are derived from the amino acids like tyrosine and phenylalanine.
Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites.
Any carboxylic ester resulting from the formal condensation of a carboxy group with methanol.
Any polyatomic entity that is an electrically neutral entity consisting of more than one atom.
An isoquinoline alkaloid based on a morphinan skeleton and its substituted derivatives.
Any organic ion with a net negative charge.
Any organic ion with a net positive charge.
Compounds of the general formula SO3HOR where R is an organyl group
An alcohol derived from an aliphatic compound.
An oxide is a chemical compound of oxygen with other chemical elements.
Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests.
Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives.
Any alkali metal salt having sodium(1+) as the cation.
An ester of an alcohol and sulfuric acid.
A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom.
A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid.
A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer).
A tropane alkaloid obtained from leaves of the South American shrub Erythroxylon coca.
A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised.
An onium cation obtained by protonation of ammonia.
A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid.
The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated.
A monoatomic monocation obtained from sodium.
A divalent inorganic anion resulting from the removal of two protons from ammonia.
A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom.
A 1,2-benzisothiazole having a keto-group at the 3-position and two oxo substituents at the 1-position. It is used as an artificial sweetening agent.
An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
Intended use of the molecular entity or part thereof by humans.
A particle not known to have substructure.
A monoatomic entity is a molecular entity consisting of a single atom.
An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system.
Any substituent group which does not contain carbon.
Any substituent group or skeleton containing carbon.
Any organic substituent group, regardless of functional type, having one free valence at a carbon atom.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.
Some people may be uncomfortable calling every proton an atomic nucleus
atomic nucleus
Heavy nuclear particle: proton or neutron.
A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.
A derivative of two oxoacids RkE(=O)l(OH)m (l =/= 0) in which two acyl groups are attached to the amino or substituted amino group.
A molecular entity all atoms of which have the same atomic number.
An organosulfur compound is a compound containing at least one carbon-sulfur bond.
An anion consisting of more than one atom.
A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans.
A nutrient is a food component that an organism uses to survive and grow.
A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.
A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life.
An energy-rich substance that can be transformed with release of usable energy.
A molecular entity containing one or more atoms of an alkali metal.
Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth.
A p-block molecular entity containing any pnictogen.
Any p-block element belonging to the group 16 family of the periodic table.
Any p-block molecular entity containing a chalcogen.
An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl.
An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.
An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity.
An amino-acid anion obtained by deprotonation of any alpha-amino acid.
Any main group element atom belonging to the p-block of the periodic table.
A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.
A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.
Any molecule that consists of a series of atoms joined together to form a ring.
A cyclic compound having as ring members atoms of the same element only.
A homocyclic compound in which all of the ring members are carbon atoms.
A molecule that features two fused rings.
A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.
A polycyclic compound in which at least one of the rings contains at least one non-carbon atom.
A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.
An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element.
A main group molecular entity that contains one or more atoms of a p-block element.
Hydrides are chemical compounds of hydrogen with other chemical elements.
A macromolecule formed by a living organism.
A cation consisting of more than one atom.
An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group.
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
A carboxylic acid containing one or more amino groups.
An organic compound having at least one hydroxy group attached to a carbon atom.
Any organic molecule that consists of atoms connected in the form of a ring.
A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).
Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion.
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring.
A substance used in a chemical reaction to detect, measure, examine, or produce other substances.
Any nutrient required in large quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Macronutrients are usually chemical elements (carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur) that humans consume in the largest quantities. Calcium, sodium, magnesium and potassium are sometimes included as macronutrients because they are required in relatively large quantities compared with other vitamins and minerals.
Saturated acyclic nitrogen hydrides having the general formula NnHn+2.
A substance that diminishes the rate of a chemical reaction.
A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction.
The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group.
A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc).
Any drug that enhances the activity of the central nervous system.
Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.
Any heteroorganic entity containing at least one carbon-nitrogen bond.
An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.
A substance used in the prophylaxis or therapy of infectious diseases.
A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system.
A loosely defined grouping of drugs that have effects on psychological function.
A traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behaviour.
Anxiolytic drugs are agents that alleviate anxiety, tension, and anxiety disorders, promote sedation, and have a calming effect without affecting clarity of consciousness or neurologic conditions.
An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms.
A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood.
A loosely defined group of drugs that tend to reduce the activity of the central nervous system.
A drug that mimics the effects of stimulating postganglionic adrenergic sympathetic nerves. Included in this class are drugs that directly stimulate adrenergic receptors and drugs that act indirectly by provoking the release of adrenergic transmitters.
A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume.
A food additive that is used to added improve the taste or odour of a food.
A drug used to cause dilation of the blood vessels.
Adrenergic uptake inhibitors are drugs that block the transport of adrenergic transmitters into axon terminals or into storage vesicles within terminals. The tricyclic antidepressants and amphetamines are among the therapeutically important drugs that may act via inhibition of adrenergic transport. Many of these drugs also block transport of serotonin.
Any carboxylic acid containing two carboxy groups.
A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter.
A xenobiotic (Greek, xenos "foreign"; bios "life") is a compound that is foreign to a living organism. Principal xenobiotics include: drugs, carcinogens and various compounds that have been introduced into the environment by artificial means.
A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function.
Esters of benzoic acid or substituted benzoic acids.
A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.
Any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block.
Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).
Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).
Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.
subatomic particle
A subatomic particle known to have substructure (i.e. consisting of smaller particles).
Hadron is a subatomic particle which experiences the strong force.
A nucleus or any of its constituents in any of their energy states.
Any molecular entity consisting of more than one atom.
An ion consisting of more than one atom.
Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.
Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element.
Compounds based on a biladiene skeleton.
A monoatomic or polyatomic species having one or more elementary charges of the proton.
An organochalcogen compound is a compound containing at least one carbon-chalcogen bond.
An organochalcogen compound containing at least one carbon-oxygen bond.
Any of the group of polysaccharides composed of alternating units from uronic acids and glycosamines, and commonly partially esterified with sulfuric acid.
An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
A molecular entity consisting of two or more chemical elements.
An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.
Any imide in which the acyl substituents are any two from carboacyl, sulfonyl and phosphoryl
A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid.
Any agent that acts on an adrenergic receptor or affects the life cycle of an adrenergic transmitter.
A compound composed of two or more pyrrole units.
Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.
Any of a class of heterocyclic amines having a saturated five-membered ring.
Any drug used for its actions on cholinergic systems. Included here are agonists and antagonists, drugs that affect the life cycle of acetylcholine, and drugs that affect the survival of cholinergic neurons.
Any drug that binds to and activates cholinergic receptors.
isoquinoline alkaloid fundamental parent
Any agent that affects the transport of molecular entities across a biological membrane.
An agent that inhibits sodium influx through cell membranes.
Any dianion containing at least one carboxy group.
Substance which produces loss of feeling or sensation.
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
A molecular entity capable of accepting a hydron from a donor (Bronsted acid).
A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct.
A 3-(1-methylpyrrolidin-2-yl)pyridine in which the chiral centre has R-configuration.
A liquid that can dissolve other substances (solutes) without any change in their chemical composition.
Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc.
An agonist that selectively binds to and activates a nicotinic acetylcholine receptor.
nicotinic acetylcholine receptor agonist
A substance used locally on humans and other animals to destroy harmful microorganisms or to inhibit their activity (cf. disinfectants, which destroy microorganisms found on non-living objects, and antibiotics, which can be transported through the lymphatic system to destroy bacteria within the body).
An antimicrobial agent that is applied to non-living objects to destroy harmful microorganisms or to inhibit their activity.
A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds.
A polar solvent that is capable of acting as a hydron (proton) donor.
Solvent that is capable of acting as a hydron (proton) acceptor.
Self-ionizing solvent possessing both characteristics of Bronsted acids and bases.
A drug used for its effects on dopamine receptors, on the life cycle of dopamine, or on the survival of dopaminergic neurons.
Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own.
Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances.
A drug that acts principally at one or more sites within the peripheral neuroeffector systems, the autonomic system, and motor nerve-skeletal system.
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
Synthetic or natural substance which is given to prevent a disease or disorder or are used in the process of treating a disease or injury due to a poisonous agent.
Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families.
Substance that sweeten food, beverages, medications, etc.
Drug used to cause constriction of the blood vessels.
An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position.
Biologically active substance whose activity affects or plays a role in the functioning of the immune system.
Any molecular entity that contains carbon.
A chemical compound, or part thereof, which causes the onset of an allergic reaction by interacting with any of the molecular pathways involved in an allergy.
A role played by a chemical compound in biological systems with adverse consequences in embryo developments, leading to birth defects, embryo death or altered development, growth retardation and functional defect.
A role is particular behaviour which a material entity may exhibit.
A poison that interferes with the functions of the nervous system.
A compound that specifically inhibits the reuptake of serotonin in the brain. This increases the serotonin concentration in the synaptic cleft which then activates serotonin receptors to a greater extent.
A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups.
A dopaminergic agent that blocks the transport of dopamine into axon terminals or into storage vesicles within terminals. Most of the adrenergic uptake inhibitors also inhibit dopamine uptake.
A role played by the molecular entity or part thereof within a chemical context.
An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case.
Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s).
An organic anion that is the conjugate base of methanol.
An organic anion that is the conjugate base of ethanol.
A biological role played by the molecular entity or part thereof within a biochemical context.
A role played by the molecular entity or part thereof which causes the development of a pathological process.
A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties.
Any substance introduced into a living organism with therapeutic or diagnostic purpose.
A chemical substance that encourages a cell to commence cell division, triggering mitosis.
The biological role played by a material entity when bound by a receptor of the adaptive immune system. Specific site on an antigen to which an antibody binds.
A polymer carrying multiple negative charges.
A macromolecule containing ionic groups.
A compound that exhibits agonist activity at the mu-opioid receptor.
A benzothiazole consisting of a benzene ring fused to an isothiazole.
A cyclic compound having as ring members atoms of at least two different elements.
A dicarboxylic acid dianion obtained by deprotonation of the two carboxy groups of bilirubin; major species at pH 7.3.
The conjugate acid of morphine arising from protonation of the tertiary amino group; major species at pH 7.3.
An organic anion of general formula RS(=O)2O(-) where R is an organyl group.
A substance used as an indicator of a biological state.
An organic anion arising from deprotonation of a acyclic tetrapyrrole compound.
A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons.
The conjugate acid of (S)-nicotine arising from selective protonation of the tertiary amino group; major species at pH 7.3.
A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.
A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind.
A polymer is a mixture, which is composed of macromolecules of different kinds and which may be differentiated by composition, length, degree of branching etc..
The conjugate base of cocaine arising from protonation of the tertiary amino group; major species at pH 7.3.
An ionic polymer is a polymer, composed of ionic macromolecules.
An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one.
Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged.
Any agent that acts on an opioid receptor or affects the life cycle of an opioid transmitter.
Any agent that acts on a mu-opioid receptor.
An agent that selectively binds to and activates an opioid receptor.
Any substance that inhibits the action of N-methyl-D-aspartate (NMDA) receptors. They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs.
Any substance which inhibits the action of receptors for excitatory amino acids.
A racemate is an equimolar mixture of a pair of enantiomers.
A polymer, composed of polyanion macromolecules.
An ester where the ester linkage is bonded directly to an aromatic system.
Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds.
A carbohydrate derivative that is formally obtained from a carbohydrate acid.
A carboxylic acid anion resulting from the deprotonation of the carboxy group of a carbohydrate acid derivative.
An agonist that selectively binds to and activates a protein kinase C receptor
Any substance which is added to food to preserve or enhance its flavour and/or appearance.
An agonist that selectively binds to and activates a protein kinase receptor.
An organic molecular entity containing a single carbon atom (C1).
Any organic molecular entity that is acidic and contains carbon in covalent linkage.
Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism.
A carbohydrate derivative that is any derivative of a polysaccharide.
Any molecule that consists of at least one carbon atom as part of the electrically neutral entity.
A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment.
Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms.
Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals.
Any animal metabolite produced during a metabolic reaction in mammals.
Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus).
Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae).
Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea.
A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'.
Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*).
Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*).
EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor
An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*).
EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor
Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms.
Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds.
Any prokaryotic metabolite produced during a metabolic reaction in bacteria.
Any bacterial metabolite produced during a metabolic reaction in Escherichia coli.
Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens).
An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4).
A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants.
Any minor or unwanted substance introduced into the environment that can have undesired effects.
A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure.
An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3.
Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation.
carbohydrates and carbohydrate derivatives
The conjugate acid of (R)-nicotine arising from selective protonation of the tertiary amino group; major species at pH 7.3.
Any inorganic anion with a valency of two.
Any inorganic anion with a valency of one.
Any drug which causes the onset of an allergic reaction.
A mixed diacylamine resulting from the formal condensation of the nitrogen of a carboxamide with a sulphonic acid.
A carboxylic acic anion obtained by deprotonation of the carboxy group of any aromatic carboxylic acid. Major species at pH 7.3.
A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
This atom is closely related to ChEBI's atom, but not exactly equivalent to.
atom
A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom.
This molecular entity is different than ChEBI's 'molecular entity'.
We would like to have cardinality restrictions on the logic, but there are some technical limitations.
molecular entity
A complex of two or more molecular entities that are not covalently bound.
>=2 parts (not we cannot use cardinality with transitive properties)
This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead.
Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'.
Note that this term refers to a mode of migration rather than to any particular cell type.
An instance of intramembranous ossification may also be classified as metaplastic; the former classifies based on tissue type location, and the latter based on mechanism/cell division.
positive regulation of mesenchymal cell proliferation
regulation of respiratory gaseous exchange by nervous system process
This term was obsoleted because it is outside the scope of GO.
organ or tissue specific immune response
Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501).
negative regulation of immune system process
positive regulation of immune system process
negative regulation of peptide secretion
positive regulation of peptide secretion
developmental process involved in reproduction
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.
This is the same as GO molecular function
gene product or complex activity
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer.
Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term.
Note that this term refers to a projection from a single cell, and should not be confused with 'microvillus' as used to refer to a multicellular structure such as that found in the placenta.
regulation of glycogen biosynthetic process
regulation of glycogen catabolic process
generation of precursor metabolites and energy
regulation of carbohydrate metabolic process
phosphate-containing compound metabolic process
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
Note that this term was 'developmental process'.
respiratory gaseous exchange by respiratory system
1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).
groom
fly
See also the biological process term 'behavior ; GO:0007610'.
A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
A biological process is an evolved process
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
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
positive regulation of cell population proliferation
negative regulation of cell population proliferation
See also the biological process term 'locomotory behavior ; GO:0007626'.
Note that 'radiation' refers to electromagnetic radiation of any wavelength.
embryo development ending in birth or egg hatching
negative regulation of biosynthetic process
positive regulation of biosynthetic process
negative regulation of metabolic process
positive regulation of metabolic process
negative regulation of catabolic process
positive regulation of catabolic process
This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.
regulation of mesenchymal cell proliferation
regulation of macromolecule biosynthetic process
positive regulation of macromolecule biosynthetic process
negative regulation of macromolecule biosynthetic process
positive regulation of phosphorus metabolic process
negative regulation of phosphorus metabolic process
regulation of cellular ketone metabolic process
positive regulation of macromolecule metabolic process
negative regulation of macromolecule metabolic process
positive regulation of cell communication
negative regulation of cell communication
negative regulation of norepinephrine secretion
positive regulation of norepinephrine secretion
positive regulation of steroid biosynthetic process
negative regulation of steroid biosynthetic process
positive regulation of glucose metabolic process
regulation of glucan biosynthetic process
negative regulation of serotonin secretion
positive regulation of serotonin secretion
urinary bladder smooth muscle contraction
energy derivation by oxidation of organic compounds
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.
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
transferase activity, transferring phosphorus-containing groups
regulation of phosphate metabolic process
Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.
cellular process involved in reproduction in multicellular organism
regulation of anatomical structure morphogenesis
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.
regulation of cellular metabolic process
negative regulation of cellular metabolic process
positive regulation of cellular metabolic process
regulation of cellular biosynthetic process
negative regulation of cellular biosynthetic process
positive regulation of cellular biosynthetic process
regulation of cellular catabolic process
negative regulation of cellular catabolic process
positive regulation of cellular catabolic process
negative regulation of nervous system process
positive regulation of nervous system process
locomotion involved in locomotory behavior
positive regulation of insulin secretion
regulation of response to external stimulus
negative regulation of response to external stimulus
positive regulation of response to external stimulus
negative regulation of intracellular transport
positive regulation of intracellular transport
plasma membrane bounded cell projection cytoplasm
regulation of polysaccharide metabolic process
regulation of polysaccharide biosynthetic process
negative regulation of organic acid transport
positive regulation of organic acid transport
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
This is not covalently bonded, which conflicts with changes to the parent definition.
protein-containing macromolecular complex
regulation of intracellular protein transport
negative regulation of catecholamine secretion
positive regulation of catecholamine secretion
Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior.
establishment of protein localization to extracellular region
positive regulation of embryonic development
regulation of cell population proliferation
regulation of circadian sleep/wake cycle, REM sleep
negative regulation of circadian sleep/wake cycle, sleep
negative regulation of circadian sleep/wake cycle, REM sleep
negative regulation of circadian sleep/wake cycle, non-REM sleep
circadian sleep/wake cycle, non-REM sleep
regulation of circadian sleep/wake cycle
Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (e.g. yeast with mating projections) that do have projections.
positive regulation of catalytic activity
negative regulation of catalytic activity
intracellular membrane-bounded organelle
intracellular non-membrane-bounded organelle
regulation of carbohydrate biosynthetic process
extracellular non-membrane-bounded organelle
positive regulation of monoatomic ion transport
negative regulation of monoatomic ion transport
regulation of generation of precursor metabolites and energy
regulation of carbohydrate catabolic process
regulation of respiratory gaseous exchange
regulation of respiratory system process
negative regulation of molecular function
positive regulation of molecular function
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
regulation of circadian sleep/wake cycle, sleep
regulation of circadian sleep/wake cycle, non-REM sleep
This term was obsoleted because it was not precisely defined.
negative regulation of glycogen biosynthetic process
positive regulation of glycogen biosynthetic process
negative regulation of glycogen catabolic process
positive regulation of glycogen catabolic process
negative regulation of heart contraction
positive regulation of heart contraction
negative regulation of lipid metabolic process
positive regulation of lipid metabolic process
negative regulation of carbohydrate metabolic process
positive regulation of carbohydrate metabolic process
negative regulation of muscle contraction
positive regulation of muscle contraction
negative regulation of phosphate metabolic process
positive regulation of phosphate metabolic process
positive regulation of circadian sleep/wake cycle, sleep
negative regulation of steroid metabolic process
positive regulation of steroid metabolic process
negative regulation of smooth muscle contraction
positive regulation of smooth muscle contraction
negative regulation of embryonic development
positive regulation of circadian sleep/wake cycle, REM sleep
positive regulation of circadian sleep/wake cycle, non-REM sleep
negative regulation of insulin secretion
positive regulation of hormone secretion
negative regulation of hormone secretion
positive regulation of lipid biosynthetic process
regulation of lipid biosynthetic process
positive regulation of biological process
negative regulation of biological process
regulation of post-embryonic development
negative regulation of post-embryonic development
positive regulation of post-embryonic development
positive regulation of response to stimulus
negative regulation of response to stimulus
multicellular organismal reproductive process
Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.
anatomical structure formation involved in morphogenesis
branching morphogenesis of an epithelial tube
multicellular organismal-level homeostasis
negative regulation of protein secretion
positive regulation of protein secretion
regulation of steroid biosynthetic process
neuromuscular process controlling balance
detection of stimulus involved in sensory perception
detection of chemical stimulus involved in sensory perception
detection of light stimulus involved in visual perception
detection of mechanical stimulus involved in sensory perception of sound
detection of chemical stimulus involved in sensory perception of smell
detection of chemical stimulus involved in sensory perception of taste
sensory perception of temperature stimulus
sensory perception of electrical stimulus
sensory perception of mechanical stimulus
detection of temperature stimulus involved in thermoception
detection of temperature stimulus involved in sensory perception
detection of light stimulus involved in sensory perception
detection of electrical stimulus involved in sensory perception
detection of temperature stimulus involved in sensory perception of pain
detection of mechanical stimulus involved in sensory perception of pain
detection of electrical stimulus involved in sensory perception of pain
detection of chemical stimulus involved in sensory perception of pain
detection of mechanical stimulus involved in equilibrioception
detection of mechanical stimulus involved in sensory perception
detection of mechanical stimulus involved in sensory perception of touch
negative regulation of lipid biosynthetic process
negative regulation of developmental process
positive regulation of developmental process
regulation of cellular component organization
negative regulation of cellular component organization
positive regulation of cellular component organization
regulation of phosphorus metabolic process
positive regulation of protein transport
negative regulation of protein transport
regulation of multicellular organismal process
positive regulation of multicellular organismal process
negative regulation of multicellular organismal process
Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
This term is useful for grouping, but is too general for manual annotation. Please use a child term instead.
positive regulation of transferase activity
negative regulation of transferase activity
visual perception involved in equilibrioception
biological process involved in intraspecies interaction between organisms
regulation of sensory perception of pain
regulation of nervous system development
negative regulation of nervous system development
positive regulation of nervous system development
smooth muscle contraction involved in micturition
regulation of macromolecule metabolic process
positive regulation of gastric acid secretion
negative regulation of gastric acid secretion
positive regulation of digestive system process
negative regulation of digestive system process
regulation of morphogenesis of a branching structure
positive regulation of cartilage development
negative regulation of cartilage development
regulation of nematode larval development
positive regulation of nematode larval development
negative regulation of nematode larval development
regulation of small molecule metabolic process
positive regulation of small molecule metabolic process
negative regulation of small molecule metabolic process
collagen-containing extracellular matrix
detection of stimulus involved in sensory perception of pain
extracellular membrane-bounded organelle
negative regulation of glucagon secretion
positive regulation of glucagon secretion
regulation of establishment of protein localization
regulation of bile acid biosynthetic process
negative regulation of bile acid biosynthetic process
positive regulation of bile acid biosynthetic process
regulation of glycogen metabolic process
negative regulation of glycogen metabolic process
positive regulation of glycogen metabolic process
protein localization to extracellular region
cellular component organization or biogenesis
negative regulation of mesenchymal cell proliferation
monocarboxylic acid biosynthetic process
positive regulation of somatostatin secretion
negative regulation of somatostatin secretion
positive regulation of peptide hormone secretion
negative regulation of peptide hormone secretion
positive regulation of intracellular protein transport
negative regulation of intracellular protein transport
regulation of locomotion involved in locomotory behavior
positive regulation of locomotion involved in locomotory behavior
negative regulation of locomotion involved in locomotory behavior
Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass.
organic cyclic compound metabolic process
organic cyclic compound biosynthetic process
organic hydroxy compound metabolic process
organic hydroxy compound biosynthetic process
negative regulation of male mating behavior
positive regulation of male mating behavior
positive regulation of response to water deprivation
negative regulation of blood circulation
positive regulation of blood circulation
negative regulation of secretion by cell
positive regulation of secretion by cell
negative regulation of protein localization
positive regulation of protein localization
negative regulation of respiratory gaseous exchange
positive regulation of respiratory gaseous exchange
negative regulation of sensory perception of pain
positive regulation of sensory perception of pain
regulation of bile acid metabolic process
negative regulation of bile acid metabolic process
positive regulation of bile acid metabolic process
regulation of smooth muscle contraction involved in micturition
negative regulation of smooth muscle contraction involved in micturition
positive regulation of smooth muscle contraction involved in micturition
negative regulation of establishment of protein localization
positive regulation of establishment of protein localization
An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay).
negative regulation of epithelial tube formation
positive regulation of epithelial tube formation
regulation of morphogenesis of an epithelium
negative regulation of morphogenesis of an epithelium
positive regulation of morphogenesis of an epithelium
regulation of detection of mechanical stimulus involved in sensory perception of touch
negative regulation of detection of mechanical stimulus involved in sensory perception of touch
positive regulation of detection of mechanical stimulus involved in sensory perception of touch
negative regulation of mechanosensory behavior
positive regulation of mechanosensory behavior
negative regulation of mesoderm formation
positive regulation of mesoderm formation
negative regulation of lipid localization
positive regulation of lipid localization
regulation of multicellular organismal development
regulation of response to water deprivation
negative regulation of reproductive process
positive regulation of reproductive process
negative regulation of mesoderm development
positive regulation of mesoderm development
negative regulation of ectoderm development
positive regulation of ectoderm development
A change of place or position of part of an organism that does not involve the entire organism [NBO:SMAC]
Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences.
Observable characteristic of behaviour related to involuntary movement in response to a stimulus.
Behavior related to the acquisition and processing of information and/or the storage and retrieval of this information over time.
The act of moving any of the tissues and hard structures surrounding the mouth other than teeth, jaws or filter structures [NBO:AC]
Observable characteristic of behavior associated with the specific movement from place to place of an organism.
Behavior directly related to the production of offspring [NBO:AC]
reproduction
"A behavior that occurs predominantly or only, in individuals that are part of a group." [Wikipedia:Social_behavior]
Movement from place to place of an organism." [GO:0007626]
locomotion
Behavior related to the interactions between organisms for the purpose of mating.
A behavioral interaction between organisms in which one organism has the intention of inflicting damage on another individual using physical or verbal means.
"Behavior relate to the usually upward movement off the ground or other surface through sudden muscular effort in the legs." [GO:0007630]
jump
The act of seizing with teeth or jaws an object or organism so as to grip or break the surface covering [NBO:AC]
bite
Emotional behavior related to fear or anxiety.
The act of stroking or touching with the tongue [NBO:AC]
lick
A change in place or position of the portion of the organism containing the brain, mouth and main sense organs [NBO:SMAC]
move head
Behavior associated with any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
Movement of the head in the horizontal plane.
shake head
Behavior related to the readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals.
An uncontrolled, paroxysmal neuronal discharge in any part of the brain; it may cause physical or mental symptoms and may be convulsive or nonconvulsive
The act of moving the head in a plane, circularly, pivoting at the neck [NBO:SMAC]
rotate head
The act of using body parts to pick at, rub and or remove material from exterior covering, e.g., fur, scales, feathers, skin [NBO:SMAC]
A kinesthetic behavior which relatively increased.
A kinesthetic behavior which relatively decreased.
"Loss of power of voluntary movement in a muscle through injury or disease of its nerve supply." [JAX:<new dbxref>]
"Paralysis of the extensors of the wrist and fingers." [JAX:<new dbxref>]
Carpoptosis is most often caused by a lesion of the radial nerve.
Behaviour related to the activity which primary purpose is the sexual reproduction.
produce sound
behavioral control of production of sound
A behavior in which an organism produces sounds by a mechanism involving its respiratory system.
vocalize
The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
The behavioral control of defecation. [wikipedia:defecation]
Excretion behaviour that controls liquid waste expulsion.
urinate
Behavior associated with and resulting in the production and subsequent release of any substance or product elaborated, and released by a cell or gland [NBO:SMAC]
secrete
behavioral control of external secretion
The regulated release of the aqueous layer of the tear film from the lacrimal glands.
tear release
A behavior that occurs between two individuals, such as parent and child, and involves an emotional attachment that implies a special and focused relationship.
Behavior associated with protection, or assisting growth and development of young. [NBO:AC]
Behavior that serves to regulate the temperature around offspring.[NBO:AC]
Parental behavior that promotes the breaking of an offspring's dependence on parental resources.
Immelmann K, Beer C. A dictionary of ethology. Harvard University Press; 1989.
Especially food resources, and we know that many male birds provide offspring food.
Behavior related the protection of offspring.
protection of offspring
"Play behavior that is associated with the socialization of an individual into the group." [web:http\://www.bio.davidson.edu/people/vecase/behavior/Spring2009/Sacco/Pages/Play%20Fighting.html]
Behavior related to the actions by which an organism modulates its internal body temperature.
Behavior associated with two or more individuals' achieving or maintaining close and extensive bodily contact; to nestle closely with another [NBO:AC]
huddle
Exposure of body to sunlight, either by modification of body posture, by movement to specific areas or both [NBO:SMAC]
basking
sunning
sunning behavior
Specific actions of a newborn or infant mammal that result in the derivation of nourishment from the breast.
The act of locomoting on limbs with body off the ground such that periodically none of the limbs are touching the ground [NBO:SMAC]
run
The act of locomoting on limbs with body off the ground such that at least one limb is always touching the ground [NBO:AC]
walking
The act of dragging claws or nails over a surface [NBO:AC]
scratch
scratching behavior
Male's insertion of sperm-transfer organ into the body of the female [NBO:SMAC]
copulate
Loss of power of voluntary movement in muscles of the forelimb through injury or disease of it or its nerve supply.
Behavior related to the washing or cleansing of the body in a fluid, usually water or an aqueous solution.
bathe
A feeding behavior associated with the intake or the frequency of intake or preference or manner of intake of food.
A feeding behavior associated with the intake or the frequency of intake or preference or manner of intake of liquids.
Behavior related to a variety of aspects of the relationship between the mind and the world with which it interacts.
"Behavior related to the state of being conscious and engages in a coherent cognitive and behavior responses to the external world." [NBO:SD, wikipedia:Wakefulness]
Behavior related to reduced or absent consciousness, relatively suspended sensory activity, and inactivity of nearly all voluntary muscles.
Behavior related to the movement facilitated by the generation of hole or tunnel dug into the ground.
The act of repeated grinding, tearing, and or crushing with teeth or jaws [NBO:SMAC]
chew
gnaw
A very broad category including the partial or complete performance of adult functional behaviors in non-functional contexts, as well as interactive behaviors peculiar to immature animals [NBO:AC]
play
Undirected behavior involving exercise and coordination, and often associated with repetition and 'practice' of adult behavior patterns in a non-functional context [NBO:AC]
motor play
Many different actions are included in locomotor play. Some of the actions include a vertical leap, running in circles, chasing an animals own tail, lolloping, bouncing, bucking, rolling, whirling, dangling, spinning, back flips, hand stands, somersaults, and hanging upside down. The vertical leap is seen in mammals like in primates, hares, and mice. Along with running and bouncing, the vertical leap is important for strengthening leg muscles for self defense, escaping, or chasing. Activities like dangling and hanging upside down are important for improving climbing ability. These many different examples of locomotor play are important in strengthening muscles and improving motor skills. By participating in locomotor play, individuals will be able to improve skills like fighting, hunting, fleeing, and climbing.
The behavioral interactions between organisms for the purpose of attracting sexual partners.
courtship
Behavior related to the specific actions or reactions of an organism following mating.
post-copulatory behavior
The act of bringing an object or substance into the body by swallowing, surrounding or absorbing it [NBO:SMAC]
The act of moving the body core lower, closer to the ground [NOB:SMAC]
sit down
The act of moving the body core higher, away from the ground [NBO:SMAC]
stand up
writhe
Behavior related to any biological process in an organism that recurs with a regularity of approximately 24 hours.
Emotional behavior related to a state of low mood and aversion to activity.
Behavior related to the exploration/investigation of a novel object, situation or environment.
Behavior related to defence against predation or predators.
antipredator behavior
Behavior related to the preparation of the body to \"fight\" or \"flee\" from perceived attack, harm or threat.
A physical aggression behavior involving attack on prey by a predator.
Behavior directed at a predator that signifies hostility and predicts an increased probability of attack [NBO:SMAC]
threaten predator
An emotional behavior related to a feeling of uneasiness or nervousness triggered by a specified triggering stimulus such as pain or the threat of danger.
An emotional behavior related to a feeling of uneasiness or nervousness triggered by an identifiable triggering stimulus.
An emotional behavior related to a feeling of uneasiness or nervousness in respect to an object.
An emotional behavior related to a feeling of uneasiness or nervousness in respect to a particular situation or environment.
fear behavior towards situation/environment
An emotional behavior related to a feeling of uneasiness or nervousness in respect to a living thing.
A phobia characterised by fear of open spaces.
Behavior related to the exploration/investigation of a novel environment.
Behavior related to the exploration/investigation of a novel obhject.
Behavior related to the exploration/investigation of a novel odor.
Moving backwards in response to a fear stimulus.
Behavioral response to the presidency of the stressor where it becomes necessary to attempt some means of coping with the stress.
Exhibiting a domineering, assault posture and/or hostile physical action towards humans.
Exhibiting a domineering, assault posture and/or hostile physical action towards animals.
Exhibiting a domineering, assault posture and/or hostile physical action toward any type of object.
Exhibiting a domineering, assault posture and/or hostile physical action towards mice.
Exhibiting a domineering, assault posture and/or hostile physical action towards women.
Exhibiting a domineering, assault posture and/or hostile physical action towards men.
Exhibiting a domineering, assault posture and/or hostile physical action towards male mice.
Exhibiting a domineering, assault posture and/or hostile physical action towards female mice.
Exhibiting a domineering, assault posture and/or hostile physical action toward inanimate objects.
aggressive behavior towards inanimate objects
Exhibiting a domineering, assault posture and/or hostile physical action toward animate objects.
aggressive behavior towards animate objects
Exhibiting a domineering, assault posture and/or hostile physical action towards children.
Exhibiting a domineering, assault posture and/or hostile physical action towards pups.
Gender related exhibition of a domineering, assault posture and/or hostile physical action.
Exhibiting a domineering, assault posture and/or hostile physical action towards female animals.
Exhibiting a domineering, assault posture and/or hostile physical action towards male animals.
A behavior that occur quickly without control, planning, or consideration of the consequences of that behavior.
An aggressive behavior that aims to inflicting damage on another entity using physical means.
agonism
Any behavior that tends to prevent further or future attack, often by signalling a willingness to yield or surrender [NBO:AC]
A behavior associated with the tendency of an organism towards being passive and willing to yield to male animals.
A behavior associated with the tendency of an organism towards being passive and willing to yield to female animals.
A behavior associated with the tendency of an organism towards being passive and willing to yield towards male mice.
Behavior by which an animal removes itself spatially from an agonistic encounter in which it is not the winner [NBO:AC]
retreat
Behavior characterized by a quick excitability to annoyance, impatience, or anger.
Emotional behavior related to excitement or restlessness.
A behavior associated with the intake of liquid.
A drinking behavior associated with the intake of alcohol.
A drinking behavior associated with the intake of water.
A feeding behavior associated with the intake of food.
A feeding behavior associated with the intake of saccharin.
Predilection to ingest a liquid over other substances.
Purposeful avoidance of a liquid due to dislike.
Purposeful avoidance of liquid alcohol due to dislike. [NBO:LKSR]
Predilection to ingest alcohol over other substances.
Behavior of a mother towards her offspring.
Behavior of a father towards his offspring.
Maternal behavior related to the brining up her offspring.
Paternal behavior related to the brining up his offspring.
Behavior related to the parent's tendency to collect stray offspring and return them to a defined location.
retrieval
Behavior related to all sleep stages in the circadian sleep/wake cycle other than REM sleep.
These stages are characterized by a slowing of brain waves and other physiological functions.
Endogenously driven roughly 24-hour cycle in biochemical, physiological, or behavioral processes.
Behavior related with the ability of an organism's ability to store, retain, and recall information and experiences.
"Learning by associating a stimulus (the cause) with a particular outcome (the effect)." [Wikipedia:Learning#Associative_learning]
The formation of associations among stimuli and responses.
"A behavioral process whose outcome is a relatively long-lasting adaptive behavioral change whereby an organism modifies innate vocalizations to imitate or create new sounds." [GO:0042297]
A decrease in a behavioral response to a repeated stimulus.
Gradual decrease in behavioral responses with repeated encounters of a particular stimulus, which proves of no consequence.
An increase in behavioral responses following repeated applications of a particular stimulus.
A type of memory that allows the recall of something from several seconds to as long as a minute.
This type of memory, lasting hours to months, critically depends on a transfer of the information from short term memory using repeated rehearsal.
Report great detail about a complex stimulus immediately following its presentation. This ability forms within a few tens of milliseconds and decays again rapidly within a few hundred milliseconds.
A memory that last for months to lifetime.
A type of memory that allows the recall of something from minutes to several hours.
Ability to become conscious of, or declare, facts and experiences.
Encoded by the hippocampus, entorhinal cortex, and perirhinal cortex but store possibly in the medial temporal lobe.
Ability to consciously recall knowledge of facts that are independent of a specific time and place.
Ability to explicitly recall information about a specific event that has occurred at a specific time and place.
Non-declarative memory type of memory, which does not need to involve conscious awareness in the act of recollection.
Encoded and probably stored by the cerebellum and the striatum but store in the amygdala.
Consolidating a specific motor task into memory through repetition.
Depends on the cerebellum and basal ganglia.
"A type of memory associated with emotional experiences." [wikipedia:http\://www.scholarpedia.org/article/Emotional_memory]
Remembering to perform an intended action.
Remembering to perform an intended action in respect to a particular event.
Remembering to perform an intended action in respect to a particular time reference.
A type of memory for particular events within one's own life.
"Ability to store and retrieve previously experienced visual sensations and perceptions when the stimuli that originally evoked them are no longer present." [wikipedia:Visual_memory]
"The ability to recall images, sounds, or objects in memory with extreme precision and in abundant volume." [wikipedia:Eidetic_memory]
Ability to orient oneself in space, to recognize and follow an itinerary, or to recognize familiar places.
An implicit memory effect in which exposure to a stimulus influences response to a later stimulus.
A type of priming where the prime and the target are from the same semantic category and share features.
A type of priming where the target is a word that has a high probability of appearing with the prime, and is \"associated\" with it but not necessarily related in semantic features.
A type of priming based on the meaning of a stimulus and is enhanced by semantic task.
A type priming based on the form of the stimulus and is enhanced by the match between the early and later stimuli.
Change in the responsiveness of a sensory system when confronted with a constant stimulus.
A form of associative learning that requires an unconditional reflex, where an unconditional stimulus (US)brings about an automatic, unlearned (unconditional) response (UR). If a neutral stimulus (NS) tends to precede it, an association is made and the conditional response (CR) becomes transferred onto the (previously neutral) conditional strimulus (CS); a conditional reflex has been learned.
A type of associative learning that allows organisms to acquire affective responses, such as fear, in situations where a particular context or stimulus is predictably elicits fear via an aversive context.
"Operant conditioning is the use of a behavior's antecedent and/or its consequence to influence the occurrence and form of behavior." [wikipedia:Operant_conditioning]
Operant conditioning is distinguished from classical conditioning in that operant conditioning deals with the modification of "voluntary behavior" or operant behavior.
Avoidance learning when the action occurs.
Avoidance learning when no action occurs.
Associative learning behavior that arises from observing or interacting with another individual.
Original definition: "The sociological process of training individuals in a society to act or respond in a manner generally approved by the society in general and peer groups within society." [wikipedia:Social_conditioning]
"Perception of objects remains the same despite changes in their image on the retina." [:http\://science.jrank.org/pages/5094/Perception.html]
Observable characteristic of behavior related to the awareness of body balance and movement.
Behavior related to the tendency of an organism to maintain internal equilibrium.
Behavior related to the deprivation of water.
Behavior related to the deprivation of food.
Behavior related to the drive of an organism to engage in sexual activity.
Any process which modulates the physical craving for food.
Any process which modulates the physical craving for food over short term food deprivation.
Any process which modulates the physical craving for food over long term food deprivation.
An observable characteristic of the behavior of an organism.
"A pathological anxiety characterized by long-lasting anxiety that is not focused on any one object or situation." [wikipedia:Generalized_anxiety_disorder]
A pathological anxiety characterized by fear or anxiety triggered by a specific stimulus or situation.
"A pathological anxiety characterized by brief attacks of intense terror and apprehension, often marked by trembling, shaking, confusion, dizziness, nausea, difficulty breathing." [wikipedia:Panic_disorder]
"A pathological anxiety primarily characterized by repetitive obsessions (distressing, persistent, and intrusive thoughts or images) and compulsions (urges to perform specific acts or rituals)." [wikipedia:Obsessive%E2%80%93compulsive_disorder]
"A pathological behavior characterized by one or more symptoms of a physical dysfunction but for which there is no identifiable organic cause." [wikipedia:Somatoform_disorder]
"A somatoform disorder characterised by a physical dysfunction (blindness, deafness, paralysis, numbness, etc. ) that has no underlying organic basis." [wikipedia:Conversion_disorder]
A somatoform disorder characterised by a continuing belief that one has one or more serious illnesses although no medical evidence supports the belief.
"A mood disorder formerly characterised by alternating periods of mania and depression (and in some cases rapid cycling, mixed states, and psychotic symptoms)." [wikipedia:Bipolar_disorder]
disorganized (hebephrenic) schizophrenia
Observable characteristic of behaviour related to cognitive processes.
Observable characteristic of behavior associated with the intake of food or liquids.
Behaviors that are described for or done by groups of animals, not individual animals [NBO:SMAC]
group actions
A behavioral interaction between organisms in which one organism exhibits aggression using vocal or verbal means.
A discriminatory behavior that is related to age.
Behavior related to having a generally positive attitude toward another person.
A helping behavior (without expectation of extrinsic rewards and sometimes involving personal risk or sacrifice) that benefits individuals or society.
"Prosocial behavior is caring about the welfare and rights of others, feeling concern and empathy for them, and acting in ways that benefit others." [wikipedia:Prosocial_behavior]
"Helping behavior refers to voluntary actions intended to help the others, with reward regarded or disregarded." [wikipedia:Helping_behavior]
"Reciprocal altruism is the idea that the incentive for an individual to help in the present is based on the expectation of the potential receipt in the future." [wikipedia:Helping_behavior]
Behavior related to one or more capacities of the mind.
"Behavior stemming from the ability to identify, assess, and control the emotions of oneself, of others, and of groups." [wikipedia:Emotional_intelligence]
behavior stemming from emotional intelligence
Behavior that facilitates the restoration of normal interactions between parties that recently engaged in a conflict.[NBO:AC]
reconciliation
reconciliation behavior
"Behavior associated with problem finding and problem shaping." [wikipedia:Problem_solving]
Behavior stemming from intelligence associated with the capacity of conveying information. (Example: behavior adaptation in chimpanzees in order to communicate with humans.)
behavior stemming from communication intelligence
A domineering, assault posture and/or hostile physical action towards animals exhibited by male animals.
A domineering, assault posture and/or hostile physical action towards animals exhibited by female animals.
A domineering, assault posture and/or hostile physical action towards animals exhibited by a mother or attending female.
A domineering, assault posture and/or hostile physical action towards animals exhibited by a father or attending male.
Behavior related with the gradual loss of information and experiences stored in the memory of an organism.
Behavior related with the ability of an organism's ability to store information and experiences.
Behavior related with the ability of an organism's ability to recall information and experiences.
Cognitive perception of a sensation by any of the five senses -- vision, touch, smell, taste, and hearing.
Example: moving head to watch passing object.
A phobia characterised by fear of social or performance situations in which embarrassment may occur.
A phobia characterised by fear of high places.
Behavior related to the actions of an organism in relation to sleep.
Any process that modulates the frequency, rate or extent of sleep.
"The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610]
"Behavior related to the actions or reactions of an organism in response to a visual stimulus." [GO:0007632]
"Behavior related to the actions or reactions of an organism pertaining to movement of the eyes and of objects in the visual field, as in nystagmus." [GO:0007634]
"Behavior related to the actions or reactions of an organism in response to a sound." [GO:0031223]
Behavior related to the awareness of body balance and movement.
Behavior as a result of the sensation of chemicals.
Behavior related to the sensation of odors.
Taste can be described as five basic sensations, sweet, sour, salty, bitter and umamy which can be combined in various ways to make all other taste sensations.
Behavior related to environmental temperature.
Behavior related to the sensations arising from the skin and from the muscles, tendons, and joints.
Sensations arising from the internal organs (the viscera), such as pain or the sense of fullness of the stomach or bladder, may therefore be included, although they are usually considered separately as visceral sensations. Pain arising from the viscera is often felt as though it comes from some part of the body surface or underlying tissue.
Behavior related to the detection of high environmental temperature.
Behavior related to the detection of low environmental temperature.
chemically-elicited antinociception behaviour
chemically-elicited antinociceptive behavior
"Movement behavior of the body or its parts."
"The coordination of combinations of body movements created with the kinematic (such as spatial direction) and kinetic (force) parameters that result in intended actions." [wikipedia:Motor_coordination]
"The coordinated control of eye movement with hand movement, and the processing of visual input to guide reaching and grasping along with the use of proprioception of the hands to guide the eyes." [wikipedia:Eye%E2%80%93hand_coordination]
Optic apraxia - total inability of a person to coordinate eye and hand movements.\nOptic ataxia - inability of a person to coordinate eye and hand movements.
Coordination that results in spatial and temporal planning of reaching and grasping.
Coordination that results in bimanual synchronization and temporal association of the hands.
The coordination of lower limb movement.
The coordination of upper limb movement.
The coordination of large muscle groups and whole body movement.
Coordination of small muscle movements which occur usually in coordination with the eye.
The coordination of the whole body movement.
The coordination of the lower body movement.
The coordination of the upper body movement.
Intentionally or habitually assumed arrangement of the body and its limbs.
Intentionally or habitually assumed arrangement of the body.
Intentionally or habitually assumed arrangement of the limbs.
Intentionally or habitually assumed arrangement of the body and its limbs in inactivity.
Behavior associated with surface locomotion.
Behavior related to the upward thrust produced by the rapid, simultaneous extension of the hind legs with the intend to cross wide gaps in the locomotor surface.
"The pattern of movement of the limbs of animals, characterized by elements of progression, stability, speed and length over the ground." [MP:0001406]
A behavioral pattern characterized by the distance covered by as many steps as there are legs.
Behavior related to the movement resulting by dragging the body close to the ground.
crawl
"Behavior related to the locomotion of animals in trees." [wikipedia:Arboreal_locomotion]
arm over arm swinging movement through arboreal environment [NBO:AC]
Arguably the epitome of arboreal locomotion, it involves swinging with the arms from one handhold to another.
Behavior related to the movement of an organism from one location to another through the air.
Behavior related to the self-propelled movement of an organism from one location to another through the air, usually by means of active wing movement.
Behavior related to the ascending a steep object.
Behavior related to the expansion lateral surface of the body with the intention of increasing the wind resistance against the body and hence reducing the speed of falling.
Behavior related to the upward thrust produced by the rapid, simultaneous extension of the hind legs with the intend to rise in the air.
Behavior related to the movement of an organism from one location to another through a liquid medium.
Behavior related to the control of the direction of locomotion.
Behavior related to the ability of an animal to determine and to alter its position in the environment.
Alteration of speed or direction of movement in response to a sensory stimulus.
Locomotory orientation in a specific spatial relationship to a stimulus.
Behavior related to the mechanical alteration of the locomotor pattern through which the animal adjusts its position.
"Locomotory orientation in response to specific chemical concentration gradient." [GO:0006935]
"Locomotory orientation in response to gravity." [GO:0048062]
"Locomotory orientation away from the source of gravity." [GO:0048060]
"Locomotory orientation towards the source of gravity." [GO:0048061]
"Locomotory orientation in response to touch." [GO:0001966]
"Locomotory orientation in response to physical parameters involved in energy generation." [GO:0009453]
"Locomotory orientation in response to light." [GO:0042331]
"Locomotory orientation in response to a temperature gradient." [GO:0043052]
Locomotory orientation in response to sound.
Locomotory orientation in response to mechanical stimulus.
Locomotory orientation in response to pressure.
Behavior related to movements that occur independent of planning.
Movevents listed here are involuntary, but may be also generated by free will, like blinking of the eyelids and respiratory movements.
Behavior related to involuntary movement in response to a stimulus.
"Reflex actions originating in the central nervous system that are exhibited by normal infants in response to particular stimuli." [wikipedia:Primitive_reflexes]
"An action or movement due to the application of a sudden unexpected stimulus." [wikipedia:Startle_reflex]
"A reflex that arises when tilting the head back while lying on the back causes the back to stiffen and even arch backwards, the legs to straighten, stiffen, and push together, the toes to point, the arms to bend at the elbows and wrists, and the hands to become fisted or the fingers to curl." [wikipedia:Tonic_labyrinthine_reflex]
"A reflex that assists in the birthing process and helps to develop muscle tone, kicking and stimulates vestibular function in utero." [wikipedia:Asymmetrical_tonic_neck_reflex]
A reflex that causes the eyes to alternately fixate at far and near, expanding vision development from arms length to far away.
"It is elicited by holding the newborn in ventral suspension (face down) and stroking along the one side of the spine. A reflex that caused the laterally flex toward the stimulated side when a newborn is held in ventral suspension (face down) and stroking along the one side of the spine." [NBO:Galant_reflex]
"A reflex elicited by the application of pressure to both palms resulting varying responses such as head flexion, head rotation or opening of the mouth, or a combination of these responses." [wikipedia:Primitive_reflexes]
"A reflex that causes the infant to begin to paddle and kick in a swimming motion upon its placement face down in a pool of water." [NBO:Primitive_reflexes]
"A reflex elicited when the sole of the foot is stimulated with a blunt instrument." [wikipedia:Plantar_reflex]
"A reflex elicited by the placement of an object in the infant's hand and strokes their palm, causing its fingers to close and grasp it." [wikipedia:Primitive_reflexes]
"A reflex that causes a newborn infant to turn his head toward anything that strokes his cheek or mouth, searching for the object by moving his head in steadily decreasing arcs until the object is found." [wikipedia:Primitive_reflexes]
"A reflex that causes the infant to instinctively suck at anything that touches the roof of their mouth and suddenly starts to suck simulating the way they naturally eat." [wikipedia:Primitive_reflexes]
"A reflex that causes the infant to attempt to 'walk' by placing one foot in front of the other when the soles of their feet touch a flat surface." [wikipedia:Primitive_reflexes]
Behavior related to movements executed with intent.
"A muscle contraction in response to stretching within the muscle." [wikipedia:Stretch_reflex]
A deep tendon reflex that elicits involuntary contraction of the biceps brachii muscle.
"A deep tendon reflex elicited by striking the lateral surface of the forearm proximal to the distal head of the radius, characterized by normal slight elbow flexion and forearm supination." [Medical disctionary:http\://medical-dictionary.thefreedictionary.com/brachioradialis+reflex]
A reflex that elicits involuntary contraction of the extensor digitorum muscle.
"A deep tendon reflex that elicits involuntary contraction of the triceps brachii muscle." [wikipedia:Triceps_reflex]
A deep tendon reflex that elicits extension of the leg resulting from a sharp tap on the patellar tendon.
"A reflex bending of the foot resulting from contraction of the calf muscles when the Achilles tendon is sharply struck." [Medical Dictionary:http\://medical-dictionary.thefreedictionary.com/Achilles+reflex]
"A reflex that controls the diameter of the pupil, in response to the intensity (luminance) of light that falls on the retina of the eye, thereby assisting in adaptation to various levels of darkness and light, in addition to retinal sensitivity." [wikipedia:Pupillary_light_reflex]
"A reflex action of the eye, in response to focusing on a near object, then looking at distant object (and vice versa), comprising coordinated changes in vergence, lens shape and pupil size." [wikipedia:Accommodation_reflex]
"An involuntary blinking of the eyelids elicited by stimulation of the cornea." [wikipedia:Corneal_reflex]
"A reflex eye movement that stabilizes images on the retina during head movement by producing an eye movement in the direction opposite to head movement, thus preserving the image on the center of the visual field." [wikipedia:Vestibulo-ocular_reflex]
"A form of involuntary eye movement that is part of the vestibulo-ocular reflex (VOR). It is characterized by alternating smooth pursuit in one direction and saccadic movement in the other direction." [wikipedia:Physiologic_nystagmus]
"A reflex contraction of the back of the throat, evoked by touching the soft palate." [wikipedia:Gag_reflex]
Observable characteristic of behavior related to the readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals.
A NREM parasomnia characterised by Involuntarily grinding of teeth while sleeping.
"A circadian rhythm sleep disorder characterized by a much later than normal timing of sleep onset and offset and a period of peak alertness in the middle of the night." [wikipedia:Delayed_sleep_phase_syndrome]
Inability to fall asleep and/or remain asleep for a reasonable amount of time.
A dyssomnia characterised by excessive daytime sleepiness (EDS) in which a person experiences extreme fatigue and possibly falls asleep at inappropriate times.
A NREM parasomnia characterised by abrupt awakening from sleep with behavior consistent with terror and a temporary inability to regain full consciousness.
"A reflex that results in the contraction of the muscles of the abdominal wall in response to stimulation of the overlying skin." [web:http\://www.merriam-webster.com/medical/abdominal%20reflex]
"Reflexive contraction of the external anal sphincter upon stroking of the skin around the anus." [wikipedia:Anal_wink]
"A reflex is elicited by lightly stroking the superior and medial (inner) part of the thigh resulting in a contraction of the cremaster muscle that pulls up the scrotum and testis on the side stroked." [wikipedia:Cremasteric_reflex]
"A reflex in mammals which optimises respiration to allow staying underwater for extended periods of time." [wikipedia:Mammalian_diving_reflex]
"An increase in tonus (normal tension) of the tissues of the abdominal muscles resulting from painful stimuli originating in a viscus." [:http\://www.wordinfo.info/words/index/inf]
"A reflex of the abdominal muscles to contract upon mechanical force to the abdomen, and serves as protection." [wikipedia:Muscular_defense]
"A response to activation of sensory neurons whose peripheral terminals are located on the surface of the body." [wikipedia:Scratch_reflex]
An action or movement due to the application of a sudden unexpected loud noise.
A reflex where the body reacts to pain or unpleasant stimuli by trying to move itself away from the source.
"A reflex where the flexors in the withdrawing limb contract and the extensors relax, while in the other limb, the opposite occurs." [wikipedia:Crossed_extensor_reflex]
"An involuntary muscle contraction that occurs in the middle ear of mammals in response to high-intensity sound stimuli." [wikipedia:Acoustic_reflex]
"A reflex in which joint movement can reflexively cause muscle activation or inhibition." [wikpedia:Arthrokinetic_reflex]
"A reflex by which the body rids the lower respiratory tract of any irritant that enters through the air and less frequently any fluids (drinks) and solids (food) that may spill into the respiratory tract." [XX:http\://www.healthhype.com/cough-reflex-physiology-process-ear-cough-reflexes.html]
"A pouting or pursing of the lips that is elicited by light tapping of the closed lips near the midline." [wikipedia:Snout_reflex]
"A reflex elicited by repetitive tapping on the forehead which result in blinking to the first several taps." [wikipedia:Glabellar_reflex]
"A skeletal muscle contraction causes the muscle to simultaneously lengthen and relax." [wikipedia:Golgi_tendon_reflex]
A reflex in which muscle groups around the vital organs begin to shake in small movements in an attempt to create warmth by expending energy.
The shivering reflex is triggered to maintain homeostasis.
A reflex in which mucus containing foreign particles or irritants is expelled and the nasal cavity is cleanses.
"A contraction of muscles in the gastrointestinal tract in response to distension of the tract following consumption of food and drink." [wikipedia:Vagus_reflex]
Selective tracking that follows a moving object by eye.
Original definition: Selectively track a moving object (Source: NBO:GVG).
Kinesthetic behavior initiated in the absence of specific sensory input.
"Behavior related to the activity in which individuals in a group clean or maintain one another's body or appearance." [wikipedia:Social_grooming]
allo-hygiene behavior
allohygiene
"Behavior related to the promotion of personal hygiene." [wikipedia:Social_grooming]
autohygiene
Behavior related to the state or ability to perceive, to feel, or to be conscious of events, objects or sensory patterns.
obsolete behavior related to feelings experiencing
The sustained focus of cognitive resources on information while filtering or ignoring extraneous information. Intended to encompass only attention to perceptual stimuli.
Behavior involving responding discretely to specific visual, auditory or tactile stimuli.
Behavior involving maintaining a behavioral or cognitive set in the face of distracting or competing stimuli.
Behavior involving mental flexibility that allows individuals to shift their focus of attention and move between tasks having different cognitive requirements.
Behavior involving maintaining a consistent behavioral response during continuous and repetitive activity.
Behavior involving responding simultaneously to multiple tasks or multiple task demands.
"The perception of familiar objects as approximately the same size regardless of their distance from the observer." [Jrank:http\://science.jrank.org/pages/5094/Perception.html]
"The perception of a color as constant under changing conditions of illumination." [wikipedia:Color_constancy]
The perception of familiar objects as approximately the same shape regardless of their distance or angle of view from the observer.
"Perception relating to the process of inferring the speed and direction of elements in a scene based on visual, vestibular and proprioceptive inputs." [wikipedia:Motion_perception]
"Perception related to the identification of objects and their distinction from each other." [:http\://science.jrank.org/pages/5094/Perception.html]
"Behavior involving an active reception and coordination of information relating to depth received through the sensory systems in order to perceive the three-dimensionality of the world and objects within it." [:erceiving the three-dimensionality of the world and objects Read more\: Perception - Perceptual Systems\, Historical Background\, Innate And Learned - Classical perceptual phenomena\, Broad theoretical approaches\, Current research/future developments http\://science.jrank.org/pages/5094/Perception.html#ixzz1It3oOobp]
Perception of the distance of an object.
"Misperception of stimuli, where what is perceived does not correspond to the actual dimensions or qualities of the physical stimulus." [jrank:http\://science.jrank.org/pages/5094/Perception.html]
"Behavior related to how the body reacts to a stressor ( a stimulus that causes stress), real or imagined." [wikipedia:Stress_(biological)]
It refers to the consequence of the failure of an organism to respond adequately to mental, emotional or physical demands, whether actual or imagined.
"Behavior related to the identification or realization of a threat or a stressor." [wikipedia:Stress_(biological)]
Behavior related to the depletion of the body resources for coping to stress.
A pathological sleeping behavior related to the initiating or maintaining sleep or of excessive sleepiness and are characterized by a disturbance in the amount, quality, or timing of sleep.
A dyssomnia characterized by excessive amounts of sleepiness.
"A dyssomnia where the patient moves limbs involuntarily during sleep, and has symptoms or problems related to the movement." [wikipedia:Periodic_limb_movement_disorder]
"A dyssomnia characterized by an irresistible urge to move one's body to stop uncomfortable or odd sensations." [wikipedia:Restless_legs_syndrome]
"A sleep breathing disorder characterized by abnormal pauses in breathing or instances of abnormally low breathing, during sleep." [wikipedia:Sleep_apnea]
"A dyssomnia characterized by a mistakenly perception of one's sleep as wakefulness." [wikipedia:Sleep_state_misperception]
A dyssomnia associated with alcohol intake.
A insomnia associated with food allergies.
"A pathological circadian behavior primarily related to the timing of sleep." [wikipedia:Circadian_rhythm_sleep_disorder]
"An extrinsic circadian rhythm sleep disorder characterized by insomnia and excessive sleepiness affecting people whose work hours are scheduled during the typical sleep period." [wikipedia:Shift_work_sleep_disorder]
extrinsic circadian rhythm sleep disorder
intrinsic circadian rhythm sleep disorder
"An extrinsic circadian rhythm sleep disorder resulting from rapid long distance transmeridian (east west or west east) travel." [wikipedia:Jet_lag]
"A circadian rhythm sleep disorder characterized by difficulty staying awake in the evening and staying asleep in the morning." [wikipedia:Advanced_sleep_phase_syndrome]
"A circadian rhythm sleep disorder which the affected individual's sleep occurs later and later each day, with the period of peak alertness also continuously moving around the clock from day to day." [wikipedia:Circadian_rhythm_sleep_disorder]
circadian rhythm sleep disorder, free running type
circadian rhythm sleep disorder, nonentrained type
"A circadian rhythm sleep disorder characterized by numerous naps throughout the 24-hour period, no main night time sleep episode and irregularity from day to day." [wikipedia:Irregular_sleep-wake_rhythm]
A sleeping behavior phenotype that involve abnormal and unnatural movements, emotions, perceptions, and dreams that occur while falling asleep, sleeping, between sleep stages, or during arousal from sleep.
An intrinsic sleep disorder characterised by breathing abnormalities.
A sleeping behavior characterised by vibration of respiratory structures and the resulting sound, due to obstructed air movement during breathing while sleeping.
"A sleep breathing disorder characterized by airway resistance to breathing during sleep." [wikipedia:Upper_airway_resistance_syndrome]
A hypersomnia characterized by recurrent episodes.
A hypersomnia that occurs as a result of a traumatic event involving the central nervous system.
A type of parasomnia that occurs during NREM sleep.
A NREM parasomnia characterised by the risef rom the slow wave sleep stage in a state of low consciousness and perform activities that are usually performed during a state of full consciousness.
A NREM parasomnia characterised by involuntary urination while asleep after the age at which bladder control usually occurs.
A NREM parasomnia characterised by talking during sleep.
"A REM parasomnia characterised by the lack of muscle atonia during sleep." [wikipedia:REM_Sleep_Behavior_Disorder]
A type of parasomnia that occurs during REM sleep.
A RBD that occurs mostly as a result of a side-effect in prescribed medication- usually antidepressants.
Idiopathic or associated with neurological disorders REM sleep behavior disorder.
A REM parasomnia consisting of breath holding and expiratory groaning during sleep that is distinct from both somniloquy and obstructive sleep apnea.
"An isolted sleep paralysis that is characterized by frequent episodes or a complex of sequential episodes whose total duration may exceed one hour, and particularly by the range and sense of perceived reality of the subjective phenomena experienced during episodes." [web:http\://www.theconsciousdreamer.org/SSE.HTM]
"A sleep paralaysis characterised by the absence of narcolepsy." [wikipedia:Sleep_paralysis]
"A REM parasomnia characterised by periods of inability to perform voluntary movements either when going to sleep or when waking up." [wikipedia:Sleep_paralysis]
"A sleep paralysis which upon falling asleep the person remains aware while the body shuts down for REM sleep." [wikipedia:Sleep_paralysis]
"A sleep paralysis which upon awakening, the person becomes aware before the REM cycle is complete,." [wikipedia:Sleep_paralysis]
Behavior related to the ascending stairs.
A dyssomnia characterised by fear of sleep.
depressive disorder not otherwise specified
"A major depressive disorder characterized by mood reactivity (paradoxical anhedonia) and positivity, significant weight gain or increased appetite (\"comfort eating\"), excessive sleep or somnolence (hypersomnia), a sensation of heaviness in limbs known as leaden paralysis, and significant social impairment as a consequence of hypersensitivity to perceived interpersonal rejection." [wikipedia:Atypical_depression]
"A major depressive disorder characterized by a loss of pleasure (anhedonia) in most or all activities, a failure of reactivity to pleasurable stimuli, a quality of depressed mood more pronounced than that of grief or loss, a worsening of symptoms in the morning hours, early morning waking, psychomotor retardation, excessive weight loss (not to be confused with anorexia nervosa), or excessive guilt." [wikipedia:Melancholic_depression]
"A major depressive disorder characterized by a major depressive episode, particularly of melancholic nature, where the patient experiences psychotic symptoms such as delusions or, less commonly, hallucinations." [wikipedia:Psychotic_major_depression]
A major depressive disorder characterized by psychological and motorological disturbances.
"A major depressive disorder characterized by a intense, sustained and sometimes disabling depression experienced by women after giving birth." [wikipedia:Postpartum_depression]
"A major depressive disorder usually characterized seasonal pattern with depressive episodes coming on in the winter or summer, spring or autumn, repeatedly, year after year." [wikipedia:Seasonal_affective_disorder]
A depressive disorder characterized by chronic, different mood disturbance.
For humans: where a person reports a low mood almost daily over a span of at least two years.
"A depressive disorder characterized by intermittent depressive episodes, in women not related to menstrual cycles, occurring at least once a month over at least one year or more fulfilling the diagnostic criteria for major depressive episodes except for duration which in RBD is less than 14 days, typically 2 to 4 days." [wikipedia:Recurrent_brief_depression]
"A depressive disorder that does not meet full criteria for Major depressive disorder but in which at least two depressive symptoms are present for two weeks." [wikipedia:Minor_Depressive_Disorder]
"A type of bipolar disorder distinguished by the presence or history of one or more manic episodes or mixed episodes with or without major depressive episodes." [wikipedia:Bipolar_I]
"A bipolar disorder characterised by recurrent intermittent hypomanic and depressive episodes." [wikipedia:Mood_disorder]
A bipolar disorder characterised by recurrent hypomanic and dysthymic episodes, but no full manic episodes or full major depressive episodes.
"A bipolar disorder characterised by symptoms in the bipolar spectrum (e.g. manic and depressive symptoms) but does not fully qualify for any of the three types of bipolar disorder." [wikipedia:Bipolar_Disorder_Not_Otherwise_Specified]
bipolar disorder not otherwise specified
"A pathological anxiety which results from a traumatic experience." [wikipedia:Post-traumatic_stress_disorder]
"A pathological anxiety characterized by feeling of excessive and inappropriate levels of anxiety over being separated from a person or place." [wikipedia:Separation_anxiety_disorder]
Any process in which an organism modulates its heart rate at different values with a regularity of approximately 24 hours.
"Any process in which an organism modulates its blood pressure at different values with a regularity of approximately 24 hours." [GO:GO\:0003052]
circadian regulation of systemic arterial blood pressure
Any homeostatic process in which an organism modulates its internal body temperature at different values with a regularity of approximately 24 hours.
Observable characteristic of feeding behavior that relates to eating.
Observable characteristic of feeding behavior that relates to drinking.
A pathological drinking behavior characterised by an excessive desire to drink.
'participates in' some ('regulation of drinking behavior' and (has_quality some ('increased frequency' and towards some 'liquid consumption' and owl:qualifier some chronic)))
A pathological drinking behavior characterised by large intake of fluids by mouth, usually due to excessive thirst that is relatively prolonged.
'participates in' some ( 'regulation of drinking behavior' and regulates some ('liquid consumption' and has-input some ('liquid substance' and has_quality some 'increased mass')) and owl:qualifier some 'temporally extended')
A pathological drinking behavior characterised by an excessive relative temporal desire to drink.
'participates in' some ('regulation of drinking behavior' and (has_quality some ('increased frequency' and (towards some 'liquid consumption') and (owl:qualifier some 'temporally extended'))))
A pathological feeding behavior characterised by failure to eat.
The act of moving food from the mouth cavity to the esophagus through coordinated muscular movements [NBO:AC]
swallow
A pathological eating behavior characterised by an abnormally large intake of food by mouth, usually due to excessive hunger that is relatively prolonged.
Lack of ability to enjoy a sense of pleasure.
Behaviour related to the male activity which primary purpose is the sexual reproduction.
Behaviour related to the female activity which primary purpose is the sexual reproduction.
"Ability to correctly remember something that has been encountered before." [wikipedia:Recognition_memory]
"Ability to perceive the physical properties of an object (such as shape, colour and texture) and apply semantic attributes to the object, which includes the understanding of its use, previous experience with the object and how it relates to others." [wikipedia:Cognitive_Neuroscience_of_Visual_Object_Recognition]
A visual object recognition that lasts hours to months and critically depends on a transfer of the information from short term object recognition memory using repeated rehearsals.
"A type of memory responsible for recording information about one's environment and its spatial orientation." [wikipedia:Spatial_memory]
"A type of memory that allows one to temporarily store and manage information about one's environment and its spatial orientation." [wikipedia:Spatial_memory]
Behavior related to the activity in which a mother cleans or maintains the body or the appearance of her offsprings.
Behavior relating to the plucking of fur/hair or whiskers/vibrissae.
Behavior related to the barbering of other individuals of a cohort.
Behavior related to the barbering of oneself.
A pathological behavior characterized by muscular rigidity and fixation of posture regardless of external stimuli, as well as decreased sensitivity to pain.
Observable characteristic of behavior that occurs predominantly or only, in individuals that are part of a group.
A pathological behavior associated with repetitive or ritualistic movement, posture, or utterance.
Observable characteristic of behavior related to the movement of the body's muscles, tendons, and joints.
Exhibiting abnormal exhaustion due to mental or physical exertion.
Movement of the head in the vertical plane. [NBO:GVG]
nod head
Movement of the head in multiple directions.
"A degenerative state of the brain resulting in impairment of memory, judgment, attention span, problem solving skills, the inability to perform previously learned skills that cannot be attributed to deficits of motor or sensory function, and a global loss of cognitive abilities." [MeSH:National Library of Medicine_Medical Subject Headings]
"A reflex allows the eye to follow objects in motion when the head remains stationary." [wikipedia:Optokinetic_reflex]
"A reflex that elucidates goose bumps (bumps on a person's skin at the base of body hairs) which may involuntarily develop when a person is cold or experiences strong emotions such as fear, awe, admiration or sexual arousal" [wikipedia:Goose_bumps]
A reflex that elucidates a characteristic ear twitch in response to an auditory stimulus.
A reflex that maintains body position and equilibrium either during rest or during movement.
A reflex process in which an animal immediately tries to turn over after being placed in a supine position.
A pathological behavior characterised by pronounced startle responses to tactile or acoustic stimuli and hypertonia.
"A reflex that elucidates an automatic positioning of the limbs in response to a movement of the head on trunk (neck)." [web:http\://www.dizziness-and-balance.com/anatomy/vspine.htm]
A reflex which results from activation of afferents from the vestibular organs and uses neck movements to stabilize the head position in space.
A reflex that originates with vestibular stimulation and control body posture.
"Change position in response to stimulation of the whiskers." [JAX:<new dbxref>]
A mouse reflex that elicidated the clasping of front and/or hind feet almost immediately upon being lifted by tail.
A form of tetanic spasm in which the head and feet are drawn forward and the spine arches backward.
A form of tetanic spasm in which the head, neck and spine are bent backward and the body is bowed forward.
A sudden, involuntary contraction of a muscle or group of muscles associated with strychnine poisoning and tetanus.
A sudden, involuntary contraction of a muscle or group of muscles.
An involuntary rhythmical, oscillatory movement of a body part.
Inability to coordinate voluntary muscular movements.
Observable characteristic of behavior related to the coordination of combinations of body movements created with the kinematic (such as spatial direction) and kinetic (force) parameters that result in intended actions.
Lack of coordination of movement typified by the undershoot or overshoot of intended position with the hand, arm, leg, or eye.
Observable characteristic of behavior related with the Intentionally or habitually assumed arrangement of the body and its limbs.
"Posture distinguished by a faltering gait while walking and/or a swaying motion of the trunk or head while resting." [JAX:<new dbxref>]
Loss of power of voluntary movement in the muscles of the hindlimb through injury or disease of it or its nerve supply.
A locomotory disorder in which sustained muscle contractions cause twisting and repetitive movements or abnormal postures.
A type of memory that allows one to store and manage information about one's environment and its spatial orientation lasting hours to months.
"Agitation characterised by a series of unintentional and purposeless motions that stem from mental tension and anxiety of an individual." [wikipedia:Psychomotor_agitation]
Observable characteristic of behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences.
"Exhibiting indifference, or suppression of emotions such as concern, excitement, motivation and passion." [wikipedia:Indifference_(emotion)]
A belief that is either mistaken or not substantiated that is held with vehemence.
"A social behavior characterised by conscious or unconscious constraint of a behavior that might be considered objectionable in a social setting." [wikipedia:Social_inhibition]
"A social behavior characterised by conscious or unconscious constraint or curtailment of behavior relating to specific sexual matters or practices." [wikipedia:Sexual_inhibition]
Loss of information already encoded and stored in an individual's long term memory.
Behaviour related to cognitive processes.
Perception in the absence of a stimulus.
A form of hallucination that involves perceiving images without visual stimulus.
"A form of hallucination that involves perceiving sounds without auditory stimulus." [wikipedia:Auditory_hallucination]
A form of hallucination that involves perceiving odors without odor stimulus.
A social behavior related to the activity of conveying information.
"Communication behavior related to the process of conveying meaning in the form of non-word messages through for example gesture, body language or posture; facial expression and eye contact etc." [wikipedia:.wikipedia.org/wiki/Nonverbal_communication]
"Communication behavior related to the conveyance of ideas and information through creation of visual representations." [wikipedia:Visual_communication]
"Communication behavior related to the process of conveying meaning in the form of word messages." [wikipedia:Oral_communication#Oral_communication]
"A nonverbal communication behavior that is characterised by the meeting the eyes between two individuals." [wikipedia:Eye_contact]
The behavior in which an organism sheds tears, often accompanied by non-verbal vocalizations and in response to external or internal stimuli.
Behavior stemming from understanding of a specific cause and effect in a specific context.
An emotional behavior that arises from the perceived resistance to the fulfillment of individual will.
"A communication disorder in which a person, most often a child, who is normally capable of speech is unable to speak in given situations, or to specific people." [wikipedia:Selective_mutism]
Any highly repetitive behavior, where the repetition is unusual, difficult to disrupt, and neither the behavior nor repetition serve an obvious function [NBO:AC]
Stereotypic behavior characterised by a tendency to repeat vocalizations.
Play behavior associated with the manipulation of objects.
Object play is important in developing skills important in adulthood, especially hunting.
"Behavior associated with interactions which resemble sexual behavior but do not lead to copulation." [web:http\://www.bio.davidson.edu/people/vecase/behavior/Spring2009/Sacco/Pages/Sex%20Play.html]
"Play behavior associated to fighting simulation, although fighting is much slower and gentler with no intention of actual hurt." [web:http\://www.bio.davidson.edu/people/vecase/behavior/Spring2009/Sacco/Pages/Play%20Fighting.html]
Play fighting helps learning to evaluate oneself and an opponent. This skill is crucial for serious adult situations. Being able to size up an opponent quickly is very important in knowing when to give up or fight for a resource (food, mate, territory, etc. ). Play fighting is one of the most important categories of play because it prepares animals for actual fighting.
Play behavior that is associated with the pursuit of an individual.
Play behavior associated with the exhibition of parenting behavior by non-parents.
"Play behavior related to the copying the actions of another." [web:http\://www.bio.davidson.edu/people/vecase/behavior/Spring2009/Sacco/Pages/Imitative%20Play.html]
Imitative play is an excellent means of learning how to perform a task that an adult has perfected. Therefore, imitative play is one of the best ways for animals to learn from the adults in the group.
Harassment of and-or attack of a presumed predator or intruder by multiple individuals at once [NBO:SMAC]
mobbing
"Behavior associated with signals made by the mobbing species while harassing a predator." [wikipedia:Mobbing_(animal_behavior)]
Aggressive behavior related to the defence of a fixed area against intruders, typically conspecifics.
"Behavior related to the activity seen in animals exposed to adverse stimuli, in which the tendency to act defensively is stronger than the tendency to attack." [web:http\://www.britannica.com/EBchecked/topic/45916/avoidance-behavior]
Behavior related to the activity seen in animals exposed to potential danger in which they exhibit the tendency to act defensively.
The actions or reactions of a male, for the purpose of attracting a sexual partner.
The actions or reactions of a female, for the purpose of attracting a sexual partner.
Any process which modulates the physical craving for water over long term water deprivation.
Any process which modulates the physical craving for water over short term water deprivation.
Two or more unprovoked recurrent seizures.
Observable characteristic of behavior related to movements that occur independent of planning.
Observable characteristic of behavior related to movements executed with intent.
A rapid and repeated body muscle contract that results in an uncontrolled shaking of the body.
"A seizure which affect only a part of the brain at onset." [wikipedia:http\://en.wikipedia.org/wiki/Focal_seizures]
Partial seizures begin with an electrical discharge in one limited area of the brain.
"A partial seizure which affect only a small region of the brain, often the temporal lobes and/or hippocampi whilst consciousness is unaffected." [wikipedia:http\://en.wikipedia.org/wiki/Simple_partial_seizure]
Depending on the area of cerebral cortex involved, symptoms may be motor, cognitive, sensory, autonomic, or affective. Consciousness is not impaired.
"A seizure that is associated with bilateral cerebral hemisphere involvement and causes impairment of awareness or responsiveness, i.e. loss of consciousness." [wikipedia:http\://en.wikipedia.org/wiki/Complex_partial_seizures]
"A type of focal epilepsy characterized by recurrent seizures." [NBO:http\://en.wikipedia.org/wiki/Temporal_lobe_epilepsy]
A simple partial seizure affecting the kinesthetic behavior.
A simple partial seizure affecting any of the five senses -- vision, touch, smell, taste, and hearing.
Some simple partial seizures consist of a sensory experience. The person may see lights, hear a buzzing sound, or feel tingling or numbness in a part of the body.
simple partial seizure with sensory symptoms
A simple partial seizure affecting the part of the nervous system that automatically controls bodily functions.
These seizures are accompanied by autonomic symptoms or signs, such as abdominal discomfort or nausea which may rise into the throat (epigastric rising), stomach pain, the rumbling sounds of gas moving in the intestines (borborygmi), belching, flatulence and vomiting. Other symptoms may include pallor, flushing, sweating, hair standing on end (piloerection), dilation of the pupils, alterations in heart rate and respiration, and urination. A few people may experience sexual arousal, penile erection, and orgasm.
simple partial seizure with autonomic symptoms or signs
A simple partial seizure affecting the emotional behavior.
simple partial seizures of temporal lobe origin
Simple partial seizures which arise in or near the temporal lobes often take the form of an odd experience. One may see or hear things that are not there. One feels emotions, often fear, but sometimes sadness, anger, or joy. There may be a bad smell or a bad taste, a funny feeling in the pit of the stomach or a choking sensation.
simple partial seizure with psychic symptoms
Observable characteristic of behavior related any of the five senses -- vision, touch, smell, taste, and hearing.
A phenotype manifested by a behavior related to the sensations arising from the skin and from the muscles, tendons, and joints.
somatic sensation related behavior phenotype
Observable characteristic of behavior related to the actions or reactions of an organism in response to a sound.
A phenotype manifested by a behavior related to the actions or reactions of an organism in response to a visual stimulus.
Observable characteristic of behavior related to the sensation of chemicals.
Observable characteristic of behavior related to the sensation of odors.
A seizure which affect the whole of the brain at onset.
Primary generalized seizures begin with a widespread electrical discharge that involves both sides of the brain at once.
partial seizure evolving to secondarily generalized seizure
simple partial seizure evolving to generalized seizure
complex partial seizure evolving to generalized seizure
simple partial seizure evolving to complex partial seizure evolving to generalized seizure
simple partial onset, followed by impairment of consciousness
with impairment of consciousness at onset
"An absence seizure is a brief (usually less that 20 seconds), generalized epileptic seizure of sudden onset and termination." [wikipedia:http\://en.wikipedia.org/wiki/Absence_seizure]
"A type of generalized seizure that consist of a brief lapse in muscle tone that are caused by temporary alterations in brain function." [wikipedia:http\://en.wikipedia.org/wiki/Atonic_seizure]
A type of seizure that is characterised by a very brief symmetric alternating contraction and relaxation of a muscle or a group of muscles.
A type of seizure that is characterised by rhythmic symmetric alternating contraction and relaxation of a muscle or a group of muscles.
A type of epilepsy characterised by myoclonic seizures usually involving the neck, shoulders, and upper arms.
A type of epilepsy characterised by multiple different types of seizures, particularly including tonic (stiffening) and atonic (drop) types of seizures.
A type of seizure generated by sudden sensor stimulation caused by the environment.
A type of generalized seizure characterised by a combination of tonic stiffening (extensions) followed by clonic flexion motions.
The seizures are divided into two phases, the tonic phase and the clonic phase, hence the name of the seizure, though a tonic clonic seizure will often be preceded by an aura.
A type of seizure characterised by muscle rigidity.
"A type of seizure associated with a significant rise in body temperature." [wikpedia:http\://en.wikipedia.org/wiki/Febrile_seizure]
"A febrile seizure that lasts less than 15 minutes , does not recur in 24 hours, and involves the entire body." [wikipedia:http\://en.wikipedia.org/wiki/Febrile_seizure]
"A febrile seizure characterized by longer duration, recurrence, or focus on only part of the body." [wikipedia:http\://en.wikipedia.org/wiki/Febrile_seizure]
"Benign rolandic epilepsy is characterized by either simple partial seizures involving the mouth and face or generalized tonic-clonic seizures." [wikipedia:http\://en.wikipedia.org/wiki/Rolandic_epilepsy]
benign (childhood) epilepsy with centrotemporal (EEG) spikes
"A temporal lobe epilepsy arises in the hippocampus, parahippocampal gyrus and amygdala which are located in the inner aspect of the temporal lobe." [wikipedia:http\://en.wikipedia.org/wiki/Temporal_lobe_epilepsy]
"A temporal lobe epilepsy arises in the neocortex on the outer surface of the temporal lobe of the brain." [wikipedia:http\://en.wikipedia.org/wiki/Temporal_lobe_epilepsy]
"Paroxysmal events that mimic an epileptic seizure but do not involve abnormal, rhythmic discharges of cortical neurons." [wikipedia:http\://en.wikipedia.org/wiki/Non-epileptic_seizure]
"A type of seizure of psychological origin that superficially resembles an epileptic seizure, but without the characteristic electrical discharges associated with epilepsy." [wikipedia:http\://en.wikipedia.org/wiki/Psychogenic_non-epileptic_seizures]
A type of epilepsy that is characterised by myoclonic seizures.
"A myoclonic epilepsy characterised by a combination of myoclonic and tonic-clonic seizures." [wikipedia:http\://en.wikipedia.org/wiki/Progressive_myoclonic_epilepsy]
"Continuous unremitting seizure lasting longer than 30 minutes or recurrent seizures without regaining consciousness between seizures for greater than 30 minutes." [wikipedia:http\://en.wikipedia.org/wiki/Status_epilepticus]
generalised convulsive status epilepticus
"A convulsive status epilepticus characterized by seizures involving long-lasting stupor, staring and unresponsiveness." [wikipedia:http\://en.wikipedia.org/wiki/Complex_partial_status_epilepticus]
"Subtle status epilepticus consists of electrical seizure activity in the brain that endures when the associated motor responses are fragmentary or even absent." [web:http\://emedicine.medscape.com/article/1164462-overview]
"Simple partial SE consists of seizures that are localized to a discrete area of cerebral cortex and produce no alteration in consciousness." [web:http\://emedicine.medscape.com/article/1164462-overview]
"A type of epilepsy characterized by brief, recurring seizures that arise in the frontal lobes of the brain, often while the patient is sleeping." [wikipedia:http\://en.wikipedia.org/wiki/Frontal_lobe_epilepsy]
A type of epilepsy characterised by seizure, usually tonic clonic, that occur only during sleep.
"A type of reflex seizure caused by visual stimuli that form patterns in time or space, such as flashing lights, bold, regular patterns, or regular moving patterns." [wikipedia:http\://en.wikipedia.org/wiki/Photosensitive_epilepsy]
A type of seizure induced by exposure to an auditory stimulus.
An absence seizure induced by hyperventilation.
An absence seizure not induced by hyperventilation.
A generalized seizure that was initiated as a partial seizure.
A generalized seizure that was initiated as a partial seizure but very rapidly spread to both hemispheres.
Purposeless repetitive motor activities that often occur during a seizure.
Automatisms may occur during complex partial or absence seizures.
An automatism characterised by involuntary oral activity such as lip smacking and swallowing.
An automatism characterised by involuntary movement of the limbs or body such as fumbling, picking and rubbing.
An automatism characterised by stereotyped series of motor actions usually involving the limbs bilaterally such as swimming \nmovements, kicking movements and bicycling movements.
A type of seizure induced by the administration of a drug.
A type of seizure induced by accidental or intentional ingestion or application of a drug in quantities greater than recommended.
A type of seizure induced by termination of drug administration.
A type of seizure induced by lower than normal level of blood glucose levels.
A type of seizure induced by the administration of cocaine.
A type of seizure induced by the administration of isoniazide.
A type of seizure induced by the administration of amphetamine.
A type of seizure induced by the administration of antidepressant.
A type of seizure induced by the administration of theophylline.
A type of seizure induced by the administration of penicillin.
A type of seizure induced by termination of alcohol administration.
A type of seizure induced by termination of benzodiazepine administration.
benzodiazepine withdrawal induced seizure
A type of seizure induced by termination of barbiturates administration.
A type of seizure induced by termination of heroin administration.
A type of seizure induced by lower than normal level of blood magnesium levels.
A type of seizure induced by exposure to an electrical stimulus.
A type of seizure induced by the administration of a brain trauma.
A type of seizure induced by kindling, a repeated administration of seizure invoking stimulus which eventually results changes in the brain.
A type of seizure induced by kindling, a repeated administration of electrical stimulus which eventually results changes in the brain.
A type of seizure induced by kindling, a repeated administration of chemical stimulus which eventually results changes in the brain.
A type of seizure induced by kindling, a repeated administration of auditory stimulus which eventually results changes in the brain.
A simple partial seizure affecting the kinesthetic behavior of one side of the body.
A simple partial seizure affecting the kinesthetic behavior of left side of the body.
A simple partial seizure affecting the kinesthetic behavior of right side of the body.
A type of epileptic seizures occurring in infants and characterised by clusters of myoclonic spasms.
A type of seizure induced by lower than normal level of blood calcium levels.
A generalized tonic clonic seizure that was initiated as a partial seizure.
secondary generalized tonic clonic seizure
A type of seizure induced by exposure to a light stimulus.
A type of epilepsy that is characterised a sudden burst of energy, usually in the form of laughing.
"A type of epilepsy that is characterised a sudden paroxysmal crying." [NBO:<new dbxref>, NBO:GVG]
An aggressive behavior towards other members of the society.
A social behavior related to the activity of conveying information by means of a system of arbitrary signals, such as voice sounds, gestures, or written symbols.
The act of displacing part or all of the tongue from its current position [NBO:SMAC]
Observable characteristic of behavior related to all sleep stages in the circadian sleep/wake cycle other than REM sleep.
non-rapid eye movement sleep behavior phenotype
Observable characteristic of behavior related to the stage in the circadian sleep cycle during which dreams occur and the body undergoes marked changes including rapid eye movement, loss of reflexes, and increased pulse rate and brain activity.
Observable characteristic of behavior related to the actions or interactions of an organism that are associated with reproduction.
Observable characteristic of behavior related to the interactions between organisms for the purpose of mating.
Observable characteristic of behavior related to the specific actions or reactions of an organism following mating.
Observable characteristic of behavior related to the activity which primary purpose is the sexual reproduction.
Observable characteristic related to the behavioral interactions between organisms for the purpose of attracting sexual partners.
Observable characteristic of behavior related to the actions or reactions of a female, for the purpose of attracting a sexual partner.
Observable characteristic of behavior related to the actions or reactions of a male, for the purpose of attracting a sexual partner.
Observable characteristic of behavior related to the act of sexual union between male and female, involving the transfer of sperm.
Observable characteristic of behavior related to the female activity which primary purpose is the sexual reproduction.
Observable characteristic of behavior related to the male activity which primary purpose is the sexual reproduction.
Observable characteristic of behaviour related to the acquisition and processing of information and/or the storage and retrieval of this information over time.
learning and/or memory behavior phenotype
Observable characteristic of behaviour associated with any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
Observable characteristic of behaviour related to the ability of an organism's ability to store, retain, and recall information and experiences.
Observable characteristic of behaviour related to the elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds.
behavioral control of excretion phenotype
Observable characteristic of behaviour related to the expulsion of feces from the rectum.
behavioral control of defecation phenotype
Observable characteristic of behaviour related to the regulation of body fluids process by which parasympathetic nerves stimulate the bladder wall muscle to contract and expel urine from the body.
behavioral control of urination phenotype
behavioral control of production of sound phenotype
behavioral control of external secretion phenotype
Observable characteristic of behaviour related to the regulated release of the aqueous layer of the tear film from the lacrimal glands.
behavioral control of lacrimation phenotype
Observable characteristic of behaviour in which an organism sheds tears, often accompanied by non-verbal vocalizations and in response to external or internal stimuli.
Observable characteristic of behaviour associated with signals made by the mobbing species while harassing a predator.
Observable characteristic of behaviour in which an organism produces sounds by a mechanism involving its respiratory system.
increased amount of liquid in a single drinking act
increased amount of liquid in drinking regulation
'participates in' some ('regulation of drinking behavior' and (has_quality some (frequency and (towards some 'liquid consumption'))))
frequency of drinking
increased frequency of drinking
decreased frequency of drinking
Behavior as a result of an electromagnetic radiation stimulus.
behavioral response to radiation
Behavior as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
behavioral response to light
Behavior as a result of a chemical stimulus.
behavioral response to chemical stimulus
Behavior as a result of a xenobiotic compound (compound foreign to living organisms) stimulus.
behavioral response to xenobiotics
Behavior as a result of sensitivity to an addictive substance intake.
behavioral response to addictive substance
Behavior as a result of sensitivity to cocaine alcohol.
behavioral response to alcohol
"Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GO:0050795]
regulation of behavior
Any process that modulates the frequency, rate or extent of alcohol consumption, the specific actions or reactions of an organism in response to external or internal stimuli.
regulation of alcohol consumption
Behavior related to the intake of substances.
consumption behavior
Behavior related to the intake of addictive substances.
consumption of an addictive substance
Behavior related to the intake of cocaine.
cocaine consumption
Behavior related to the intake of morphine.
morphine consumption
Behavior as a result of sensitivity to cocaine intake.
behavioral response to cocaine
Behavior as a result of sensitivity to morphine
behavioral response to morphine
Behavior as a result of sensitivity to nicotine intake.
behavioral response to nicotine
Behavior related to the intake of nicotine.
nicotine consumption
Any process that modulates the frequency, rate or extent of cocaine consumption, the specific actions or reactions of an organism in response to external or internal stimuli.
regulation of cocaine consumption
Any process that modulates the frequency, rate or extent of consumption behavior, the specific actions or reactions of an organism in response to external or internal stimuli.
regulation of consumption behavior
Any process that modulates the frequency, rate or extent of consumption of an addictive substance, the specific actions or reactions of an organism in response to external or internal stimuli.
regulation of consumption of an addictive substance
Any process that modulates the frequency, rate or extent of nicotine consumption, the specific actions or reactions of an organism in response to external or internal stimuli.
regulation of nicotine consumption
Any process that modulates the frequency, rate or extent of morphine consumption, the specific actions or reactions of an organism in response to external or internal stimuli.
regulation of morphine consumption
Behavior as a result of sensitivity to an anasthetic intake.
behavioral response to anesthetic
Maternal behavior related to the nursing offspring.
nursing behavior
Any process that modulates the frequency, rate or extent of consumption of food or liquid
regulation of feeding behavior
Any process that modulates the frequency, rate or extent of water consumption, the specific actions or reactions of an organism in response to external or internal stimuli.
regulation of water consumption
Any process that modulates the frequency, rate or extent of saccharin consumption, the specific actions or reactions of an organism in response to external or internal stimuli.
regulation of saccharin consumption
A pathological drinking behavior characterised by a lack of desire to drink.
adipsia
Increase in core body termperature in response to stress or anticipatory anxiety.
stress-induced hypothermia
Any process that modulates the frequency, rate or extent of sexual activity, the specific actions or reactions of an organism in response to external or internal stimuli.
regulation of sexual activity
A regulation of drinking behavior process associated with the preference over the type of liquids that are consumed.
regulation of drinking preference behavior
A regulation of drinking behavior process associated with the preference over alchohol consumption.
regulation of alcohol preference behavior
A regulation of drinking behavior process associated with the preference over the type of food that is consumed.
regulation of eating preference behavior
A regulation of drinking behavior process associated with the preference over saccharing consumption.
regulation of saccharin preference behavior
A regulation of consumption of an addictive sustance behavior process associated with the preference over the type of addictive sustance that is consumed.
regulation of addictive substance consumption preference
A regulation of consumption of an addictive sustance behavior process associated with the preference over cocaine consumption.
regulation of cocaine consumption preference
A regulation of sexual activity process associated with the preference over a males or females.
regulation of mating preference
A vestibular reflex by which a response to an angular acceleration stimulus begins with an afferent nerve impulse from a receptor in the semi-circular canal and ends with the compensatory action of eye muscles. Signaling never reaches a level of consciousness. [GOC:dph]
angular vestibuloocular reflex
A vestibular reflex by which a response to a linear acceleration stimulus begins with an afferent nerve impulse from a receptor in the otolith and ends with the compensatory action of eye muscles. [GOC:dph]
linear vestibuloocular reflex
Behavior response to addictive substance resulting from the discontinuation of an addictive substance. [NBOC:GVG]
withdrawal response
Any process that modulates the frequency, rate or extent of behavioral response to chemical stimulus.
regulation of behavioral response to chemical stimulus
Any process that modulates the frequency, rate or extent of behavioral response to addictive substance.
regulation of behavioral response to addictive substance
Any process that modulates the frequency, rate or extent of withdrawal response.
regulation of withdrawal response
Behavior response to an addictive substance resulting from dependence of that addictive substance as well as unctronllable cravings of that substance. [NBOC:GVG]
addiction response
Any process that modulates the frequency, rate or extent of addiction response.
regulation of addiction response
rotation behavior
locomotor inactivation behavior
A predator behavior involving actively stalking prey over a distance.
hunting behavior
A predator behavior involving a surprise attack on unsuspecting prey. The predator remains in one place and waits for prey to come near. The predator conceals itself and then subdues its prey with its own body or body parts.
ambush behavior
An avoidance behavior engaged in by prey that reduces the success of a predator without the prey actually attacking the predator.
predator avoidance behavior
A predator behavior involving subduing prey using a structure or modification of the environment created by the predator for that purpose.
trapping behavior
Feeding behavior during which a living entity acquires food and energy by actively searching for food resources.
active foraging behavior
OBSOLETE. Feeding behavior during which a living entity acquires food and energy by actively searching for food resources.
obsolete active foraging behavior
Consumption behavior that involves burning a substance and inhaling the particulate and gas suspension emitted.
smoking behavior
Smoking behavior that involves burning a substance such as tobacco and tasting or inhaling the smoke through a pipe.
pipe smoking behavior
Smoking behavior that involves burning a substance such as tobacco wrapped in paper and inhaling the smoke.
cigarette smoking behavior
Smoking behavior that involves burning a substance such as tobacco wrapped in tobacco leaf and inhaling the smoke.
cigar smoking behavior
Consumption behavior that involves inhaling a material (such as finely ground tobacco leaves) through the nose.
snuffing behavior
Consumption of specific compounds that facilitate processing of food items.
aiding digestion
Assessment of cues and signals from encountered individual to determine reproductive condition.
reproductive status assessment
Postures or signals that alert other animals to presence or approach of a predator.
warn other prey
Behavior in which one animal causes the death of another.
killing
kill
Signal or behavior that reveals presence of the signaller directed to multiple receivers and not limited to particular receivers.
broadcast advertisement
Threat that will not be acted upon.
bluff
Agonistic behavior involving direct physical contact including (but not limited to) biting, kicking, grabbing.
contact aggression
Perform behaviors that may induce one or more other animals to share food with the performer.
beg food
Surveillance for presence or approach of predators.
vigilance
Active pursuit of fleeing prey.
chase prey
Behaviors in which predator forces potential prey to emerge from cover.
flush prey
Behavior associated with deposition of material by male following ejaculation to block access to female's reproductive tract during her future matings.
insert genital plug
Deposition of eggs either into the medium, or onto a substrate.
facilitating oviposition
One member of a recently mating pair prevents the other from subsequent matings with other individuals.
mate guarding
Currently reside in constructed or existing structure that provides reduced predator and/or environmental risk.
occupy refuge
Forcible alteration of behavior of one animal by another.
coercion
Facilitating release or transfer of gametes.
gamete release function
Caching or hoarding of food for later use and for protection from competitors, or use of specific substrates for cultivation.
food storage
Displays or other behaviors performed by pairs in longer term pair bonds to advertise relationship to each other and to other animals nearby.
pair affirmation
Performance of behaviors that demonstrate physical condition of performer to a detected predator.
display condition (to predator)
Emission of signals in such a way as to prevent effective use of signals emitted by other parties.
jamming
Active search for possible mates.
mate finding behavior
Postures or signals performed to other animals to indicate the presence, and in some cases, the location, quantity, and quality, of a resource.
resource advertisement
Sensory assessment of a resource (usually using olfaction or taste), for suitability of subsequent usage.
suitability assessment
A behavior on the part of one individual associated with evaluating the fighting ability or correlates of fighting ability of a potential opponent.
assessment behavior
Locomotion to a resource guided by visual or olfactory cues created by a prior finder and/or user of that resource.
trail following to resource
Behavior by one animals soliciting food provision by a potential mate.
courtship begging
Consumption of one member of a mating pair, usually the male, usually after the mating.
sexual cannibalism
Process of retaining developing eggs in the mouth cavity.
mouth brooding
Construction of a structure in which builder can benefit from reduced predation risk and/or environmental stress.
create refuge
Behavior that signifies hostility and predicts an increased probability of attack.
threat
Use of specialized male organs to remove sperm already deposited in female's reproductive tract.
sperm scraping
Behavior in which one animal causes bodily damage to another.
injuring
injure
Carrying or manipulation of infants or equivalent items to reduce chances of aggression on carrier by other animals.
agonistic buffering
Use of behavioral tactics or chemical weapons to deter predation. Example: flashing eye spots (behavioral tactic) or expulsion of noxious liquid (chemical).
deploy defense
Insertion of sperm not in a spermatophore into female body.
insemination
Building of a trap, web, net, or other structure to help ensnare potential food items.
construct capturing device
Behaviors that reduce detectability of performer against background.
enhance crypsis
Chasing of one animal by another during an agonistic conflict.
agonistic chase
The identification, avoidance, or neutralization of toxic substances in food.
dealing with toxins
Removal of food resource from previously-stored supply of food.
recovery from cache
Alarm behavior triggered by agonistic actions or postures.
agonistic alarm
Signals emitted by an animal trapped or captured by a presumed predator.
distress signaling
Behaviors that serve to reduce body temperature as by moving to shade or panting.
cooling behaviour
Approach to prey in manner designed to avoid early detection by prey.
stalk prey
Behaviors that reveal a hidden food resource, such as digging, cracking, or breaking.
food exposure
Behaviors in which animals solicit or allow other animals to utilize a resource they currently control.
share food
Release of gametes one or both sexes into the ambient medium.
spawning
Halting or diminution of activity to minimize detection by predator.
reduce activity
Obtaining food that has been procured by other conspecifics or heterospecifics.
social acquisition of food
Increasing intensity of directed agonistic behavior.
escalation
Movement directed to the detection of new resources.
nutrient locating
Become immobile and reduce other evidence of living state.
feign death
Spawning in which male and female are clasped or attached to ensure close proximity of released gametes
mating amplexus
Behaviors directed towards presumed predators to redirect their attention away from a location of importance to the performer.
misdirect predator
Behavior that serves to exlude an animal from a group.
exclusion
Conspicuous orientation towards and/or approach to detected predator.
inspect predator
Perform physically violent acts on a presumed predator.
attack predator
Display behavior by the winner of a prior agonistic contest.
triumph
Performance of a behavior that indicates the performer's willingness to mate or bond
mating solicitation
Creation of or modification of a structure or area that is used in attraction of mates.
build display structure
Behaviors, anatomical structures, or signals that imitate aposematic animals, plants, or inanimate objects that are undesirable to predators of performer.
mimicry enhancement
Erratic movements or similar behaviors that would confuse a predator.
promote confusion
Behavior that serves to demonstrate non-aggressive intent by one member of a courting or potentially mating pair to the other.
mating appeasement
Any of several behaviors directed towards one animal unwilling to mate by another eager to do so.
sexual harassment
An acitvity that seems irrelevant to its behavioral context to a human observer and often occurs when its performer is in a conflict situation.
displacement behavior
Provision of food to a potential mate
courtship feeding
Deposition of spermatophore either on substrate or in body of female.
spermatophore deposition
Depart [from] current location of predator.
flee
Active searching of potential mate
hunt for mate
Actions resulting in establishment or use of one locale for reproductive activity.
breeding site selection
Behaviors that appear to signifiy lack of hostility and to reduce chances of attack.
appeasement
General category of behaviors including sampling of medium to detect presence of possible mates, and sampling of encountered individuals to determine mate suitability.
mate sampling
Behaviors related to acquisition and utilization of external resources.
nutrient acquisition
Removal of food items from location by use of appendage or tool.
food extraction
Conspicuous postures or signals (often coloration) that potential predators learn to associate with strong defense mechanisms of performer
aposematism
Postures or signals that can communicate to predator that it has been detected by performer.
(predator) detection notification
Behavior that precedes and facilitates attaining food.
nutrient preparation
Suite of behaviors involved in securing a prey item once it has been located.
capturing behaviour
Behaviors that result in ending flight of prey with successful predation.
capturing prey
The act of putting a food resource in a location in which it can be stored or protected until a future time.
caching behavior
Behaviors that prepare food for consumption, such as nut-cracking or peeling.
food processing
Uninvited taking of food from another animal.
scrounge
Behavior associated with locating and acquiring food that has been killed or procured by another animal.
scavenge
Usually interference by members of one sex in the completion of courtship or mating activities by one or more members of the same sex.
sexual interference
Behavior associated with refusing courtship or solicitation behaviors by avoidance, retreat, or other active repulsion of suitor.
mate rejection
A behavior associated with the gathering of organisms together in some locality. [Wikipedia:Aggregation_(ethology)]
aggregation behavior
A type of aggregation behavior in which organisms (especially fish or tadpoles) come together in an interactive way, aware of the other members of the group as shown by the way they adjust their behavior. [Wikipedia:Shoaling_and_schooling]
shoaling behavior
A type of shoaling behavior in which organisms (especially fish or tadpoles) are tightly organized and move in the same direction in a coordinated manner. [Wikipedia:Shoaling_and_schooling]
schooling behavior
A behavior in which action is rapidly taken by an organism in response to possible predation, examples of which include camouflage, freezing behavior, and fleeing. [Wikipedia:Escape_response]
escape behavior
A behavior involving an organism (especially fish or tadpoles) breathing at or near the surface of water where the concentration of dissolved oxygen is highest. [NBO:EJS]
surface breathing
A behavior involving avoidance of or escape from approaching visual stimuli, threats, or objects which are on a collision course. [PMID:23364572]
visually guided collision avoidance behavior
Any habitual use of the tobacco plant leaf and its products.
tobacco consumption
A behavior of chewing a type of smokeless tobacco maked from cured tobacco leaves. Often the tobacco is left in the mouth and chewed but the leaves are not swallowed.
tobacco chewing behavior
The inhalation and exhalation of tobacco smoke.
tobacco smoking behavior
The inhalation and exhalation of tobacco aerosol, referred to as vapor, which is produced by an e-cigarette or other device.
tobacco vaping behavior
cannabis consumption
The inhalation and exhalation of marijuana smoke.
cannabis smoking behavior
The inhalation and exhalation of cannabis aerosol, referred to as vapor, which is produced by an e-cigarette or other device.
cannabis vaping behavior
The consuming of cannabis through eating or applying the oil sublingually.
cannabis oil consumption
A feeding behavior during which an animal ingests biomass produced by a plant or other primary producer
Behavior related to the movement of an organism from one location to another using an inchworm like motion. This motion consists of extending the front part of the body and pulling the rear along the surface to meet the front.
Behavior related to the repeating or looping movement of the whole organism along a circular or round path.
Protective behavior that sheds or discards an animal's body part.
Tara Lynne Maginnis, The costs of autotomy and regeneration in animals: a review and framework for future research, Behavioral Ecology, Volume 17, Issue 5, September/October 2006, Pages 857–872
This is most often understood to mean an appendage such as a lizard's tail, or an insect's leg, which may already be in the clutches of a predator, fouled in a portion of molted cuticle, or caught in a spider's web. Some animals can even shed a body part spontaneously, perhaps to distract a predator. But some echinoderms can autotomize part of their digestive tract whilst some mammals can slough off some skin, which are not so much appendages as organs, yet with the same effects.
Rhythmic behavior that involves cue-initiated, persistent, direct, focused movement between habitats.
Dingle H. Migration: the biology of life on the move. Oxford University Press, USA; 2014.
Migration that involves regular movement up and down in the water column.
Bandara K, Varpe Ø, Wijewardene L, Tverberg V, Eiane K. Two hundred years of zooplankton vertical migration research. Biological Reviews. 2021 Aug;96(4):1547-89.
Migration that involves regular movement laterally between distant ranges in seasonal cycles.
Display that involves taking all four legs off the ground simultaneously and holding the legs stiff and straight.
Caro TM. The functions of stotting: a review of the hypotheses. Animal Behaviour. 1986 Jun 1;34(3):649-62.
characteristic
We should name the inverse in COB and avoid the confusing inverse(..) construct
For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood).
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
TODO: define this or obsolete it and move children somewhere else.
This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.
For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism.
mass
We recommend using the new absent terms (physical absence, absent anatomical entity, or absent process) instead of this class. This is a legacy term and will ultimately be obsoleted. See https://github.com/pato-ontology/pato/issues/331.
See comments of relational quality of a physical entity.
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
This refers to the disposition of the bearer.
Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2.
Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type.
In polydactyly, the bearer of the quality is the hand, and the entity type being counted is 'finger'. In EQ syntax, E=hand, Q=<this> E2=finger.
Use this term or an is_a child of this term when the entire shape of the object is known.
Becoming flat but not necessarily completely flat.
quality of interaction of a substance with electromagnetic radiation
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
create a separate class for distributed pancreas, eg cyclostomes?
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
this is currently a subtype of organism subdivision - which would exclude feathers
TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.
in humans, consists of adventitial, muscular and mucoa layers
In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening.
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
currently defined in a very broad sense, may be replaced by more specific classes in the future
Uberon includes clade-specific subclasses, e.g. nematod larva
proximo-distal subdivision of respiratory tract
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
mixed endoderm/mesoderm-derived structure
mixed ectoderm/mesoderm/endoderm-derived structure
In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney
By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]
During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis
This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass]
Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg. [Wikipedia:Trophoblast]
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
consider adding a preceding stage 'morula stage' as part of cleavage
it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces
A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]
Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate.
requires alignment with EHDAA2 and complete developmental relationships
In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca
Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs
this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals.
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
TODO - add layer relations. 'tendon sheath' GAT in FMA.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
defined generically to encompass both vertebrates and invertebrates
We model the digestive tract as consisting of two parts: the wall and the lumen.
Note that some sources treat 'intestinal gland' as synonymous with crypts
Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html]
Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
TODO - split body and mc organism? body continues after death stage
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
see also conceptus extraembryonic component in EHDAA2.
changed label and definition to reflect CARO2
Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it?
needs to be synchronized with CL - there is no distinct cuboidal cell in CL
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male.
All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
requires review for applicability to invertebrate structures, e.g. synganglion
this term should be ceded to the arthropod anatomy ontology
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water
This class excludes compound eye corneal lenses.
The lens is avascular and nourished by diffusion from the aqueous and vitreous humors.
Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved
consider splitting genitalia from reproductive system
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here
the cardiovascular system and the lymphatic system are parts of the circulatory system
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)]
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
Consider generalizing to deuterostome pharynx
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class
In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html
in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO
The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]
kidney excreta from some taxa (e.g. in aves) may not be liquid
It provides nutrients and lubrication for articular cartilage
The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts
check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
todo - add developmental relationships for other taxa
TODO - abstract this such that it legitimately covers all vertebrates
In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]
In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]
it extracts water and salt from solid wastes before they are eliminated from the body[WP]
we include this as zone of stomach even though it is not distinguished by gland type
We follow Kardong in defining stomach regions by glands
The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP]
TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part
renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability.
The right [renal artery] passes behind the inferior vena cava, the right renal vein, the head of the pancreas, and the descending part of the duodenum[WP]
The left [renal artery] is somewhat higher than the right; it lies behind the left renal vein, the body of the pancreas and the splenic vein, and is crossed by the inferior mesenteric vein[WP]
duodenum, 1st part serosa, 2nd - 4th adventitia
currently defined as equivalent to any submucosal gland in the duodenum.
in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine
In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter
In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]
The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]
Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue
we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different
The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented
The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver.
Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct)
kidney terms require review for cross-vertebrate compatibility and developmental relationships.
The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP]
this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831).
TODO - find a home for: FMA:24139 ! skeleton of upper limb
birds have right aortic arch, mammals left.
results from fusion of left and right dorsal aortae
Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates
we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'
This class represents the adult and developing structures'
in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae
Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)
in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery
proximal part arises from right 4th aortic arch in humans
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
in humans, branches off the arch of aorta
arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans
The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green).
The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]
in aves, stromal mesenchymal cells may migrate to the iris and become skeletal
In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted]
WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure
It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina
Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system.
TODO - check with MA - vein vs venous blood vessel
In humans A vein in the abdominal cavity that drains blood from the gastrointestinal tract and spleen. It is usually formed by the confluence of the superior mesenteric and splenic veins, and also receives blood from the inferior mesenteric, gastric, and cystic veins. The hepatic portal vein is a major component of the hepatic portal system, one of the main portal venous systems in the body. Conditions involving the hepatic portal vein cause considerable illness and death. An important example of such a condition is elevated blood pressure in the hepatic portal vein. This condition, called portal hypertension, is a major complication of cirrhosis worldwide. [WP,unvetted]
we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves
TODO - add class 'pulmonary artery tree organ'
consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks)
In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process
It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
TODO - move ZFA:0001227 (it is the entire jaw skeleton).
There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
See notes for jaw w.r.t skeletal element vs subdivision of head
in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence.
Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods
The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions
In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish.
arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN:1607950324 (todo - request cell terms from CL)
See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship
TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal
TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus
The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]
In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei
In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson].
Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709].
Disease notes: implicated in rheumatoid arthritis.
Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'.
Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here.
check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA
classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN.
See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6
this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former
synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens
In humans, they are situated in the upper, outer portion of each orbit
Innervation is highly complex and species-specific
developmental relationships need revised
In human embryonic development, the rhombomeres are present by day 29
DHBA divides this into A(1-3),B(4),C(5-7) and D(8)
the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA].
'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum.
aids the process of digestion of lipids in the small intestine
bile salts function to emulsify dietary fats and facilitate their intestinal absorption
major excretory route for potentially harmful exogenous lipophilic substances
many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates
protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine
TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
annelids have blood vessels, but this class is not applicable to annelids.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]
provides some protection from trauma and damage.
The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule]
Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung.
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
see also: vascular system. Consider merging?
GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form
In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616]
In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu
Consider adding a layer-of-skin grouping class for all skin layers
In mammals continuous with the pulmonary arteries
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
consider 'integumentary system' for invertebrates
'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'
Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm
In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron
It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells
An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988)
Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104
In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718]
The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates.
TODO - check ZFA/pons. also GO says part of dorsorostral pons
fixed in GO to reflect FMA. See email to David/Varsha June 18 2010
In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
WP considers epiphyseal plates as subtypes of this
consider adding link to hyaline cartilage
In many species, the diaphragm separates thoracic and abdominal cavities
TODO - add superclass to unify with VNC?
we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)
covers the brain dorsally in chondrichthyans
An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation.
It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain.
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
check the FMA placement here; ncit placement of body cavity here probably not correct
In mammals it forms the peritoneal, pleural, and pericardial cavities
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
distinction between abdomen muscle and abdomen musculature
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.
The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]
TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium
EHDAA2 divides the system from the tissue
most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]
Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx).
capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288
some ontologies consider dura mater part of the CNS, others dispute this and claim it surrounds it (e.g. DOI:10.1111/joa.12381)[https://github.com/obophenotype/uberon/issues/1261]
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
check FMA, use plural for now as general class not there
The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008]
consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)
the formal definition is very inclusive, and includes sesamoids
cannot find singular in FMA, using Set class
see https://github.com/obophenotype/uberon/issues/27
May be composed of smooth muscle and elastic tissue
the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass
TODO discriminate between stages and organisms
involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum]
consider adding class for organizer. Consider adding separate class for isthmus as a structure
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150]
TODO - check; developmental relationship to anterior hypoblast in ZFA?
The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode
Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...'
Consider adding subclasses for male and female specific variants
TODO - mesonephric portion of the nephric duct
In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts.
TODO - add grouping class for the anterior end of the neural tube at all stages
The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.
should probably be merged with heart rudiment.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007
Disappears early in development in tetrapods
Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta
In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"]
consider changing genus to subdivision of meninx
TODO - change mesenchyme relationships to precursor_of
examples: tongue squamous epithelium, keratined, non-keratinized and parakeratinized epithelium, as well as gustatory epithelium. Note that not all these subtypes are named in individual anatomy ontologies.
cardiac muscle tissue of interventricular septum
Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle
added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea
consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve
Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
test whether 'facial bone' is an exact synonym
respiratory system capillary endothelium
only in MA - supertype of artery, arteriole, aorta.
TODO - check free limb vs pectoral complex
TODO - check free limb vs pelvic complex
lower respiratory tract connective tissue
check whether to classify as part of splanchoncranium
in mammals the rings are incomplete, in avians the rings are complete.
respiratory system arterial blood vessel
Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses
Design pattern notes: check whether this fits the foramen design pattern
includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct
includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts
All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers
this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
revisit after standardizing terms 'primordium', 'anlagen', 'bud'
The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]
the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship.
Not to be confused with 'dermatome segment of skin'.
As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye
The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389]
Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
consider splitting out lymph organ, compare with lymph node
The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]
note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap
Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93
review as part of general integumentary system review - part of skin, or more generally, integumental system
It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP]
respiratory system blood vessel smooth muscle
distinction between trophectoderm and trophoblast unclear/inconsistent in many sources
developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm
note that media, dorsal fins etc have AERs.
maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop
Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056]
Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods
The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches
The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed)
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376
define generically to encompass both vertebrates and invertebrates
originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose
currently defined by location rather than attachment
cardiac muscle tissue of interatrial septum
Note placement of MA class based on parthood relationship
smooth muscle tissue of terminal bronchiole
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP]
we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei'
respiratory system blood vessel endothelium
TODO - check relationship to bulbus arteriosus
this class is the union of the classes limb, pectoral fin and pelvic fin.
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted
revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)
In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular.
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
Do not manually classify under here - bones are automatically classified
TODO - split respiratory tract mucosa from respiratory system mucosa
The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468
See https://github.com/obophenotype/uberon/issues/1305
composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0]
Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal
this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips
Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands
splanchnic layer of lateral plate mesoderm
Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/
sources differ as to whether this is part-of or develops-from the LPM
part_of or develops_from urogenital ridge?
Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II)
neuron projection bundle connecting eye with brain
after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]
TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
class added for consistency with GO - consider merging with kidney mesenchyme.
TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same
the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
directing or focusing light onto light receptors
This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries
the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
alimentary part of gastrointestinal system
Genes: Tbx5 specifies forelimbs. Wnt2b restricts Fgf10 in chick // In tetrapods, the position of the forelimb is associated with the anterior expression border of Hoxc6 in the paraxial mesoderm (Burke et al., 1995)
Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick.
at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future
at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future
pectoral appendage apical ectodermal ridge
pelvic appendage apical ectodermal ridge
todo - epidermis? todo - track down EHDAA2 class in new release
After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm.
Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998).
todo - compare ZFA and EHDAA2 representation
Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm
includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries
In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein
stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)]
the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney
consider splitting into main and accessory. See also: vomeronasal organ
we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system
In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP].
we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this.
the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995)
TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
TODO - check ridge vs cord vs nephrogenic cord vs blastema
Development notes:; the vitelline arteries give rise to the celiac artery, superior mesenteric artery, and inferior mesenteric artery in the adult[MP:0010664]
add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
the collection consisting of the two lateral swellings and the medial swelling
TODO - check ordering; awaiting confirmation from JB
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints
check if it is valid to group ZFA class here.
currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)
typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle.
The thyroid initially develops caudal to the tuberculum impar . This embryonic swelling arises from the first pharyngeal arch and occurs midline on the floor of the developing pharynx, eventually helping form the tongue as the 2 lateral lingual swellings overgrow it. [http://emedicine.medscape.com/article/845125-overview]
This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343
consider splitting epithelium from epithelial tissue
Surface groove is modelled as immaterial - see https://github.com/obophenotype/uberon/issues/2667 for discussion
this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future.
merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland.
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
consider FBbt:00005541 ! cardiogenic mesoderm
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract.
mesenchyme derived from head neural crest
mesenchyme derived from trunk neural crest
relationship to Meckel's cartilage to be added
this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future.
In mice many lobules lack islets, in contrast to other mammals including humans
this class groups together accessory (dorsal) and main (ventral) pancreatic ducts
this grouping class exists primarily to align with GO - see GO:0008544.
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species
this class will be an important part of the NC reorganization
In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system
Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]
decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx
check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
characteristically low in protein and cellular content (unless there has been secondary concentration)
check sacrum, coccyx (MA does NOT include these)
typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone
need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)
the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).
subclasses of this should be checked for taxonomic consistency
Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]
this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class.
The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5.
Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing
a reasoner should automatically classify all the vertebrate ontology brain classes here
in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10
The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this
many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
other AOs are not yet in sync with this classification
We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA
typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321]
Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion
Epibranchial ganglia orchestrate the development of the cranial neurogenic crest
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA
associated mesenchyme of foregut-midgut junction
TODO - developmental relationships for lines
midbrain hindbrain boundary neural plate
A major contributor to neurocranium [PMID:16313393]
decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts
this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules
We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach
see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish.
Their name is potentially misleading -- the 'medullary' refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla
in mouse has left ventricular identity[PMID:22855565]
todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland)
Alternate definition: One of the subdivisions of the kidney, consisting of a medullary ray and that portion of the convoluted port (renal corpuscles and convoluted tubules) associated with its collecting duct. -http://www.mondofacto.com/facts/dictionary?lobulus+corticalis+renalis
Includes: trigeminal, otic, lateral line and epibranchial placodes.
in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
entire pharyngeal arch associated mesenchyme
develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN:1607950324
TODO - coordinate with CL, add cuboidal cell
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton
Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6?
1st arch mandibular mesenchyme from neural crest
mesenchyme from rhombencephalic neural crest
In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process).
we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed
The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288
non-keratinized stratified squamous epithelium
structure with developmental contribution from neural crest
we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium
mandibular process mesenchyme from neural crest
mandibular process mesenchyme from head mesenchyme
1st arch mandibular mesenchyme from head mesenchyme
1st arch mesenchyme from head mesenchyme
2nd arch mesenchyme from head mesenchyme
3rd arch mesenchyme from head mesenchyme
4th arch mesenchyme from head mesenchyme
6th arch mesenchyme from head mesenchyme
Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
pharyngeal arch mesenchyme from neural crest
pharyngeal arch mesenchyme from head mesenchyme
This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO
consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen')
Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen')
the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives
In an adult mammal, most red blood cells are formed in flat bones
Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment
Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs
Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia.
pseudostratified ciliated columnar epithelium
It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]
note the distinction between this and skeleton of limb
considering adding pectoral and pelvic complex skeleton classes
In some primitive organisms, the meningeal cluster includes only the primitive meninx
forelimb bone pre-cartilage condensation
the MA class belongs here, based on its current child classes
primary subdivision of cranial skeletal system
central nervous system cell part cluster
Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath]
synovial membrane of synovial tendon sheath
fibrous membrane of synovial tendon sheath
In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
consider obsoleting, coordinate with VSAO
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
subdivision of organism along main body axis
The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP]
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
The Epimysium also protects muscles from friction against other muscles and bones
as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts
Contains nerves, blood vessels, lymphatics and lymph nodes
respiratory system arterial smooth muscle
a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction
increases the surface area of a cell lining whilst minimizing increase in volume
includes the cloacal lumen, in species where this is present
lumen of terminal part of digestive tract
TODO mirror representation of abdominal aorta
this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein
the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938).
Groupings may vary - typically pulmonary vessels and aorta and vena cavae
In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis
this class may be merged with 'respiratory system muscle'; check intercostals
consider merging into myocardial compact layer
the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]
the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]
The class name or definition should not be taken to mean strictly in the lateral ocular region. We place the extraocular lacrimal glands, even though they are as the name suggests outside the ocular region. The class exists as the division between lateral vs medial (Harderian, nictitans) glands is standard, e.g. http://www.ncbi.nlm.nih.gov/pubmed/7559104
This class is primarily to implement taxon constraints. It may be removed in the future.
smooth muscle layer in fatty layer of subcutaneous tissue
central nervous system gray matter layer
epithelium of terminal part of digestive tract
muscle tissue of terminal part of digestive tract
In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault.
In humans, they begin in the deep veins of the penis which issue from the corpus cavernosum penis, accompany the internal pudendal artery, and unite to form a single vessel, which ends in the internal iliac vein. They receive the veins from the urethral bulb, and the perineal and inferior hemorrhoidal veins
Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104
responsible for gut movement, such as peristalsis
see notes in inclusivity in class 'intestine'
See also: Wikipedia:Spinal_accessory_nucleus
in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe
this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum
Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat
he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]
myocardium of anterior wall of left ventricle
myocardium of anterior wall of right ventricle
vasculature of central nervous system plus retina
Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305
insect embryonic/larval head sense organ
The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum.
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'
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).