An ontology of human and animal behaviours. Neuro Behaviour Ontology GO 2023-07-04 definition term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive 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 part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part has part has_part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes 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 occurs in occurs in 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 has characteristic https://github.com/oborel/obo-relations/pull/284 participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant has participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of 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 contained in contains 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 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/ located_in 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. 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 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. has boundary has_2D_boundary has 2D boundary http://www.ncbi.nlm.nih.gov/pubmed/22402613 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. has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. 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. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. has component process directly regulated by directly negatively regulated by directly positively regulated by This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true 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. connected to 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 FMA:85972 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 only in taxon 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. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern 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 https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). 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 https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern 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 true 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 inverse of 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. FBbt TODO - add child relations from DOS directly develops from inverse of directly develops from developmental precursor of 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. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in capable of part of true 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 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. inverse of surrounded by 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 inverse of starts with Chris Mungall Allen 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. Chris Mungall started by 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 EHDAA2 Jonathan Bard, EHDAA2 develops in inverse of ends with Chris Mungall 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. Chris Mungall finished by 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 starts with process that occurs in 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 ends with process that occurs in 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. consumes 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. produces 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 induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 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 false 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. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. acts upstream of or within 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 replaces developmentally replaces Inverse of developmentally preceded by 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 causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of true A 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. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in inverse of enables enabled by enabled by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates 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. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member inverse of has input input of inverse of has output 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. Wikipedia:Insertion_(anatomy) 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. Wikipedia:Insertion_(anatomy) 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 https://github.com/obophenotype/uberon/issues/170 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. drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) tributary of http://en.wikipedia.org/wiki/Tributary A lump of clay and a statue 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 FMA:85994 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 inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates 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 influences (processual) causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. executes activity in is active in true 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. contributes to morphology of 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. Considering relabeling as 'pairwise interacts with' 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. interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates 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. composed primarily of 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. has part that occurs in true is kinase activity 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). existence starts during 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). existence starts with 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. existence overlaps 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) 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. existence starts and ends during 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). 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. existence ends during 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). 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. existence ends with x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships transformation of 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 immediate transformation of 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). 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. existence starts during or after 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. 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. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes depends on 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. towards The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities 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. has supporting framework 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). has skeleton causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences 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. biomechanically related to 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. Wikipedia:Antagonist_(muscle) has muscle antagonist inverse of branching part of has branching part 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. UBERON:cjm 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. conduit for 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. GOC:cjm lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity luminal space of inverse of has skeleton skeleton of p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates 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. enables subfunction 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 acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative acts upstream of, negative effect 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. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. indirectly regulates different in magnitude relative to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased in magnitude relative to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased in magnitude relative to Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has cross section 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. reciprocal of 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. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic by_means has-input has_participant in_response_to is_about qualifier has number of atomic nuclei entity Entity 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 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 per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant 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 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] occurrent Occurrent 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 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. per discussion with Barry Smith 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] ic IndependentContinuant 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 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] s-region SpatialRegion 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 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. per discussion with Barry Smith 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] process Process 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 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]) (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] disposition Disposition 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 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] realizable RealizableEntity 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 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] quality Quality 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 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] sdc SpecificallyDependentContinuant 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 role of being a doctor 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 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. per discussion with Barry Smith (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] role Role 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 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] function Function 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 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] material MaterialEntity 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 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] immaterial ImmaterialEntity 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 0 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. -1 0.000548579903 0.0 electron electron nucleic acid polymer Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. Mycoplasma genitalium metabolite 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. -1 (C14H20NO11)n.H2O hyaluronate 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. volatile organic compound An organic cation obtained by protonation of the amino group of any tertiary amino compound. +1 HNR3 15.015 15.01090 [NH+](*)(*)* tertiary ammonium ion An N-alkylpyrrolidine that consists of N-methylpyrrolidine bearing a pyridin-3-yl substituent at position 2. 0 C10H14N2 InChI=1S/C10H14N2/c1-12-7-3-5-10(12)9-4-2-6-11-8-9/h2,4,6,8,10H,3,5,7H2,1H3 SNICXCGAKADSCV-UHFFFAOYSA-N 162.232 162.11570 C=1C=C(C2N(CCC2)C)C=NC1 3-(1-methylpyrrolidin-2-yl)pyridine 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. inorganic acid Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). gas molecular entity -1 CH2NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 KXDHJXZQYSOELW-UHFFFAOYSA-M 60.03212 60.00910 NC([O-])=O carbamate 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. 0 C7H6N2O 134.136 134.04801 C(=CC(NC(=*)*)=*)(NC(C(C)=*)=O)* 24G7 epitope A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. acceptor An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms 0 H2O InChI=1S/H2O/h1H2 XLYOFNOQVPJJNP-UHFFFAOYSA-N 18.01530 18.01056 [H]O[H] water 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. 0 CH3OR 31.034 31.01839 *C(O)([H])[H] primary alcohol A peptide containing ten or more amino acid residues. C4H6N2O3R2(C2H2NOR)n polypeptide An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. 0 H3N InChI=1S/H3N/h1H3 QGZKDVFQNNGYKY-UHFFFAOYSA-N 17.03056 17.02655 [H]N([H])[H] ammonia A sulfur oxoanion obtained by deprotonation of both OH groups of sulfuric acid. -2 O4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2 QAOWNCQODCNURD-UHFFFAOYSA-L 96.06360 95.95283 [O-]S([O-])(=O)=O sulfate -1 HO InChI=1S/H2O/h1H2/p-1 XLYOFNOQVPJJNP-UHFFFAOYSA-M 17.00734 17.00329 [O-][H] hydroxide A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group. 0 C2H6O InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 LFQSCWFLJHTTHZ-UHFFFAOYSA-N 46.06844 46.04186 CCO ethanol 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. 0 (C14H21NO12)n hyaluronic acid A naturally occurring polypeptide synthesized at the ribosome. protein polypeptide chain 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. carbohydrate 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. 0 (C2H2NOR)nC2H3NOR peptide 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. glycan 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. 0 C33H36N4O6 InChI=1S/C33H36N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-14,34-35H,1-2,9-12,15H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14- BPYKTIZUTYGOLE-IFADSCNNSA-N 584.673 584.26348 CC1=C(C=C)\C(NC1=O)=C\C1=C(C)C(CCC(O)=O)=C(CC2=C(CCC(O)=O)C(C)=C(N2)\C=C2/NC(=O)C(C=C)=C2C)N1 bilirubin IXalpha A compound in which a carbohydrate component is covalently bound to a protein component. glycoprotein 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). 0 C17H19NO3 InChI=1S/C17H19NO3/c1-18-7-6-17-10-3-5-13(20)16(17)21-15-12(19)4-2-9(14(15)17)8-11(10)18/h2-5,10-11,13,16,19-20H,6-8H2,1H3/t10-,11+,13-,16-,17-/m0/s1 BQJCRHHNABKAKU-KBQPJGBKSA-N 285.33770 285.13649 [H][C@]12C=C[C@H](O)[C@@H]3Oc4c(O)ccc5C[C@H]1N(C)CC[C@@]23c45 morphine Any compound that supports healthy aging, slows the biological aging process, or extends lifespan. geroprotector 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. 0 C10H14N2 InChI=1S/C10H14N2/c1-12-7-3-5-10(12)9-4-2-6-11-8-9/h2,4,6,8,10H,3,5,7H2,1H3/t10-/m0/s1 SNICXCGAKADSCV-JTQLQIEISA-N 162.236 162.11570 [H][C@]1(CCCN1C)C1=CC=CN=C1 (S)-nicotine The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group. 0 CH4O InChI=1S/CH4O/c1-2/h2H,1H3 OKKJLVBELUTLKV-UHFFFAOYSA-N 32.04186 32.02621 CO methanol A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. donor '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. lipid Any polysaccharide containing a substantial proportion of aminomonosaccharide residues. glycosaminoglycan 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. polysaccharide A racemate composed of equimolar amounts of (R)- and (S)-nicotine. 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. acyl group alkali metal atom 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. alkaloid aminoglycan A monoatomic or polyatomic species having one or more elementary charges of the electron. anion A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. antioxidant 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). base Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. benzenes Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group. benzoic acids A sodium salt of the conjugate of any bile acid with either glycine or taurine. bile salt An insecticide compound naturally occurring in plants. phytogenic insecticide The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid. 0 CH2NO 44.03272 44.01364 *C(N)=O carbamoyl group 0 CO 28.01010 27.99491 O=C(*)* carbonyl group 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). cofactor Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular 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. drug monoatomic cation 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. enzyme inhibitor Any primary alcohol based on an ethanol skeleton. ethanols A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity A role played by the molecular entity or part thereof within a biological context. biological role A defined linked collection of atoms or a single atom within a molecular entity. group A cyclic compound having as ring members atoms of carbon and at least of one other element. organic heterocyclic compound Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). hydroxides imide 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). oxoacid inorganic anion A molecular entity that contains no carbon. inorganic molecular entity inorganic oxide Strictly, a substance intended to kill members of the class Insecta. In common usage, any substance used for preventing, destroying, repelling or controlling insects. insecticide A salt is an assembly of cations and anions. salt monoatomic ion organic salt A molecular entity having a net electric charge. ion Any alkaloid that has a structure based on an isoquinoline nucleus. They are derived from the amino acids like tyrosine and phenylalanine. isoquinoline alkaloid linear tetrapyrrole Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. metabolite metal cation Any carboxylic ester resulting from the formal condensation of a carboxy group with methanol. 0 C2H3O2R 59.044 59.01330 COC([*])=O methyl ester Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule +1 0.00000 [*+] monoatomic monocation An isoquinoline alkaloid based on a morphinan skeleton and its substituted derivatives. morphinane alkaloid 0 N 14.007 14.00307 nitrogen atom nonmetal atom organic heteromonocyclic compound Any organic ion with a net negative charge. organic anion Any organic ion with a net positive charge. organic cation organic ion Compounds of the general formula SO3HOR where R is an organyl group organic sulfate An alcohol derived from an aliphatic compound. 0 HOR 17.007 17.00274 O* aliphatic alcohol An oxide is a chemical compound of oxygen with other chemical elements. oxide 0 O InChI=1S/O QVGXLLKOCUKJST-UHFFFAOYSA-N 15.99940 15.99491 [O] oxygen atom oxygen molecular entity Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests. pesticide pyridine alkaloid Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives. pyridines pyrrolidine alkaloid 0 Na InChI=1S/Na KEAYESYHFKHZAL-UHFFFAOYSA-N 22.98977 22.98977 [Na] sodium atom sodium molecular entity Any alkali metal salt having sodium(1+) as the cation. sodium salt An ester of an alcohol and sulfuric acid. 0 O4SR2 96.06300 95.95173 [*]OS(=O)(=O)O[*] sulfuric ester Salts and esters of sulfuric acid sulfates 0 S InChI=1S/S NINIDFKCEFEMDL-UHFFFAOYSA-N 32.06600 31.97207 [S] sulfur atom sulfur molecular entity A sulfur oxoacid that consists of two oxo and two hydroxy groups joined covalently to a central sulfur atom. 0 H2O4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4) QAOWNCQODCNURD-UHFFFAOYSA-N 98.07948 97.96738 [H]OS(=O)(=O)O[H] sulfuric acid 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. tetrapyrrole organic heterobicyclic compound A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid. univalent carboacyl group 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). zwitterion 0 C InChI=1S/C OKTJSMMVPCPJKN-UHFFFAOYSA-N 12.01070 12.00000 [C] carbon atom A tropane alkaloid obtained from leaves of the South American shrub Erythroxylon coca. 0 C17H21NO4 InChI=1S/C17H21NO4/c1-18-12-8-9-13(18)15(17(20)21-2)14(10-12)22-16(19)11-6-4-3-5-7-11/h3-7,12-15H,8-10H2,1-2H3/t12-,13+,14-,15+/m0/s1 ZPUCINDJVBIVPJ-LJISPDSOSA-N 303.35290 303.14706 [H][C@]12CC[C@]([H])([C@H]([C@H](C1)OC(=O)c1ccccc1)C(=O)OC)N2C cocaine 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. 0 CH3NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4) KXDHJXZQYSOELW-UHFFFAOYSA-N 61.04006 61.01638 NC(O)=O carbamic acid An onium cation obtained by protonation of ammonia. +1 H4N InChI=1S/H3N/h1H3/p+1 QGZKDVFQNNGYKY-UHFFFAOYSA-O 18.03850 18.03383 [H][N+]([H])([H])[H] ammonium A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid. -2 C2O4R 88.019 87.97966 [O-]C(=O)[*]C([O-])=O dicarboxylic acid dianion The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. -1 CO2R 44.00950 43.98983 [O-]C([*])=O carboxylic acid anion A monoatomic monocation obtained from sodium. +1 Na InChI=1S/Na/q+1 FKNQFGJONOIPTF-UHFFFAOYSA-N 22.98977 22.98922 [Na+] sodium(1+) -1 H2N InChI=1S/H2N/h1H2/q-1 HYGWNUKOUCZBND-UHFFFAOYSA-N 16.02262 16.01927 [H][N-][H] azanide A divalent inorganic anion resulting from the removal of two protons from ammonia. -2 HN InChI=1S/HN/h1H/q-2 DZQYTNGKSBCIOE-UHFFFAOYSA-N 15.01468 15.01200 [N--][H] hydridonitrate(2-) +1 H3O InChI=1S/H2O/h1H2/p+1 XLYOFNOQVPJJNP-UHFFFAOYSA-O 19.02322 19.01784 [H][O+]([H])[H] oxonium A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. 0 HOR 17.007 17.00274 O[*] alcohol 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. 0 C7H5NO3S InChI=1S/C7H5NO3S/c9-7-5-3-1-2-4-6(5)12(10,11)8-7/h1-4H,(H,8,9) CVHZOJJKTDOEJC-UHFFFAOYSA-N 183.18500 182.99901 O=C1NS(=O)(=O)c2ccccc12 saccharin 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. amide Intended use of the molecular entity or part thereof by humans. application A particle not known to have substructure. fundamental particle A monoatomic entity is a molecular entity consisting of a single atom. monoatomic entity oxoacid derivative inorganic hydride 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. organic fundamental parent Any substituent group which does not contain carbon. inorganic group Any substituent group or skeleton containing carbon. organic group Any organic substituent group, regardless of functional type, having one free valence at a carbon atom. organyl group A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom uncharged atom 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 This is equivalent to CHEBI:33252 atomic nucleus atomic nucleus Heavy nuclear particle: proton or neutron. nucleon 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. primary amide 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. secondary amide A molecular entity all atoms of which have the same atomic number. elemental molecular entity An organosulfur compound is a compound containing at least one carbon-sulfur bond. organosulfur compound An anion consisting of more than one atom. polyatomic anion A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. antimicrobial agent A nutrient is a food component that an organism uses to survive and grow. nutrient A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. heteroorganic entity 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. food An energy-rich substance that can be transformed with release of usable energy. fuel A molecular entity containing one or more atoms of an alkali metal. alkali metal molecular entity Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogen A p-block molecular entity containing any pnictogen. pnictogen molecular entity Any p-block element belonging to the group 16 family of the periodic table. chalcogen Any p-block molecular entity containing a chalcogen. chalcogen molecular entity carbon group element atom An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. 0 CO2R2 44.010 43.98983 [*]C(=O)O[*] carboxylic ester An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group element atom sulfur oxoacid sulfur oxoacid derivative sulfur oxoanion chalcogen oxoacid chalcogen oxoanion alkali metal cation An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. metal atom An amino-acid anion obtained by deprotonation of any alpha-amino acid. alpha-amino-acid anion s-block element atom Any main group element atom belonging to the p-block of the periodic table. p-block element atom 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. 0 CHO2R 45.01740 44.99765 OC([*])=O carboxylic 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. main group molecular entity carbon group molecular entity Any molecule that consists of a series of atoms joined together to form a ring. cyclic compound A cyclic compound having as ring members atoms of the same element only. homocyclic compound A homocyclic compound in which all of the ring members are carbon atoms. carbocyclic compound hydrogen molecular entity polycyclic compound A molecule that features two fused rings. bicyclic compound 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. aromatic compound organic aromatic compound monocyclic compound heteromonocyclic compound A polycyclic compound in which at least one of the rings contains at least one non-carbon atom. heteropolycyclic compound A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compound An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity A main group molecular entity that contains one or more atoms of a p-block element. p-block molecular entity Hydrides are chemical compounds of hydrogen with other chemical elements. hydrides oxygen hydride A macromolecule formed by a living organism. biomacromolecule information biomacromolecule proteinogenic amino-acid residue A cation consisting of more than one atom. polyatomic cation An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group. 0 C2H4NO2R 74.05870 74.02420 NC([*])C(O)=O alpha-amino acid 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. amino-acid residue A carboxylic acid containing one or more amino groups. amino acid alpha-amino-acid residue carbohydrate acid carbohydrate acid anion An organic compound having at least one hydroxy group attached to a carbon atom. organic hydroxy compound Any organic molecule that consists of atoms connected in the form of a ring. organic cyclic compound 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). heteroarene benzenoid aromatic compound Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion. conjugated protein 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. macromolecule Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring. aromatic carboxylic acid A substance used in a chemical reaction to detect, measure, examine, or produce other substances. reagent 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. macronutrient nitrogen hydride Saturated acyclic nitrogen hydrides having the general formula NnHn+2. azane A substance that diminishes the rate of a chemical reaction. inhibitor A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction. catalyst The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group. amino acid zwitterion 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). ammonium ion derivative Any drug that enhances the activity of the central nervous system. central nervous system stimulant 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. 0 C19H31R 259.450 259.24258 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCCC4)C steroid Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compound An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. oxoanion A substance used in the prophylaxis or therapy of infectious diseases. antiinfective agent A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system. central nervous system drug A loosely defined grouping of drugs that have effects on psychological function. psychotropic drug A traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behaviour. tranquilizing drug 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. anxiolytic drug alkali metal salt 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. analgesic A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. opioid analgesic A loosely defined group of drugs that tend to reduce the activity of the central nervous system. central nervous system depressant alkaloid fundamental parent natural product fundamental parent steroid fundamental parent 0 C24H42 InChI=1S/C24H42/c1-5-8-17(2)20-12-13-21-19-11-10-18-9-6-7-15-23(18,3)22(19)14-16-24(20,21)4/h17-22H,5-16H2,1-4H3/t17-,18?,19+,20-,21+,22+,23+,24-/m1/s1 QSHQKIURKJITMZ-BRPMRXRMSA-N 330.59028 330.32865 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC cholane 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. sympathomimetic agent A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. cardiovascular drug carbon oxoacid A food additive that is used to added improve the taste or odour of a food. flavouring agent A drug used to cause dilation of the blood vessels. vasodilator agent 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. adrenergic uptake inhibitor 0 C16H21N InChI=1S/C16H21N/c1-2-6-13-12(5-1)11-15-14-7-3-4-8-16(13,14)9-10-17-15/h1-2,5-6,14-15,17H,3-4,7-11H2/t14-,15+,16-/m0/s1 INAXVFBXDYWQFN-XHSDSOJGSA-N 227.34468 227.16740 [H][C@@]12CCCC[C@@]11CCN[C@@H]2Cc2ccccc12 morphinan Any carboxylic acid containing two carboxy groups. dicarboxylic acid dicarboxylic acid anion 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. ester 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. xenobiotic sulfated glycosaminoglycan carbohydrate sulfate pnictogen hydride 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. neurotransmitter agent Esters of benzoic acid or substituted benzoic acids. benzoate ester cholanoid A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. protein A salt of a bile acid. bile acid salt 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. local anaesthetic Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). lepton Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). baryon Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion A particle smaller than an atom. subatomic particle subatomic particle A subatomic particle known to have substructure (i.e. consisting of smaller particles). composite particle Hadron is a subatomic particle which experiences the strong force. hadron A nucleus or any of its constituents in any of their energy states. nuclear particle Any molecular entity consisting of more than one atom. polyatomic entity An ion consisting of more than one atom. polyatomic ion 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. carbonyl compound Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. organic oxo compound Compounds based on a biladiene skeleton. biladienes chalcogen hydride inorganic ion inorganic cation A monoatomic or polyatomic species having one or more elementary charges of the proton. cation An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound An organochalcogen compound containing at least one carbon-oxygen bond. organooxygen compound amino-acid anion organic hydride mononuclear parent hydride elemental sodium tropane alkaloid Any of the group of polysaccharides composed of alternating units from uronic acids and glycosamines, and commonly partially esterified with sulfuric acid. mucopolysaccharide 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). acid A molecular entity consisting of two or more chemical elements. heteroatomic molecular entity 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. 0 CNOR3 42.01680 41.99799 [*]C(=O)N([*])[*] carboxamide Any imide in which the acyl substituents are any two from carboacyl, sulfonyl and phosphoryl mixed diacylamine sulfuric acid derivative A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid. carboacyl group benzothiazoles Any agent that acts on an adrenergic receptor or affects the life cycle of an adrenergic transmitter. adrenergic agent A compound composed of two or more pyrrole units. polypyrrole Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. organonitrogen heterocyclic compound organosulfur heterocyclic compound organic heteropentacyclic compound organic heteropolycyclic compound Any of a class of heterocyclic amines having a saturated five-membered ring. pyrrolidines azabicycloalkane 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. cholinergic drug Any drug that binds to and activates cholinergic receptors. cholinergic agonist isoquinoline alkaloid fundamental parent Any agent that affects the transport of molecular entities across a biological membrane. membrane transport modulator An agent that inhibits sodium influx through cell membranes. sodium channel blocker organic sodium salt Any dianion containing at least one carboxy group. carboxylic acid dianion Substance which produces loss of feeling or sensation. anaesthetic sodium channel modulator A molecular entity capable of donating a hydron to an acceptor (Bronsted base). Bronsted acid A molecular entity capable of accepting a hydron from a donor (Bronsted acid). Bronsted base 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. Lewis base A 3-(1-methylpyrrolidin-2-yl)pyridine in which the chiral centre has R-configuration. 0 C10H14N2 InChI=1S/C10H14N2/c1-12-7-3-5-10(12)9-4-2-6-11-8-9/h2,4,6,8,10H,3,5,7H2,1H3/t10-/m1/s1 SNICXCGAKADSCV-SNVBAGLBSA-N 162.23160 162.11570 CN1CCC[C@@H]1c1cccnc1 (R)-nicotine 0 HO 17.00734 17.00274 *O[H] hydroxy group -1 HO4S InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-1 QAOWNCQODCNURD-UHFFFAOYSA-M 97.07154 96.96010 [H]OS([O-])(=O)=O hydrogensulfate 0 O 15.99940 15.99491 O=* oxo group N-alkylpyrrolidine A liquid that can dissolve other substances (solutes) without any change in their chemical composition. solvent 0 CHO2 45.01744 44.99765 *C(=O)O carboxy group Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc. indicator An agonist that selectively binds to and activates a nicotinic acetylcholine receptor. nicotinic acetylcholine receptor agonist sulfur oxide 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). antiseptic drug An antimicrobial agent that is applied to non-living objects to destroy harmful microorganisms or to inhibit their activity. disinfectant serotonergic drug A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds. polar solvent A polar solvent that is capable of acting as a hydron (proton) donor. protic solvent Solvent that is capable of acting as a hydron (proton) acceptor. protophilic solvent Self-ionizing solvent possessing both characteristics of Bronsted acids and bases. amphiprotic solvent A drug used for its effects on dopamine receptors, on the life cycle of dopamine, or on the survival of dopaminergic neurons. dopaminergic agent Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own. agonist Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances. antagonist A drug that acts principally at one or more sites within the peripheral neuroeffector systems, the autonomic system, and motor nerve-skeletal system. peripheral nervous system drug 0 H InChI=1S/H YZCKVEUIGOORGS-UHFFFAOYSA-N 1.00794 1.00783 [H] hydrogen atom A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. organic amino compound 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. protective agent onium compound Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families. onium cation Substance that sweeten food, beverages, medications, etc. sweetening agent Drug used to cause constriction of the blood vessels. vasoconstrictor agent An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position. alkyl alcohol Biologically active substance whose activity affects or plays a role in the functioning of the immune system. immunomodulator Any molecular entity that contains carbon. organic molecular entity 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. allergen 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. teratogenic agent A role is particular behaviour which a material entity may exhibit. role A poison that interferes with the functions of the nervous system. neurotoxin 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. serotonin uptake inhibitor A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups. tertiary amino compound 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. dopamine uptake inhibitor A role played by the molecular entity or part thereof within a chemical context. chemical role nitrogen molecular entity 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. dipolar compound Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s). organodiyl group organic divalent group organic univalent group organic polycyclic compound An organic anion that is the conjugate base of methanol. -1 CH3O InChI=1S/CH3O/c1-2/h1H3/q-1 NBTOZLQBSIZIKS-UHFFFAOYSA-N 31.03390 31.01894 C[O-] methoxide An organic anion that is the conjugate base of ethanol. -1 C2H5O InChI=1S/C2H5O/c1-2-3/h2H2,1H3/q-1 HHFAWKCIHAUFRX-UHFFFAOYSA-N 45.06050 45.03459 CC[O-] ethoxide A biological role played by the molecular entity or part thereof within a biochemical context. biochemical role biophysical role A role played by the molecular entity or part thereof which causes the development of a pathological process. aetiopathogenetic role A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties. pharmacological role physiological role Any substance introduced into a living organism with therapeutic or diagnostic purpose. pharmaceutical A chemical substance that encourages a cell to commence cell division, triggering mitosis. mitogen inorganic hydroxy compound 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. epitope A polymer carrying multiple negative charges. polyanionic macromolecule A macromolecule containing ionic groups. ionic macromolecule A compound that exhibits agonist activity at the mu-opioid receptor. mu-opioid receptor agonist A benzothiazole consisting of a benzene ring fused to an isothiazole. 1,2-benzisothiazole A cyclic compound having as ring members atoms of at least two different elements. heterocyclic compound A dicarboxylic acid dianion obtained by deprotonation of the two carboxy groups of bilirubin; major species at pH 7.3. -2 C33H34N4O6 InChI=1S/C33H36N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-14,34-35H,1-2,9-12,15H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/p-2/b26-13-,27-14- BPYKTIZUTYGOLE-IFADSCNNSA-L 582.64630 582.24893 CC1=C(C=C)\C(NC1=O)=C\c1[nH]c(Cc2[nH]c(\C=C3NC(=O)C(C=C)=C/3C)c(C)c2CCC([O-])=O)c(CCC([O-])=O)c1C bilirubin(2-) The conjugate acid of morphine arising from protonation of the tertiary amino group; major species at pH 7.3. +1 C17H20NO3 InChI=1S/C17H19NO3/c1-18-7-6-17-10-3-5-13(20)16(17)21-15-12(19)4-2-9(14(15)17)8-11(10)18/h2-5,10-11,13,16,19-20H,6-8H2,1H3/p+1/t10-,11+,13-,16-,17-/m0/s1 BQJCRHHNABKAKU-KBQPJGBKSA-O 286.34560 286.14377 [H][C@]12C=C[C@H](O)[C@@H]3Oc4c(O)ccc5C[C@H]1[NH+](C)CC[C@@]23c45 morphine(1+) An organic anion of general formula RS(=O)2O(-) where R is an organyl group. -1 O4SR 96.06300 95.95173 [O-]S(=O)(=O)O[*] organosulfate oxoanion A substance used as an indicator of a biological state. biomarker An organic anion arising from deprotonation of a acyclic tetrapyrrole compound. linear tetrapyrrole anion A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons. nucleophilic reagent The conjugate acid of (S)-nicotine arising from selective protonation of the tertiary amino group; major species at pH 7.3. +1 C10H15N2 InChI=1S/C10H14N2/c1-12-7-3-5-10(12)9-4-2-6-11-8-9/h2,4,6,8,10H,3,5,7H2,1H3/p+1/t10-/m0/s1 SNICXCGAKADSCV-JTQLQIEISA-O 163.23900 163.12297 C[NH+]1CCC[C@H]1c1cccnc1 (S)-nicotinium(1+) A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. chemical substance A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. mixture 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.. polymer The conjugate base of cocaine arising from protonation of the tertiary amino group; major species at pH 7.3. +1 C17H22NO4 InChI=1S/C17H21NO4/c1-18-12-8-9-13(18)15(17(20)21-2)14(10-12)22-16(19)11-6-4-3-5-7-11/h3-7,12-15H,8-10H2,1-2H3/p+1/t12-,13+,14-,15+/m0/s1 ZPUCINDJVBIVPJ-LJISPDSOSA-O 304.36090 304.15433 [H][C@]12CC[C@]([H])([C@H]([C@H](C1)OC(=O)c1ccccc1)C(=O)OC)[NH+]2C cocaine(1+) An ionic polymer is a polymer, composed of ionic macromolecules. ionic polymer An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one. monovalent inorganic cation Zwitterionic form of any peptide where, in general, the amino terminus is positively charged and the carboxy terminus is negatively charged. 0 C2H4NO2R(C2H2NOR)n peptide zwitterion Any agent that acts on an opioid receptor or affects the life cycle of an opioid transmitter. opioid agent Any agent that acts on a mu-opioid receptor. mu-opioid agent An agent that selectively binds to and activates an opioid receptor. opioid receptor agonist 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. NMDA receptor antagonist Any substance which inhibits the action of receptors for excitatory amino acids. excitatory amino acid antagonist A racemate is an equimolar mixture of a pair of enantiomers. racemate A polymer, composed of polyanion macromolecules. polyanionic polymer An ester where the ester linkage is bonded directly to an aromatic system. aromatic ester 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. carbohydrate derivative A carbohydrate derivative that is formally obtained from a carbohydrate acid. carbohydrate acid derivative A carboxylic acid anion resulting from the deprotonation of the carboxy group of a carbohydrate acid derivative. carbohydrate acid derivative anion An agonist that selectively binds to and activates a protein kinase C receptor protein kinase C agonist Any substance which is added to food to preserve or enhance its flavour and/or appearance. food additive An agonist that selectively binds to and activates a protein kinase receptor. protein kinase agonist An organic molecular entity containing a single carbon atom (C1). one-carbon compound Any organic molecular entity that is acidic and contains carbon in covalent linkage. organic acid 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. poison A carbohydrate derivative that is any derivative of a polysaccharide. polysaccharide derivative Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. organic molecule A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment. exopolysaccharide Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms. eukaryotic metabolite Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals. animal metabolite Any animal metabolite produced during a metabolic reaction in mammals. mammalian metabolite Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus). mouse metabolite Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae). Saccharomyces cerevisiae metabolite Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. prokaryotic metabolite A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'. greenhouse gas Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*). EC 3.* (hydrolase) inhibitor 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. plant metabolite Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds. fungal metabolite Any prokaryotic metabolite produced during a metabolic reaction in bacteria. bacterial metabolite Any bacterial metabolite produced during a metabolic reaction in Escherichia coli. Escherichia coli metabolite Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens). human metabolite 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). EC 3.5.1.4 (amidase) inhibitor 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. food component Any minor or unwanted substance introduced into the environment that can have undesired effects. environmental contaminant 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. refrigerant 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. 0 C2H4NO2R 74.059 74.02420 [NH3+]C([*])C([O-])=O alpha-amino acid zwitterion 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. +1 C10H15N2 InChI=1S/C10H14N2/c1-12-7-3-5-10(12)9-4-2-6-11-8-9/h2,4,6,8,10H,3,5,7H2,1H3/p+1/t10-/m1/s1 SNICXCGAKADSCV-SNVBAGLBSA-O 163.23900 163.12297 C[NH+]1CCC[C@@H]1c1cccnc1 (R)-nicotinium(1+) Any inorganic anion with a valency of two. divalent inorganic anion Any inorganic anion with a valency of one. monovalent inorganic anion Any drug which causes the onset of an allergic reaction. drug allergen A mixed diacylamine resulting from the formal condensation of the nitrogen of a carboxamide with a sulphonic acid. 0 CNO3SR3 106.082 105.95989 C(=O)(N(S(*)(=O)=O)*)* N-sulfonylcarboxamide A carboxylic acic anion obtained by deprotonation of the carboxy group of any aromatic carboxylic acid. Major species at pH 7.3. -1 CO2R 44.010 43.98983 *C([O-])=O aromatic carboxylate 1 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 gene product A complex of two or more molecular entities that are not covalently bound. complex of molecular entities >=2 parts (not we cannot use cardinality with transitive properties) reproduction polysaccharide biosynthetic process polysaccharide catabolic process 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. response to acid chemical skeletal system development 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'. ossification temperature homeostasis Note that this term refers to a mode of migration rather than to any particular cell type. ameboidal-type cell migration gastric acid secretion formation of primary germ layer ectoderm formation endoderm formation mesoderm formation morphogenesis of a branching structure serotonin secretion embryonic epithelial tube formation neural tube formation 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. intramembranous ossification morphogenesis of an epithelium regulation of heart rate positive regulation of mesenchymal cell proliferation regulation of respiratory gaseous exchange by nervous system process aggressive behavior nematode larval development https://github.com/geneontology/go-ontology/issues/18568 This term was obsoleted because it is outside the scope of GO. obsolete predatory behavior true larval development 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). immune system process hepatic immune response regulation of immune system process negative regulation of immune system process positive regulation of immune system process peptide secretion regulation of peptide secretion negative regulation of peptide secretion positive regulation of peptide secretion developmental process involved in reproduction system process muscle system process circulatory system process renal system process heart process respiratory system process 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 molecular_function catalytic 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. cellular_component 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'. extracellular region fibrinogen complex collagen trimer fibrillar collagen trimer collagen type II trimer collagen type IV trimer Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. basement membrane 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. extracellular space https://github.com/geneontology/go-ontology/issues/17776 intracellular anatomical structure https://github.com/geneontology/go-ontology/issues/23023 cytoplasm cytoskeleton actin filament plasma membrane 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. microvillus https://github.com/geneontology/go-ontology/issues/22122 cell-cell junction cell cortex https://github.com/geneontology/go-ontology/issues/22880 carbohydrate metabolic process polysaccharide metabolic process glycogen metabolic process glycogen biosynthetic process regulation of glycogen biosynthetic process glycogen catabolic process regulation of glycogen catabolic process monosaccharide metabolic process glucose metabolic process organic acid metabolic process generation of precursor metabolites and energy regulation of carbohydrate metabolic process energy reserve metabolic process lipid metabolic process steroid biosynthetic process bile acid biosynthetic process phosphorus metabolic process phosphate-containing compound metabolic process https://github.com/geneontology/go-ontology/issues/20292 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. transport monoatomic ion transport serotonin transport extracellular transport lipid transport intracellular protein transport muscle contraction regulation of muscle contraction smooth muscle contraction regulation of smooth muscle contraction 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. response to stress immune response cell communication cell-cell signaling https://github.com/geneontology/go-ontology/issues/21234 Note that this term was 'developmental process'. multicellular organism development gamete generation gastrulation ectoderm development nervous system development endoderm development mesoderm development respiratory gaseous exchange by respiratory system digestion https://github.com/geneontology/go-ontology/issues/22368 excretion body fluid secretion sensory perception visual perception sensory perception of sound sensory perception of chemical stimulus sensory perception of smell 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). behavior mating behavior courtship behavior copulation rhythmic behavior circadian rhythm groom grooming behavior locomotory behavior fly flight behavior https://github.com/geneontology/go-ontology/issues/18547 See also the biological process term 'behavior ; GO:0007610'. feeding behavior visual behavior chemosensory behavior mechanosensory behavior blood circulation regulation of heart contraction male courtship behavior female courtship behavior https://github.com/geneontology/go-ontology/issues/23112 protein localization A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. https://github.com/geneontology/go-ontology/issues/24968 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 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. metabolic process steroid metabolic process bile acid metabolic process 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. cell population proliferation positive regulation of cell population proliferation negative regulation of cell population proliferation See also the biological process term 'locomotory behavior ; GO:0007626'. adult locomotory behavior lipid biosynthetic process catabolic process macromolecule catabolic process biosynthetic process http://amigo.geneontology.org/amigo/term/GO:0070589 macromolecule biosynthetic process glucan biosynthetic process glucan catabolic process response to temperature stimulus protein secretion Note that 'radiation' refers to electromagnetic radiation of any wavelength. response to radiation response to water deprivation response to water response to light stimulus detection of external stimulus detection of abiotic stimulus detection of light stimulus detection of visible light detection of chemical stimulus 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. response to external stimulus response to mechanical stimulus https://github.com/geneontology/go-ontology/issues/16572 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. response to abiotic stimulus anatomical structure morphogenesis embryo development post-embryonic development embryo development ending in birth or egg hatching tissue development regulation of biosynthetic process negative regulation of biosynthetic process positive regulation of biosynthetic process negative regulation of metabolic process positive regulation of metabolic process regulation of catabolic process negative regulation of catabolic process positive regulation of catabolic process hormone transport 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. cellular process response to organic substance response to inorganic substance mesenchymal cell proliferation regulation of mesenchymal cell proliferation regulation of gastrulation 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 regulation of cell communication positive regulation of cell communication negative regulation of cell communication negative regulation of norepinephrine secretion positive regulation of norepinephrine secretion regulation of hormone levels lipid localization positive regulation of steroid biosynthetic process negative regulation of steroid biosynthetic process regulation of glucose metabolic process positive regulation of glucose metabolic process regulation of glucan biosynthetic process response to auditory stimulus vesicle membrane regulation of norepinephrine secretion regulation of serotonin secretion negative regulation of serotonin secretion positive regulation of serotonin secretion phasic smooth muscle contraction urinary bladder smooth muscle contraction urinary tract smooth muscle contraction protein transport actin cytoskeleton organic cation transport organic anion transport monocarboxylic acid transport bile acid and bile salt transport peptide transport amine transport monoamine transport organic acid transport organic hydroxy compound transport norepinephrine transport energy derivation by oxidation of organic compounds membrane cellular component organization detection of temperature stimulus carbohydrate biosynthetic process carbohydrate catabolic process organic acid biosynthetic process true Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity phosphorylation morphogenesis of embryonic epithelium https://github.com/geneontology/go-ontology/issues/24787 cell migration transferase activity 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 https://github.com/geneontology/go-ontology/issues/23491 reproductive behavior regulation of lipid metabolic process regulation of steroid metabolic process regulation of phosphate metabolic process regulation of metabolic process sensory perception of pain hexose metabolic process carboxylic acid metabolic process https://github.com/geneontology/go-ontology/issues/22929 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. sexual reproduction neural tube development circadian sleep/wake cycle process cellular process involved in reproduction in multicellular organism reproductive process digestive system process regulation of anatomical structure morphogenesis regulation of signaling 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. signaling positive regulation of signaling negative regulation of signaling signal release cell junction peptide hormone secretion https://github.com/geneontology/go-ontology/issues/11255#issuecomment-426191045 insulin secretion regulation of ossification negative regulation of ossification 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'. external encapsulating structure regulation of cell migration positive regulation of cell migration negative regulation of cell migration defecation sleep peristalsis See also the biological process term 'behavior ; GO:0007610'. adult behavior cytoplasmic vesicle membrane transmembrane collagen trimer extracellular matrix organelle membrane auditory behavior 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 cytoplasmic vesicle regulation of nervous system process negative regulation of nervous system process positive regulation of nervous system process vesicle locomotion involved in locomotory behavior positive regulation of insulin secretion 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. regulation of response to external stimulus 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. negative regulation of response to external stimulus 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. positive regulation of response to external stimulus regulation of lipid transport negative regulation of lipid transport positive regulation of lipid transport regulation of intracellular transport negative regulation of intracellular transport positive regulation of intracellular transport actin filament bundle multicellular organismal process developmental process multicellular organism reproduction protein transport within lipid bilayer monocarboxylic acid metabolic process plasma membrane bounded cell projection cytoplasm regulation of localization https://github.com/geneontology/go-ontology/issues/22021 regulation of protein localization regulation of polysaccharide metabolic process regulation of polysaccharide biosynthetic process regulation of organic acid transport negative regulation of organic acid transport positive regulation of organic acid transport secretion by cell secretion by tissue 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 complex protein-containing macromolecular complex macromolecule localization regulation of intracellular protein transport negative regulation of catecholamine secretion positive regulation of catecholamine secretion negative regulation of kinase activity positive regulation of kinase activity tube formation Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. social behavior tube morphogenesis tube development establishment of protein localization to extracellular region regulation of urine volume direct ossification somatodendritic compartment locomotion regulation of locomotion negative regulation of locomotion embryonic cleavage positive regulation of locomotion positive regulation of embryonic development cell migration involved in gastrulation regulation of cell population proliferation cellular ketone metabolic process 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. response to chemical 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 regulation of phosphorylation negative regulation of phosphorylation positive regulation of phosphorylation homeostatic process circadian sleep/wake cycle circadian sleep/wake cycle, REM sleep circadian sleep/wake cycle, non-REM sleep regulation of circadian sleep/wake cycle regulation of circadian rhythm positive regulation of circadian rhythm negative regulation of circadian rhythm eating behavior drinking behavior amide transport cell projection neuron projection chordate embryonic development 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. neuronal cell body positive regulation of catalytic activity negative regulation of catalytic activity macromolecule metabolic process organelle membrane-bounded organelle https://github.com/geneontology/go-ontology/issues/21881 non-membrane-bounded organelle intracellular organelle extracellular organelle intracellular membrane-bounded organelle intracellular non-membrane-bounded organelle regulation of carbohydrate biosynthetic process extracellular non-membrane-bounded organelle regulation of monoatomic ion transport positive regulation of monoatomic ion transport negative regulation of monoatomic ion transport oxoacid metabolic process regulation of generation of precursor metabolites and energy regulation of carbohydrate catabolic process regulation of kinase activity regulation of respiratory gaseous exchange glucan metabolic process regulation of system process regulation of digestive system process regulation of endocrine process regulation of excretion regulation of respiratory system process negative regulation of molecular function positive regulation of molecular function 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. cellular metabolic process primary metabolic process cellular catabolic process cellular biosynthetic process Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule metabolic process Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule biosynthetic process 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. cell body establishment of protein localization 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. obsolete post-mating behavior true negative regulation of glycogen biosynthetic process positive regulation of glycogen biosynthetic process positive regulation of ossification 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 regulation of embryonic development positive regulation of circadian sleep/wake cycle, REM sleep positive regulation of circadian sleep/wake cycle, non-REM sleep carboxylic acid biosynthetic process negative regulation of insulin secretion acid secretion hormone secretion regulation of hormone secretion positive regulation of hormone secretion negative regulation of hormone secretion positive regulation of lipid biosynthetic process regulation of lipid biosynthetic process secretion intracellular transport carboxylic acid transport norepinephrine secretion mesoderm morphogenesis rhythmic process circadian behavior animal organ development positive regulation of biological process negative regulation of biological process positive regulation of behavior negative regulation of behavior positive regulation of cellular process negative regulation of cellular process regulation of post-embryonic development negative regulation of post-embryonic development positive regulation of post-embryonic development 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. regulation of response to stimulus 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. positive regulation of response to stimulus 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. negative regulation of response to stimulus embryonic morphogenesis 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 tissue morphogenesis system development branching morphogenesis of an epithelial tube pigment granule anatomical structure development https://github.com/geneontology/go-ontology/issues/19809 cell motility multicellular organismal-level homeostasis catecholamine secretion regulation of catecholamine secretion regulation of protein secretion negative regulation of protein secretion positive regulation of protein secretion regulation of immune response negative regulation of immune response positive regulation of immune response regulation of biological process regulation of catalytic activity regulation of developmental process regulation of cellular process regulation of behavior regulation of insulin secretion circadian sleep/wake cycle, sleep regulation of steroid biosynthetic process https://github.com/geneontology/go-ontology/issues/13824 nervous system process regulation of body fluid levels multicellular organismal movement musculoskeletal movement voluntary musculoskeletal movement neuromuscular process controlling balance endocrine process cognition 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. response to stimulus neuromuscular process detection of stimulus involved in sensory perception detection of chemical stimulus involved in sensory perception detection of light stimulus involved in visual perception sensory perception of taste 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 light stimulus sensory perception of mechanical stimulus thermoception equilibrioception 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 sensory perception of touch detection of mechanical stimulus involved in sensory perception of touch detection of electrical stimulus detection of mechanical stimulus regulation of secretion positive regulation of secretion negative regulation of secretion regulation of transport positive regulation of transport negative regulation of transport 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 localization cartilage development positive regulation of protein transport regulation of protein transport negative regulation of protein transport establishment of localization 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. cell division regulation of cell division This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. regulation of transferase activity This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. positive regulation of transferase activity This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. negative regulation of transferase activity visual perception involved in equilibrioception response to electrical stimulus detection of stimulus cellular localization establishment of localization in cell https://github.com/geneontology/go-ontology/issues/20191 biological process involved in intraspecies interaction between organisms positive regulation of cell division negative regulation of cell division regulation of sensory perception of pain regulation of sensory perception catecholamine transport regulation of amine transport negative regulation of amine transport positive regulation of amine transport regulation of nervous system development negative regulation of nervous system development positive regulation of nervous system development reflex vestibular reflex heart contraction micturition smooth muscle contraction involved in micturition male mating behavior female mating behavior regulation of macromolecule metabolic process regulation of feeding behavior crying behavior regulation of cellular localization epithelium development regulation of gastric acid secretion positive regulation of gastric acid secretion negative regulation of gastric acid secretion positive regulation of digestive system process negative regulation of digestive system process epithelial tube morphogenesis regulation of morphogenesis of a branching structure hepaticobiliary system process membrane organization regulation of cartilage development 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 morphogenesis of a branching epithelium connective tissue 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 biological regulation regulation of biological quality regulation of molecular function extracellular membrane-bounded organelle tear secretion glucagon secretion regulation of glucagon secretion negative regulation of glucagon secretion positive regulation of glucagon secretion anchoring junction regulation of establishment of protein localization somatostatin secretion mucus secretion regulation of mucus secretion negative regulation of mucus secretion positive regulation of mucus secretion cellular macromolecule 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 mastication protein localization to extracellular region organic substance transport organic substance metabolic process nitrogen compound transport cellular component organization or biogenesis cell periphery elastic fiber https://github.com/geneontology/go-ontology/issues/22302 epithelial tube formation negative regulation of mesenchymal cell proliferation monocarboxylic acid biosynthetic process regulation of primary metabolic process 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. regulation of response to stress regulation of peptide transport regulation of muscle system process regulation of somatostatin secretion positive regulation of somatostatin secretion negative regulation of somatostatin secretion regulation of peptide hormone 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 https://github.com/geneontology/go-ontology/issues/22368 renal tubular secretion intracellular vesicle Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. plasma membrane region network-forming collagen trimer banded collagen fibril complex of collagen trimers collagen network basement membrane collagen trimer membrane protein complex plasma membrane protein complex regulation of renal system process actin-based cell projection supramolecular complex supramolecular polymer supramolecular fiber polymeric cytoskeletal fiber cytoplasmic region cell cortex region cellular anatomical entity https://github.com/geneontology/go-ontology/issues/13193 plasma membrane bounded cell projection https://github.com/geneontology/go-ontology/issues/14472 neuron projection cytoplasm export from cell organic cyclic compound metabolic process organic cyclic compound biosynthetic process organic substance catabolic process organic substance biosynthetic process organic hydroxy compound metabolic process organic hydroxy compound biosynthetic process response to oxygen-containing compound response to salt regulation of male mating behavior negative regulation of male mating behavior positive regulation of male mating behavior positive regulation of response to water deprivation regulation of blood circulation negative regulation of blood circulation positive regulation of blood circulation regulation of secretion by cell negative regulation of secretion by cell positive regulation of secretion by cell extracellular vesicle https://github.com/geneontology/go-ontology/issues/22021 negative regulation of protein localization https://github.com/geneontology/go-ontology/issues/22021 positive regulation of protein localization negative regulation of respiratory gaseous exchange positive regulation of respiratory gaseous exchange regulation of eating behavior negative regulation of eating behavior positive regulation of eating behavior 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). regulation of epithelial tube formation An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). negative regulation of epithelial tube formation An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). positive regulation of epithelial tube formation An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). regulation of morphogenesis of an epithelium An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). negative regulation of morphogenesis of an epithelium An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). 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 regulation of mechanosensory behavior negative regulation of mechanosensory behavior positive regulation of mechanosensory behavior regulation of mesoderm formation negative regulation of mesoderm formation positive regulation of mesoderm formation regulation of lipid localization negative regulation of lipid localization positive regulation of lipid localization regulation of multicellular organismal development regulation of response to water deprivation regulation of cell motility negative regulation of cell motility positive regulation of cell motility regulation of reproductive process negative regulation of reproductive process positive regulation of reproductive process negative regulation of feeding behavior positive regulation of feeding behavior regulation of defecation negative regulation of defecation positive regulation of defecation regulation of mesoderm development negative regulation of mesoderm development positive regulation of mesoderm development regulation of ectoderm development negative regulation of ectoderm development positive regulation of ectoderm development negative regulation of gastrulation positive regulation of gastrulation regulation of grooming behavior A change of place or position of part of an organism that does not involve the entire organism [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos stationary movement behavior_ontology body part movement 2011-04-14T01:03:39Z George Gkoutos behavior_ontology whole body movement Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences. 2011-04-14T01:03:39Z George Gkoutos affective behaviour mood behavior_ontology emotional behavior Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences. wikipedia:Emotions Observable characteristic of behaviour related to involuntary movement in response to a stimulus. 2011-04-14T11:57:02Z George Gkoutos pathological reflexive behaviour behavior_ontology reflexive behavior phenotype Observable characteristic of behaviour related to involuntary movement in response to a stimulus. NBO:GVG Behavior related to the acquisition and processing of information and/or the storage and retrieval of this information over time. 2011-04-14T01:03:39Z George Gkoutos learning and/or memory behaviour behavior_ontology GO:0007611 learning and/or memory behavior Behavior related to the acquisition and processing of information and/or the storage and retrieval of this information over time. GO:jic The act of moving any of the tissues and hard structures surrounding the mouth other than teeth, jaws or filter structures [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos mouth part movement other moved mouth parts behavior_ontology mouth movement 2011-04-14T01:03:39Z George Gkoutos behavior_ontology GO:0007622 rhythmic behavior Observable characteristic of behavior associated with the specific movement from place to place of an organism. 2011-04-14T12:58:40Z George Gkoutos pathological locomotory behaviour behavior_ontology locomotory behavior phenotype Observable characteristic of behavior associated with the specific movement from place to place of an organism. NBO:GVG Behavior directly related to the production of offspring [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos reproduction reproductive behaviour behavior_ontology GO:0019098 reproductive behavior "A behavior that occurs predominantly or only, in individuals that are part of a group." [Wikipedia:Social_behavior] 2011-04-14T01:03:39Z George Gkoutos social behaviour behavior_ontology GO:0035176 social behavior 2011-04-14T01:03:39Z George Gkoutos behavior_ontology HP:0001250 MP:0002064 seizures/epilepsy Movement from place to place of an organism." [GO:0007626] 2011-04-14T01:03:39Z George Gkoutos locomotion behavior_ontology GO:0007626 GO:0008344 locomotory behavior Behavior related to the interactions between organisms for the purpose of mating. 2011-04-14T01:03:39Z George Gkoutos mating behaviour behavior_ontology GO:0007617 mating behavior Behavior related to the interactions between organisms for the purpose of mating. NBO:GVG A behavioral interaction between organisms in which one organism has the intention of inflicting damage on another individual using physical or verbal means. 2011-04-14T01:03:39Z George Gkoutos aggression aggressive behaviour agonism behavior_ontology GO:0002118 aggressive behavior A behavioral interaction between organisms in which one organism has the intention of inflicting damage on another individual using physical or verbal means. wikipedia:Aggression "Behavior relate to the usually upward movement off the ground or other surface through sudden muscular effort in the legs." [GO:0007630] 2011-04-14T01:03:39Z George Gkoutos jump behavior_ontology GO:0007630 jumping behavior The act of seizing with teeth or jaws an object or organism so as to grip or break the surface covering [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos bite behavior_ontology biting Emotional behavior related to fear or anxiety. 2011-04-14T01:03:39Z George Gkoutos fear/anxiety related behaviour behavior_ontology fear/anxiety related behavior Emotional behavior related to fear or anxiety. NBO:GVG The act of stroking or touching with the tongue [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos lick behavior_ontology licking A change in place or position of the portion of the organism containing the brain, mouth and main sense organs [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos move head behavior_ontology head movement Behavior associated with any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience. 2011-04-14T01:03:39Z George Gkoutos learning behaviour behavior_ontology GO:0007612 learning behavior Behavior associated with any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience. wikipedia:Learning Movement of the head in the horizontal plane. 2011-04-14T01:03:39Z George Gkoutos shake head behavior_ontology head shaking Movement of the head in the horizontal plane. NBO:GVG Behavior related to the readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals. 2011-04-14T01:03:39Z George Gkoutos behavior_ontology GO:0030431 sleeping behavior Behavior related to the readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals. NBO:GVG An uncontrolled, paroxysmal neuronal discharge in any part of the brain; it may cause physical or mental symptoms and may be convulsive or nonconvulsive 2011-04-14T01:03:39Z George Gkoutos epileptic seizure unprovoked seizure behavior_ontology seizures An uncontrolled, paroxysmal neuronal discharge in any part of the brain; it may cause physical or mental symptoms and may be convulsive or nonconvulsive NBO:GVG The act of moving the head in a plane, circularly, pivoting at the neck [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos rotate head behavior_ontology head rotation 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] 2011-04-14T01:03:39Z George Gkoutos groom grooming behaviour behavior_ontology hygiene GO:0007625 grooming behavior Absence of voluntary movement. 2011-04-14T12:59:27Z George Gkoutos behavior_ontology akinesia Absence of voluntary movement. NBO:GVG Reduction of voluntary movement. 2011-04-14T01:03:39Z George Gkoutos hypokinesia behavior_ontology bradykinesia Reduction of voluntary movement. NBO:GVG A kinesthetic behavior which relatively increased. 2011-04-14T01:09:28Z George Gkoutos behavior_ontology HP:0000752 MP:0001399 hyperactivity A kinesthetic behavior which relatively increased. NBO:GVG A kinesthetic behavior which relatively decreased. 2011-04-14T01:09:41Z George Gkoutos behavior_ontology MP:0001402 hypoactivity A kinesthetic behavior which relatively decreased. NBO:GVG "Loss of power of voluntary movement in a muscle through injury or disease of its nerve supply." [JAX:<new dbxref>] 2011-04-14T01:18:37Z George Gkoutos behavior_ontology HP:0003470 MP:0000753 paralysis "Paralysis of the extensors of the wrist and fingers." [JAX:<new dbxref>] 2011-04-14T01:19:09Z George Gkoutos behavior_ontology MP:0005162 Carpoptosis is most often caused by a lesion of the radial nerve. carpoptosis Behaviour related to the activity which primary purpose is the sexual reproduction. 2011-04-14T01:03:39Z George Gkoutos behavior_ontology sexual actions sexual activity Behaviour related to the activity which primary purpose is the sexual reproduction. NBO:GVG 2011-04-14T01:03:39Z George Gkoutos behavior_ontology emission behavior 2011-04-14T01:03:39Z George Gkoutos produce sound behavior_ontology behavioral control of production of sound A behavior in which an organism produces sounds by a mechanism involving its respiratory system. 2011-04-14T01:03:39Z George Gkoutos vocalization behaviour vocalize behavior_ontology vocalization behavior A behavior in which an organism produces sounds by a mechanism involving its respiratory system. NBO:GVG 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. 2011-04-14T01:03:39Z George Gkoutos behavior_ontology GO:0007588 behavioral control of excretion 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. wikipedia:Excretion The behavioral control of defecation. [wikipedia:defecation] 2011-04-14T01:03:39Z George Gkoutos behavior_ontology behavioral control of defecation Excretion behaviour that controls liquid waste expulsion. 2011-04-14T01:03:39Z George Gkoutos micturition urinate behavior_ontology GO:0060073 behavioral control of urination Excretion behaviour that controls liquid waste expulsion. wikipedia:urination 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] 2011-04-14T01:03:39Z George Gkoutos secrete behavior_ontology behavioral control of external secretion The regulated release of the aqueous layer of the tear film from the lacrimal glands. 2011-04-14T01:03:39Z George Gkoutos tear release tear secretion behavior_ontology behavioral control of lacrimation The regulated release of the aqueous layer of the tear film from the lacrimal glands. wikipedia:lacrimation A behavior that occurs between two individuals, such as parent and child, and involves an emotional attachment that implies a special and focused relationship. 2011-04-14T01:03:39Z George Gkoutos forming of peer relationship behavior_ontology bonding behavior A behavior that occurs between two individuals, such as parent and child, and involves an emotional attachment that implies a special and focused relationship. PMID:29327315 Behavior associated with protection, or assisting growth and development of young. [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos behavior_ontology GO:0060746 parental behavior Behavior that serves to regulate the temperature around offspring.[NBO:AC] 2011-04-14T01:03:39Z George Gkoutos thermoregulation of offspring behavior_ontology brooding behavior Parental behavior that promotes the breaking of an offspring's dependence on parental resources. 2011-04-14T01:03:39Z George Gkoutos weaning behaviour behavior_ontology 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. weaning behavior Parental behavior that promotes the breaking of an offspring's dependence on parental resources. ISBN:0674205065 Behavior related the protection of offspring. 2011-04-14T01:03:39Z George Gkoutos protection of offspring behavior_ontology protection of offspring behavior Behavior related the protection of offspring. NBO:SD "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] 2011-04-14T01:03:39Z George Gkoutos NBO:0000625 social playing behaviour behavior_ontology social play Behavior related to the actions by which an organism modulates its internal body temperature. 2011-04-14T01:03:39Z George Gkoutos behavior_ontology thermoregulation behavior Behavior related to the actions by which an organism modulates its internal body temperature. NBO:GVG Behavior associated with two or more individuals' achieving or maintaining close and extensive bodily contact; to nestle closely with another [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos huddle behavior_ontology huddling behavior Exposure of body to sunlight, either by modification of body posture, by movement to specific areas or both [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos basking sunning sunning behavior behavior_ontology basking behavior Specific actions of a newborn or infant mammal that result in the derivation of nourishment from the breast. 2011-04-14T01:03:39Z George Gkoutos NBO:0000046 nursing behaviour suckling behaviour behavior_ontology GO:0001967 suckling behavior Specific actions of a newborn or infant mammal that result in the derivation of nourishment from the breast. GOC:dph The act of locomoting on limbs with body off the ground such that periodically none of the limbs are touching the ground [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos run behavior_ontology running behavior The act of locomoting on limbs with body off the ground such that at least one limb is always touching the ground [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos walking behavior_ontology GO:0007628 walking behavior The act of dragging claws or nails over a surface [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos scratch scratching behavior behavior_ontology scratching 2011-04-14T01:03:39Z George Gkoutos behavior_ontology nuzzling Male's insertion of sperm-transfer organ into the body of the female [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos copulate behavior_ontology copulation Loss of power of voluntary movement in muscles of the forelimb through injury or disease of it or its nerve supply. 2011-04-14T01:20:02Z George Gkoutos behavior_ontology MP:0000756 forelimb paralysis Loss of power of voluntary movement in muscles of the forelimb through injury or disease of it or its nerve supply. JAX: Behavior related to the washing or cleansing of the body in a fluid, usually water or an aqueous solution. 2011-04-14T01:20:02Z George Gkoutos bathe bathing behaviour behavior_ontology bathing behavior Behavior related to the washing or cleansing of the body in a fluid, usually water or an aqueous solution. wikipedia:Bathing A feeding behavior associated with the intake or the frequency of intake or preference or manner of intake of food. 2011-04-14T01:20:02Z George Gkoutos eating behaviour behavior_ontology GO:0042755 regulation of eating behavior A feeding behavior associated with the intake or the frequency of intake or preference or manner of intake of food. NBO:GVG A feeding behavior associated with the intake or the frequency of intake or preference or manner of intake of liquids. 2011-04-14T01:20:02Z George Gkoutos drinking behaviour behavior_ontology GO:0042756 regulation of drinking behavior A feeding behavior associated with the intake or the frequency of intake or preference or manner of intake of liquids. NBO:GVG Behavior related to a variety of aspects of the relationship between the mind and the world with which it interacts. 2011-04-14T01:20:02Z George Gkoutos behavior_ontology consciousness behavior Behavior related to a variety of aspects of the relationship between the mind and the world with which it interacts. wikipedia:Consciousness "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] 2011-04-14T01:20:02Z George Gkoutos behavior_ontology wakefulness Behavior related to reduced or absent consciousness, relatively suspended sensory activity, and inactivity of nearly all voluntary muscles. 2011-04-14T01:20:02Z George Gkoutos behavior_ontology asleep Behavior related to reduced or absent consciousness, relatively suspended sensory activity, and inactivity of nearly all voluntary muscles. wikipedia:Asleep Repetitive movement of a body part. 2011-04-14T01:20:02Z George Gkoutos behavior_ontology shaking Repetitive movement of a body part. NBO:GVG 2011-04-14T01:20:02Z George Gkoutos behavior_ontology swaying 2011-04-14T01:20:02Z George Gkoutos behavior_ontology tilting Behavior related to the movement facilitated by the generation of hole or tunnel dug into the ground. 2011-04-14T01:20:02Z George Gkoutos burrowing burrowing behaviour behavior_ontology fossorial locomotion behavior Behavior related to the movement facilitated by the generation of hole or tunnel dug into the ground. NBO:GVG The act of repeated grinding, tearing, and or crushing with teeth or jaws [NBO:SMAC] 2011-04-14T01:20:02Z George Gkoutos chew gnaw mastication behavior_ontology chewing 2011-04-14T01:20:02Z George Gkoutos behavior_ontology yawning 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] 2011-04-14T01:20:02Z George Gkoutos play behavior_ontology playing behavior Undirected behavior involving exercise and coordination, and often associated with repetition and 'practice' of adult behavior patterns in a non-functional context [NBO:AC] 2011-04-14T01:20:02Z George Gkoutos exercise motor development playing behaviour motor play behavior_ontology 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. locomotor play The behavioral interactions between organisms for the purpose of attracting sexual partners. 2011-04-14T01:20:02Z George Gkoutos courtship courtship behaviour behavior_ontology GO:0007619 courtship behavior The behavioral interactions between organisms for the purpose of attracting sexual partners. GOC:dph Behavior related to the specific actions or reactions of an organism following mating. 2011-04-14T01:20:02Z George Gkoutos NBO:0000325 post mating behaviour post-copulatory behavior post-mating behaviour behavior_ontology GO:0045297 post-mating behavior Behavior related to the specific actions or reactions of an organism following mating. GOC:bf The act of bringing an object or substance into the body by swallowing, surrounding or absorbing it [NBO:SMAC] 2011-04-14T01:20:02Z George Gkoutos feeding behaviour behavior_ontology GO:0007631 feeding behavior The act of moving the body core lower, closer to the ground [NOB:SMAC] 2011-04-14T01:20:02Z George Gkoutos sit down behavior_ontology sitting down The act of moving the body core higher, away from the ground [NBO:SMAC] 2011-04-14T01:20:02Z George Gkoutos stand up behavior_ontology standing up 2011-04-14T01:20:02Z George Gkoutos writhe behavior_ontology writhing Behavior related to any biological process in an organism that recurs with a regularity of approximately 24 hours. 2011-04-14T01:20:02Z George Gkoutos behavior_ontology GO:0048512 circadian behavior Behavior related to any biological process in an organism that recurs with a regularity of approximately 24 hours. NBO:GVG Emotional behavior related to a state of low mood and aversion to activity. 2011-04-14T01:20:02Z George Gkoutos depression related behaviour behavior_ontology depression behavior Emotional behavior related to a state of low mood and aversion to activity. wikipedia:Depression Behavior related to the exploration/investigation of a novel object, situation or environment. 2011-04-14T01:20:02Z George Gkoutos behavior_ontology novelty response behavior Behavior related to the exploration/investigation of a novel object, situation or environment. NBO:GVG Behavior related to defence against predation or predators. 2011-04-14T01:20:02Z George Gkoutos antipredator behavior behavior_ontology antipredation behavior Behavior related to defence against predation or predators. NBO:GVG Behavior related to the preparation of the body to \"fight\" or \"flee\" from perceived attack, harm or threat. 2011-04-14T01:20:02Z George Gkoutos fight-or-flight response fight-or-flight-or-freeze response behavior_ontology acute stress response Behavior related to the preparation of the body to \"fight\" or \"flee\" from perceived attack, harm or threat. NBO:GVG A physical aggression behavior involving attack on prey by a predator. 2011-04-14T01:20:02Z George Gkoutos predatory aggression predatory aggressive behaviour behavior_ontology GO:0002120 predator behavior A physical aggression behavior involving attack on prey by a predator. NBO:GVG Behavior directed at a predator that signifies hostility and predicts an increased probability of attack [NBO:SMAC] 2011-04-14T01:20:02Z George Gkoutos threaten predator behavior_ontology threatening predator behavior 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. 2011-03-31T10:00:42Z George Gkoutos fear-related behaviour behavior_ontology fear-related behavior 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. NBO:GVG An emotional behavior related to a feeling of uneasiness or nervousness triggered by an identifiable triggering stimulus. 2011-03-31T10:01:25Z George Gkoutos anxiety-related behaviour behavior_ontology anxiety-related behavior An emotional behavior related to a feeling of uneasiness or nervousness triggered by an identifiable triggering stimulus. NBO:GVG An emotional behavior related to a feeling of uneasiness or nervousness in respect to an object. 2011-03-31T10:16:48Z George Gkoutos behavior_ontology fear behavior towards objects An emotional behavior related to a feeling of uneasiness or nervousness in respect to an object. NBO:GVG An emotional behavior related to a feeling of uneasiness or nervousness in respect to a particular situation or environment. 2011-03-31T10:18:11Z George Gkoutos behavior_ontology fear behavior towards situation/environment An emotional behavior related to a feeling of uneasiness or nervousness in respect to a particular situation or environment. NBO:GVG An emotional behavior related to a feeling of uneasiness or nervousness in respect to a living thing. 2011-03-31T10:18:25Z George Gkoutos behavior_ontology fear behavior towards living things An emotional behavior related to a feeling of uneasiness or nervousness in respect to a living thing. NBO:GVG A phobia characterised by fear of open spaces. 2011-03-31T10:18:39Z George Gkoutos behavior_ontology HP:0000756 agoraphobia behavior A phobia characterised by fear of open spaces. NBO:GVG Behavior related to the exploration/investigation of a novel environment. 2011-03-31T10:22:03Z George Gkoutos behavior_ontology response to novel environment Behavior related to the exploration/investigation of a novel environment. NBO:GVG Behavior related to the exploration/investigation of a novel obhject. 2011-03-31T10:23:07Z George Gkoutos behavior_ontology response to novel object Behavior related to the exploration/investigation of a novel obhject. NBO:GVG Behavior related to the exploration/investigation of a novel odor. 2011-03-31T10:24:44Z George Gkoutos behavior_ontology response to novel odor Behavior related to the exploration/investigation of a novel odor. NBO:GVG 2011-03-31T10:28:39Z George Gkoutos behavior_ontology GO:0035640 exploration behavior Moving backwards. 2011-03-31T10:32:40Z George Gkoutos behavior_ontology retropulsion Moving backwards. NBO:GVG Moving backwards in response to a fear stimulus. 2011-03-31T10:36:56Z George Gkoutos behavior_ontology fear-related retropulsion Moving backwards in response to a fear stimulus. NBO:GVG Behavioral response to the presidency of the stressor where it becomes necessary to attempt some means of coping with the stress. 2011-03-31T10:49:00Z George Gkoutos behavior_ontology coping behavior Behavioral response to the presidency of the stressor where it becomes necessary to attempt some means of coping with the stress. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards humans. 2011-03-31T10:50:52Z George Gkoutos aggressive behavior towards humans behavior_ontology aggressive behavior towards humans Exhibiting a domineering, assault posture and/or hostile physical action towards humans. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards animals. 2011-03-31T10:51:12Z George Gkoutos aggressive behavior towards animals behavior_ontology aggressive behavior towards animals Exhibiting a domineering, assault posture and/or hostile physical action towards animals. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action toward any type of object. 2011-03-31T10:51:33Z George Gkoutos aggressive behavior towards objects behavior_ontology aggressive behavior towards objects Exhibiting a domineering, assault posture and/or hostile physical action toward any type of object. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards mice. 2011-03-31T10:51:50Z George Gkoutos aggressive behavior towards mice behavior_ontology aggressive behavior towards mice Exhibiting a domineering, assault posture and/or hostile physical action towards mice. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards women. 2011-03-31T10:52:04Z George Gkoutos aggressive behavior towards women behavior_ontology aggressive behavior towards women Exhibiting a domineering, assault posture and/or hostile physical action towards women. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards men. 2011-03-31T10:52:26Z George Gkoutos aggressive behavior towards men behavior_ontology aggressive behavior towards men Exhibiting a domineering, assault posture and/or hostile physical action towards men. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards male mice. 2011-03-31T10:52:56Z George Gkoutos aggressive behavior towards male mice behavior_ontology aggressive behavior towards male mice Exhibiting a domineering, assault posture and/or hostile physical action towards male mice. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards female mice. 2011-03-31T10:53:07Z George Gkoutos aggressive behavior towards female mice behavior_ontology aggressive behavior towards female mice Exhibiting a domineering, assault posture and/or hostile physical action towards female mice. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action toward inanimate objects. 2011-03-31T10:53:44Z George Gkoutos aggressive behavior towards inanimate objects behavior_ontology aggressive behavior towards inanimate objects Exhibiting a domineering, assault posture and/or hostile physical action toward inanimate objects. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action toward animate objects. 2011-03-31T10:53:59Z George Gkoutos aggressive behavior towards animate objects behavior_ontology aggressive behavior towards animate objects Exhibiting a domineering, assault posture and/or hostile physical action toward animate objects. https://orcid.org/0000-0002-4277-2151 Exhibiting a domineering, assault posture and/or hostile physical action towards children. 2011-03-31T10:57:11Z George Gkoutos aggressive behavior towards children behavior_ontology aggressive behavior towards children Exhibiting a domineering, assault posture and/or hostile physical action towards children. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards pups. 2011-03-31T10:58:09Z George Gkoutos aggressive behavior towards pups behavior_ontology aggressive behavior towards pups Exhibiting a domineering, assault posture and/or hostile physical action towards pups. NBO:GVG Gender related exhibition of a domineering, assault posture and/or hostile physical action. 2011-03-31T11:02:17Z George Gkoutos gender-related aggressive behaviour behavior_ontology gender-related aggressive behavior Gender related exhibition of a domineering, assault posture and/or hostile physical action. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards female animals. 2011-03-31T11:03:36Z George Gkoutos behavior_ontology aggressive behavior towards females Exhibiting a domineering, assault posture and/or hostile physical action towards female animals. NBO:GVG Exhibiting a domineering, assault posture and/or hostile physical action towards male animals. 2011-03-31T11:04:03Z George Gkoutos aggressive behavior towards males behavior_ontology aggressive behavior towards males Exhibiting a domineering, assault posture and/or hostile physical action towards male animals. NBO:GVG A behavior that occur quickly without control, planning, or consideration of the consequences of that behavior. 2011-03-31T11:08:55Z George Gkoutos behavior_ontology impulsive behavior A behavior that occur quickly without control, planning, or consideration of the consequences of that behavior. NBO:GVG An aggressive behavior that aims to inflicting damage on another entity using physical means. 2011-03-31T11:14:04Z George Gkoutos physical aggression behaviour violent behaviour behavior_ontology physical aggression behavior An aggressive behavior that aims to inflicting damage on another entity using physical means. NBO:GVG 2011-03-31T11:42:15Z George Gkoutos agonism behavior_ontology agonistic behavior Any behavior that tends to prevent further or future attack, often by signalling a willingness to yield or surrender [NBO:AC] 2011-03-31T11:43:11Z George Gkoutos submissive behaviour behavior_ontology submissive behavior A behavior associated with the tendency of an organism towards being passive and willing to yield to male animals. 2011-03-31T11:43:37Z George Gkoutos submissive behavior towards males behavior_ontology submissive behavior towards males A behavior associated with the tendency of an organism towards being passive and willing to yield to male animals. NBO:GVG A behavior associated with the tendency of an organism towards being passive and willing to yield to female animals. 2011-03-31T11:44:14Z George Gkoutos submissive behavior towards females behavior_ontology submissive behavior towards females A behavior associated with the tendency of an organism towards being passive and willing to yield to female animals. NBO:GVG A behavior associated with the tendency of an organism towards being passive and willing to yield towards male mice. 2011-03-31T11:44:25Z George Gkoutos submissive behavior towards male mice behavior_ontology submissive behavior towards male mice A behavior associated with the tendency of an organism towards being passive and willing to yield towards male mice. NBO:GVG 2011-03-31T11:47:31Z George Gkoutos behavior_ontology subordination behavior Behavior by which an animal removes itself spatially from an agonistic encounter in which it is not the winner [NBO:AC] 2011-03-31T11:49:03Z George Gkoutos retreat retreat behaviour behavior_ontology retreat behavior Behavior characterized by a quick excitability to annoyance, impatience, or anger. 2011-03-31T12:16:00Z George Gkoutos behavior_ontology irritability behavior Behavior characterized by a quick excitability to annoyance, impatience, or anger. NBO:GVG Emotional behavior related to excitement or restlessness. 2011-03-31T12:22:11Z George Gkoutos behavior_ontology agitation behavior Emotional behavior related to excitement or restlessness. NBO:GVG A behavior associated with the intake of liquid. 2011-03-31T12:40:37Z George Gkoutos behavior_ontology liquid consumption A behavior associated with the intake of liquid. NBO:GVG A drinking behavior associated with the intake of alcohol. 2011-03-31T12:40:53Z George Gkoutos behavior_ontology alcohol consumption A drinking behavior associated with the intake of alcohol. NBO:GVG A drinking behavior associated with the intake of water. 2011-03-31T12:41:14Z George Gkoutos behavior_ontology GO:0045187 water consumption A drinking behavior associated with the intake of water. NBO:GVG 2011-03-31T12:41:50Z George Gkoutos behavior_ontology liquid preference/aversion A feeding behavior associated with the intake of food. 2011-03-31T12:42:46Z George Gkoutos behavior_ontology food consumption A feeding behavior associated with the intake of food. NBO:GVG 2011-03-31T12:43:07Z George Gkoutos behavior_ontology food preference/aversion A feeding behavior associated with the intake of saccharin. 2011-03-31T12:50:41Z George Gkoutos behavior_ontology saccharin consumption A feeding behavior associated with the intake of saccharin. NBO:GVG Predilection to ingest a liquid over other substances. 2011-03-31T12:55:09Z George Gkoutos behavior_ontology liquid preference Predilection to ingest a liquid over other substances. NBOC:GVG Purposeful avoidance of a liquid due to dislike. 2011-03-31T12:55:32Z George Gkoutos behavior_ontology liquid aversion Purposeful avoidance of a liquid due to dislike. NBO:GVG Purposeful avoidance of liquid alcohol due to dislike. [NBO:LKSR] 2011-03-31T12:55:46Z George Gkoutos behavior_ontology alcohol aversion Purposeful avoidance of liquid alcohol due to dislike. [NBO:LKSR] NBO:GVG Predilection to ingest alcohol over other substances. 2011-03-31T12:56:38Z George Gkoutos behavior_ontology alcohol preference Predilection to ingest alcohol over other substances. NBOC:GVG 2011-03-31T12:58:43Z George Gkoutos behavior_ontology food preference 2011-03-31T12:59:08Z George Gkoutos behavior_ontology food aversion 2011-03-31T12:59:56Z George Gkoutos behavior_ontology saccharin preference 2011-03-31T02:16:59Z George Gkoutos behavior_ontology mating frequency 2011-03-31T02:17:22Z George Gkoutos mate choice behavior_ontology mating preference 2011-03-31T02:17:36Z George Gkoutos behavior_ontology mating receptivity 2011-03-31T02:21:53Z George Gkoutos mate attraction behavior behavior_ontology sexual display behavior 2011-03-31T02:24:12Z George Gkoutos behavior_ontology social investigation 2011-03-31T02:25:12Z George Gkoutos behavior_ontology reclusive behavior Behavior of a mother towards her offspring. 2011-03-31T02:32:21Z George Gkoutos behavior_ontology GO:0042711 maternal behavior Behavior of a mother towards her offspring. NBO:GVG Behavior of a father towards his offspring. 2011-03-31T02:32:53Z George Gkoutos behavior_ontology GO:0042712 paternal behavior Behavior of a father towards his offspring. NBO:GVG Maternal behavior related to the brining up her offspring. 2011-03-31T02:33:34Z George Gkoutos behavior_ontology maternal nurturing behavior Maternal behavior related to the brining up her offspring. NBO:GVG Paternal behavior related to the brining up his offspring. 2011-03-31T02:33:49Z George Gkoutos behavior_ontology paternal nurturing behavior Paternal behavior related to the brining up his offspring. NBO:GVG 2011-03-31T02:35:33Z George Gkoutos behavior_ontology maternal crouching Behavior related to the parent's tendency to collect stray offspring and return them to a defined location. 2011-03-31T02:42:29Z George Gkoutos retrieval behavior_ontology offspring retrieval Behavior related to the parent's tendency to collect stray offspring and return them to a defined location. NBO:GVG 2011-03-31T02:53:42Z George Gkoutos behavior_ontology nesting behavior 2011-03-31T02:54:15Z George Gkoutos behavior_ontology nest building behavior 2011-03-31T02:59:33Z George Gkoutos behavior_ontology sleep pattern 2011-03-31T03:00:57Z George Gkoutos REM sleep paradoxical sleep behavior_ontology rapid eye movement sleep 2011-03-31T03:09:27Z George Gkoutos behavior_ontology sleep duration Behavior related to all sleep stages in the circadian sleep/wake cycle other than REM sleep. 2011-03-31T03:12:44Z George Gkoutos NREM sleep behavior behavior_ontology These stages are characterized by a slowing of brain waves and other physiological functions. non-rapid eye movement sleep behavior Behavior related to all sleep stages in the circadian sleep/wake cycle other than REM sleep. NBO:GVG Duration of REM sleep. 2011-03-31T03:15:38Z George Gkoutos behavior_ontology REM duration Duration of REM sleep. NBO:GVG 2011-03-31T03:15:49Z George Gkoutos behavior_ontology REM frequency Duration of NREM sleep. 2011-03-31T03:16:07Z George Gkoutos behavior_ontology NREM duration Duration of NREM sleep. https://orcid.org/0000-0002-4277-2151 2011-03-31T03:16:10Z George Gkoutos behavior_ontology NREM frequency Endogenously driven roughly 24-hour cycle in biochemical, physiological, or behavioral processes. 2011-03-31T03:22:26Z George Gkoutos behavior_ontology GO:0007623 circadian rhythm Endogenously driven roughly 24-hour cycle in biochemical, physiological, or behavioral processes. GOC:bf 2011-03-31T03:23:15Z George Gkoutos behavior_ontology circadian period 2011-03-31T03:23:58Z George Gkoutos behavior_ontology circadian persistence 2011-03-31T03:24:52Z George Gkoutos behavior_ontology circadian phase Behavior related with the ability of an organism's ability to store, retain, and recall information and experiences. 2011-04-01T01:49:03Z George Gkoutos memory behaviour behavior_ontology GO:0007613 memory behavior Behavior related with the ability of an organism's ability to store, retain, and recall information and experiences. NBO:GVG "Learning by associating a stimulus (the cause) with a particular outcome (the effect)." [Wikipedia:Learning#Associative_learning] 2011-04-01T01:49:32Z George Gkoutos conditional learning behavior_ontology GO:0008306 The formation of associations among stimuli and responses. associative learning behavior 2011-04-01T01:54:09Z George Gkoutos behavior_ontology GO:0008355 olfactory learning behavior 2011-04-01T01:54:15Z George Gkoutos behavior_ontology GO:0008542 visual learning behavior 2011-04-01T01:56:08Z George Gkoutos behavior_ontology motor learning 2011-04-01T01:57:20Z George Gkoutos behavior_ontology spatial learning "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] 2011-04-01T01:58:41Z George Gkoutos behavior_ontology GO:0042297 vocal learning A decrease in a behavioral response to a repeated stimulus. 2011-04-01T03:18:40Z George Gkoutos nonassociative learning unconditional response behavior_ontology GO:0046958 non-associative learning A decrease in a behavioral response to a repeated stimulus. NBO:GVG Gradual decrease in behavioral responses with repeated encounters of a particular stimulus, which proves of no consequence. 2011-04-01T03:19:06Z George Gkoutos behavior_ontology GO:0046959 habituation Gradual decrease in behavioral responses with repeated encounters of a particular stimulus, which proves of no consequence. wikipedia:Habituation An increase in behavioral responses following repeated applications of a particular stimulus. 2011-04-01T03:54:55Z George Gkoutos behavior_ontology sensitization An increase in behavioral responses following repeated applications of a particular stimulus. wikipedia:Sensitization A type of memory that allows the recall of something from several seconds to as long as a minute. 2011-04-01T03:59:07Z George Gkoutos behavior_ontology GO:0007614 short-term memory A type of memory that allows the recall of something from several seconds to as long as a minute. NBO:GVG This type of memory, lasting hours to months, critically depends on a transfer of the information from short term memory using repeated rehearsal. 2011-04-01T03:59:10Z George Gkoutos behavior_ontology GO:0007616 long-term memory This type of memory, lasting hours to months, critically depends on a transfer of the information from short term memory using repeated rehearsal. NBO:GVG 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. 2011-04-01T03:59:19Z George Gkoutos behavior_ontology sensory memory 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. NBO:GVG A memory that last for months to lifetime. 2011-04-01T04:00:48Z George Gkoutos behavior_ontology long-lasting memory A memory that last for months to lifetime. NBO:GVG A type of memory that allows the recall of something from minutes to several hours. 2011-04-01T04:01:02Z George Gkoutos behavior_ontology GO:0072375 medium term memory A type of memory that allows the recall of something from minutes to several hours. NBO:GVG Ability to become conscious of, or declare, facts and experiences. 2011-04-02T07:38:45Z George Gkoutos explicit memory behavior_ontology Encoded by the hippocampus, entorhinal cortex, and perirhinal cortex but store possibly in the medial temporal lobe. declarative memory Ability to become conscious of, or declare, facts and experiences. NBO:GVG Ability to consciously recall knowledge of facts that are independent of a specific time and place. 2011-04-02T07:40:26Z George Gkoutos behavior_ontology Medial temporal lobe, diencephalon. semantic memory Ability to consciously recall knowledge of facts that are independent of a specific time and place. NBO:GVG Ability to explicitly recall information about a specific event that has occurred at a specific time and place. 2011-04-02T07:41:30Z George Gkoutos behavior_ontology Medial temporal lobe, diencephalon. episodic memory Ability to explicitly recall information about a specific event that has occurred at a specific time and place. NBO:GVG Non-declarative memory type of memory, which does not need to involve conscious awareness in the act of recollection. 2011-04-02T07:42:37Z George Gkoutos NBO:0000189 implicit memory procedural memory behavior_ontology Encoded and probably stored by the cerebellum and the striatum but store in the amygdala. non-declarative memory Non-declarative memory type of memory, which does not need to involve conscious awareness in the act of recollection. NBO:GVG Consolidating a specific motor task into memory through repetition. 2011-04-02T07:54:40Z George Gkoutos muscle memory behavior_ontology Depends on the cerebellum and basal ganglia. motor memory Consolidating a specific motor task into memory through repetition. NBO:GVG "A type of memory associated with emotional experiences." [wikipedia:http\://www.scholarpedia.org/article/Emotional_memory] 2011-04-02T07:59:16Z George Gkoutos behavior_ontology emotional memory Remembering to perform an intended action. 2011-04-02T08:16:36Z George Gkoutos behavior_ontology prospective memory Remembering to perform an intended action. NBO:GVG Remembering to perform an intended action in respect to a particular event. 2011-04-02T08:19:20Z George Gkoutos behavior_ontology event-based prospective memory Remembering to perform an intended action in respect to a particular event. NBO:GVG Remembering to perform an intended action in respect to a particular time reference. 2011-04-02T08:19:37Z George Gkoutos behavior_ontology time-based prospective memory Remembering to perform an intended action in respect to a particular time reference. NBO:GVG A type of memory for particular events within one's own life. 2011-04-02T08:27:14Z George Gkoutos behavior_ontology autobiographical memory A type of memory for particular events within one's own life. NBO:GVG "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] 2011-04-02T08:33:27Z George Gkoutos behavior_ontology visual memory 2011-04-02T08:37:43Z George Gkoutos behavior_ontology iconic memory "The ability to recall images, sounds, or objects in memory with extreme precision and in abundant volume." [wikipedia:Eidetic_memory] 2011-04-02T08:39:24Z George Gkoutos photographic memory behavior_ontology eidetic memory Ability to orient oneself in space, to recognize and follow an itinerary, or to recognize familiar places. 2011-04-02T08:42:17Z George Gkoutos behavior_ontology topographic memory Ability to orient oneself in space, to recognize and follow an itinerary, or to recognize familiar places. NBO:GVG An implicit memory effect in which exposure to a stimulus influences response to a later stimulus. 2011-04-02T08:50:59Z George Gkoutos behavior_ontology priming An implicit memory effect in which exposure to a stimulus influences response to a later stimulus. NBO:GVG 2011-04-02T08:55:04Z George Gkoutos repetition behavior_ontology direct priming A type of priming where the prime and the target are from the same semantic category and share features. 2011-04-02T08:56:35Z George Gkoutos behavior_ontology semantic priming A type of priming where the prime and the target are from the same semantic category and share features. NBO:GVG 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. 2011-04-02T08:57:44Z George Gkoutos behavior_ontology associative priming 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. NBO:GVG 2011-04-02T08:58:44Z George Gkoutos behavior_ontology response priming A type of priming based on the meaning of a stimulus and is enhanced by semantic task. 2011-04-02T08:59:42Z George Gkoutos behavior_ontology conceptual priming A type of priming based on the meaning of a stimulus and is enhanced by semantic task. NBO:GVG A type priming based on the form of the stimulus and is enhanced by the match between the early and later stimuli. 2011-04-02T09:00:27Z George Gkoutos behavior_ontology perceptual priming A type priming based on the form of the stimulus and is enhanced by the match between the early and later stimuli. NBO:GVG Change in the responsiveness of a sensory system when confronted with a constant stimulus. 2011-04-02T09:07:54Z George Gkoutos behavior_ontology sensory adaptation Change in the responsiveness of a sensory system when confronted with a constant stimulus. NBO:GVG 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. 2011-04-03T08:57:28Z George Gkoutos Pavlovian conditioning respondent conditioning behavior_ontology classical conditioning 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. NBO:GVG 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. 2011-04-03T08:58:27Z George Gkoutos behavior_ontology fear conditioning 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. NBO:GVG 2011-04-03T09:01:08Z George Gkoutos behavior_ontology avoidance learning behavior 2011-04-03T09:04:57Z George Gkoutos Garcia conditioning behavior_ontology GO:0001661 conditioned taste aversion "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] 2011-04-03T09:05:54Z George Gkoutos instrumental conditioning instrumental learning behavior_ontology GO:0035106 Operant conditioning is distinguished from classical conditioning in that operant conditioning deals with the modification of "voluntary behavior" or operant behavior. operant conditioning behavior 2011-04-03T09:08:06Z George Gkoutos behavior_ontology imprinting behavior 2011-04-03T09:11:00Z George Gkoutos behavior_ontology latent learning behavior 2011-04-03T09:11:31Z George Gkoutos modeling vicarious learning behavior_ontology observational learning 2011-04-03T09:11:44Z George Gkoutos behavior_ontology language learning behavior Avoidance learning when the action occurs. 2011-04-04T03:22:16Z George Gkoutos behavior_ontology active avoidance learning behavior Avoidance learning when the action occurs. NBO:GVG Avoidance learning when no action occurs. 2011-04-04T03:22:53Z George Gkoutos behavior_ontology passive avoidance learning behavior Avoidance learning when no action occurs. NBO:GVG Avoid a situation completely. 2011-04-04T03:25:10Z George Gkoutos behavior_ontology escape learning behavior Avoid a situation completely. NBO:GVG Associative learning behavior that arises from observing or interacting with another individual. 2011-04-04T03:34:46Z George Gkoutos behavior_ontology 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] social learning 2011-04-04T03:36:48Z George Gkoutos behavior_ontology conditioned emotional response 2011-04-04T03:40:11Z George Gkoutos behavior_ontology conditioned place preference behavior 2011-04-04T03:42:37Z George Gkoutos behavior_ontology contextual conditioning behavior 2011-04-04T03:43:11Z George Gkoutos behavior_ontology cued conditioning behavior "Perception of objects remains the same despite changes in their image on the retina." [:http\://science.jrank.org/pages/5094/Perception.html] 2011-04-04T03:47:32Z George Gkoutos behavior_ontology perceptual constancy behavior 2011-04-04T03:48:50Z George Gkoutos behavior_ontology spinal conditioning 2011-04-04T03:55:46Z George Gkoutos behavior_ontology eye blink conditioning behavior 2011-04-04T03:57:01Z George Gkoutos behavior_ontology jaw movement conditioning behavior Observable characteristic of behavior related to the awareness of body balance and movement. 2011-04-04T06:34:21Z George Gkoutos pathological vestibular behaviour behavior_ontology vestibular behavior phenotype Observable characteristic of behavior related to the awareness of body balance and movement. NBO:GVG 2011-04-04T07:49:51Z George Gkoutos behavior_ontology pleasure behavior 2011-04-04T07:50:00Z George Gkoutos behavior_ontology excitement behavior 2011-04-04T07:50:20Z George Gkoutos behavior_ontology distress behavior Behavior related to the tendency of an organism to maintain internal equilibrium. 2011-04-04T08:29:40Z George Gkoutos NBO:0000050 behavioral homeostasis maintenance behaviour perception of need behavior_ontology motivation behavior Behavior related to the tendency of an organism to maintain internal equilibrium. NBO:GVG Behavior related to the deprivation of water. 2011-04-04T08:29:55Z George Gkoutos behavior_ontology thirst motivation behavior Behavior related to the deprivation of water. NBO:GVG Behavior related to the deprivation of food. 2011-04-04T08:30:11Z George Gkoutos appetite related behaviour behavior_ontology hunger motivation behavior Behavior related to the deprivation of food. NBO:GVG Behavior related to the drive of an organism to engage in sexual activity. 2011-04-04T08:30:39Z George Gkoutos behavior_ontology sexual motivation behavior Behavior related to the drive of an organism to engage in sexual activity. NBO:GVG Any process which modulates the physical craving for food. 2011-04-04T08:33:16Z George Gkoutos behavior_ontology GO:0032098 hunger regulation Any process which modulates the physical craving for food. NBO:GVG Any process which modulates the physical craving for food over short term food deprivation. 2011-04-04T08:33:34Z George Gkoutos behavior_ontology short term hunger regulation Any process which modulates the physical craving for food over short term food deprivation. NBO:GVG Any process which modulates the physical craving for food over long term food deprivation. 2011-04-04T08:33:49Z George Gkoutos behavior_ontology long term hunger regulation Any process which modulates the physical craving for food over long term food deprivation. NBO:GVG 2011-04-04T08:35:53Z George Gkoutos behavior_ontology anorexia nervosa 2011-04-04T08:36:00Z George Gkoutos behavior_ontology bulimia nervosa 2011-04-04T08:36:17Z George Gkoutos behavior_ontology obesity An observable characteristic of the behavior of an organism. 2011-04-04T08:51:24Z George Gkoutos behavior_ontology HP:0000708 behavioral phenotype An observable characteristic of the behavior of an organism. NBO:RH 2011-04-04T08:51:52Z George Gkoutos hysteria pathological anxiety disorder behavior_ontology pathological anxiety "A pathological anxiety characterized by long-lasting anxiety that is not focused on any one object or situation." [wikipedia:Generalized_anxiety_disorder] 2011-04-04T08:52:08Z George Gkoutos GAD behavior_ontology generalized anxiety A pathological anxiety characterized by fear or anxiety triggered by a specific stimulus or situation. 2011-04-04T08:52:18Z George Gkoutos phobic disorder behavior_ontology phobia A pathological anxiety characterized by fear or anxiety triggered by a specific stimulus or situation. NBO:GVG "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] 2011-04-04T08:52:30Z George Gkoutos behavior_ontology panic "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] 2011-04-04T08:52:42Z George Gkoutos OCD behavior_ontology HP:0000722 obsessive-compulsive 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] 2011-04-04T08:53:04Z George Gkoutos pathological somatoform behaviour behavior_ontology somatoform behavior phenotype "A somatoform disorder characterised by a physical dysfunction (blindness, deafness, paralysis, numbness, etc. ) that has no underlying organic basis." [wikipedia:Conversion_disorder] 2011-04-04T08:53:18Z George Gkoutos hysteria behavior_ontology 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. 2011-04-04T08:53:49Z George Gkoutos health anxiety health phobia hypochondria behavior_ontology hypochondriasis A somatoform disorder characterised by a continuing belief that one has one or more serious illnesses although no medical evidence supports the belief. wikipedia:Hypochondriasis 2011-04-04T08:54:15Z George Gkoutos behavior_ontology dissociative disorders 2011-04-04T08:54:26Z George Gkoutos behavior_ontology dissociative amnesia 2011-04-04T08:54:36Z George Gkoutos behavior_ontology dissociative fugue 2011-04-04T08:54:45Z George Gkoutos behavior_ontology dissociative identity disorder 2011-04-04T08:55:19Z George Gkoutos behavior_ontology mood disorder 2011-04-04T08:55:36Z George Gkoutos MDD clinical depression major depression unipolar depression behavior_ontology major depressive disorder "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] 2011-04-04T08:55:45Z George Gkoutos BD bipolar affective disorder manic depression behavior_ontology NBO:0000258 bipolar disorder 2011-04-04T08:56:39Z George Gkoutos behavior_ontology HP:0000709 psychotic disorder 2011-04-04T08:56:56Z George Gkoutos behavior_ontology paranoid schizophrenia 2011-04-04T08:57:08Z George Gkoutos behavior_ontology catatonic schizophrenia 2011-04-04T08:57:19Z George Gkoutos behavior_ontology disorganized (hebephrenic) schizophrenia 2011-04-04T08:57:32Z George Gkoutos behavior_ontology undifferentiated schizophrenia 2011-04-04T08:57:44Z George Gkoutos behavior_ontology residual schizophrenia 2011-04-04T08:59:01Z George Gkoutos behavior_ontology HP:0000751 (http://www.cliffsnotes.com/study_guide/Classifying-Psychological-Disorders.topicArticleId-25438,articleId-25396.html). personality disorder Observable characteristic of behaviour related to cognitive processes. 2011-04-04T09:01:18Z George Gkoutos behavior_ontology cognitive behavior phenotype Observable characteristic of behaviour related to cognitive processes. NBO:RH 2011-04-04T09:01:41Z George Gkoutos behavior_ontology delirium 2011-04-04T09:01:50Z George Gkoutos behavior_ontology HP:0000726 dementia 2011-04-04T09:02:00Z George Gkoutos behavior_ontology amnestic disorder Observable characteristic of behavior associated with the intake of food or liquids. 2011-04-04T09:02:16Z George Gkoutos behavior_ontology feeding behavior phenotype Observable characteristic of behavior associated with the intake of food or liquids. NBO:GVG Behaviors that are described for or done by groups of animals, not individual animals [NBO:SMAC] 2011-04-04T09:05:23Z George Gkoutos group actions behavior_ontology group behavior 2011-04-04T09:05:38Z George Gkoutos behavior_ontology social facilitation 2011-04-04T09:05:52Z George Gkoutos social loafing behavior_ontology social interference 2011-04-04T09:06:11Z George Gkoutos behavior_ontology group polarization 2011-04-04T09:06:30Z George Gkoutos behavior_ontology groupthink A behavioral interaction between organisms in which one organism exhibits aggression using vocal or verbal means. 2011-04-04T09:07:58Z George Gkoutos verbal aggression behaviour behavior_ontology vocal aggression behavior A behavioral interaction between organisms in which one organism exhibits aggression using vocal or verbal means. NBO:GVG 2011-04-04T09:11:04Z George Gkoutos <new synonym> discrimination prejudice behavior_ontology discriminatory behavior 2011-04-04T09:12:21Z George Gkoutos sexism behavior_ontology gender specific discriminatory behavior A discriminatory behavior that is related to age. 2011-04-04T09:12:49Z George Gkoutos ageism behavior_ontology age specific discriminatory behavior A discriminatory behavior that is related to age. NBO:GVG 2011-04-04T09:16:35Z George Gkoutos behavior_ontology attraction-related behavior Behavior related to having a generally positive attitude toward another person. 2011-04-04T09:16:54Z George Gkoutos behavior_ontology affiliation Behavior related to having a generally positive attitude toward another person. MBP:GVG Wanting to be with another person. 2011-04-04T09:17:02Z George Gkoutos behavior_ontology liking Wanting to be with another person. NBO:GVG 2011-04-04T09:17:59Z George Gkoutos behavior_ontology friendship 2011-04-04T09:18:24Z George Gkoutos behavior_ontology love A helping behavior (without expectation of extrinsic rewards and sometimes involving personal risk or sacrifice) that benefits individuals or society. 2011-04-04T09:19:33Z George Gkoutos behavior_ontology altruism behavior A helping behavior (without expectation of extrinsic rewards and sometimes involving personal risk or sacrifice) that benefits individuals or society. NBO:GVG "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] 2011-04-04T09:22:04Z George Gkoutos behavior_ontology prosocial behavior "Helping behavior refers to voluntary actions intended to help the others, with reward regarded or disregarded." [wikipedia:Helping_behavior] 2011-04-04T09:23:26Z George Gkoutos behavior_ontology 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] 2011-04-04T09:25:04Z George Gkoutos behavior_ontology reciprocal altruism 2011-04-04T09:26:44Z George Gkoutos behavior_ontology social influence related behavior 2011-04-04T09:27:04Z George Gkoutos behavior_ontology conformity 2011-04-04T09:27:43Z George Gkoutos behavior_ontology obedience to authority 2011-04-04T09:27:57Z George Gkoutos behavior_ontology bystander intervention Behavior related to one or more capacities of the mind. 2011-04-04T09:30:27Z George Gkoutos behavior_ontology behavior stemming from intelligence Behavior related to one or more capacities of the mind. wikipedia:Intelligence "Behavior stemming from the ability to identify, assess, and control the emotions of oneself, of others, and of groups." [wikipedia:Emotional_intelligence] 2011-04-04T09:30:47Z George Gkoutos behavior_ontology behavior stemming from emotional intelligence 2011-04-18T10:37:53Z George Gkoutos behavior_ontology satiation Behavior that facilitates the restoration of normal interactions between parties that recently engaged in a conflict.[NBO:AC] 2011-04-19T09:50:09Z George Gkoutos reconciliation reconciliation behavior behavior_ontology conciliation behavior "Behavior associated with problem finding and problem shaping." [wikipedia:Problem_solving] 2011-04-04T09:31:35Z George Gkoutos behavior_ontology behavior stemming from problem solving Behavior stemming from intelligence associated with the capacity of conveying information. (Example: behavior adaptation in chimpanzees in order to communicate with humans.) 2011-04-04T09:31:52Z George Gkoutos behavior_ontology behavior stemming from communication intelligence Behavior stemming from intelligence associated with the capacity of conveying information. (Example: behavior adaptation in chimpanzees in order to communicate with humans.) NBO:GVG 2011-04-04T09:36:53Z George Gkoutos behavior_ontology alloparental behavior A domineering, assault posture and/or hostile physical action towards animals exhibited by male animals. 2011-04-04T09:39:19Z George Gkoutos male aggressive behaviour behavior_ontology GO:0001966 male aggressive behavior A domineering, assault posture and/or hostile physical action towards animals exhibited by male animals. NBO:GVG A domineering, assault posture and/or hostile physical action towards animals exhibited by female animals. 2011-04-04T09:39:49Z George Gkoutos female aggressive behaviour behavior_ontology female aggressive behavior A domineering, assault posture and/or hostile physical action towards animals exhibited by female animals. NBO:GVG A domineering, assault posture and/or hostile physical action towards animals exhibited by a mother or attending female. 2011-04-04T09:39:58Z George Gkoutos maternal aggression behavior_ontology GO:0002125 maternal aggressive behavior A domineering, assault posture and/or hostile physical action towards animals exhibited by a mother or attending female. NBO:GVG A domineering, assault posture and/or hostile physical action towards animals exhibited by a father or attending male. 2011-04-04T09:40:11Z George Gkoutos paternal aggression behavior_ontology paternal aggressive behavior A domineering, assault posture and/or hostile physical action towards animals exhibited by a father or attending male. NBO:GVG Behavior related with the gradual loss of information and experiences stored in the memory of an organism. 2011-04-04T09:49:14Z George Gkoutos forgetting behavior_ontology memory loss behavior Behavior related with the gradual loss of information and experiences stored in the memory of an organism. NBO:GVG 2011-04-04T09:49:41Z George Gkoutos behavior_ontology memory encoding behavior Behavior related with the ability of an organism's ability to store information and experiences. 2011-04-04T09:53:48Z George Gkoutos memory storage behaviour behavior_ontology memory storage behavior Behavior related with the ability of an organism's ability to store information and experiences. NBO:GVG Behavior related with the ability of an organism's ability to recall information and experiences. 2011-04-04T09:55:36Z George Gkoutos memory retrieval behaviour behavior_ontology memory retrieval behavior Behavior related with the ability of an organism's ability to recall information and experiences. NBO:GVG Cognitive perception of a sensation by any of the five senses -- vision, touch, smell, taste, and hearing. 2011-04-04T10:00:45Z George Gkoutos NBO:0000454 behavior involving perception perception behavior behavior_ontology Example: moving head to watch passing object. sensation behavior Cognitive perception of a sensation by any of the five senses -- vision, touch, smell, taste, and hearing. NBO:GVG A phobia characterised by fear of social or performance situations in which embarrassment may occur. 2011-04-05T09:35:47Z George Gkoutos behavior_ontology social phobia A phobia characterised by fear of social or performance situations in which embarrassment may occur. NBO:GVG A phobia characterised by fear of high places. 2011-04-05T09:36:09Z George Gkoutos behavior_ontology acrophobia A phobia characterised by fear of high places. NBO:GVG Behavior related to the actions of an organism in relation to sleep. 2011-04-05T09:46:01Z George Gkoutos sleep motivation behaviour behavior_ontology sleep motivation behavior Behavior related to the actions of an organism in relation to sleep. NBO:GVG Any process that modulates the frequency, rate or extent of sleep. 2011-04-05T09:46:04Z George Gkoutos behavior_ontology regulation of sleep Any process that modulates the frequency, rate or extent of sleep. GOC:jl "The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610] 2011-04-05T09:53:10Z George Gkoutos NBO:0000000 behavior behaviour behavior_ontology GO:0007610 behavior process "Behavior related to the actions or reactions of an organism in response to a visual stimulus." [GO:0007632] 2011-04-05T10:36:24Z George Gkoutos behavioral response to visual stimulus behavioural response to visual stimulus visual behaviour behavior_ontology visual behavior "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] 2011-04-05T10:37:02Z George Gkoutos behavior_ontology GO:0007634 optokinetic behavior "Behavior related to the actions or reactions of an organism in response to a sound." [GO:0031223] 2011-04-05T10:38:17Z George Gkoutos hearing behaviour behavior_ontology GO:0031223 auditory behavior Behavior related to the awareness of body balance and movement. 2011-04-05T10:40:36Z George Gkoutos proprioception behavior_ontology vestibular behavior Behavior related to the awareness of body balance and movement. MBP:GVG 2011-04-05T10:44:05Z George Gkoutos behavior_ontology balance 2011-04-05T10:44:19Z George Gkoutos behavior_ontology body rotation sensation behavior 2011-04-05T10:44:34Z George Gkoutos behavior_ontology gravitation sensation behavior 2011-04-05T10:44:55Z George Gkoutos behavior_ontology movement sensation behavior Behavior as a result of the sensation of chemicals. 2011-04-05T10:48:17Z George Gkoutos behavior_ontology GO:0007635 chemosensory behavior Behavior as a result of the sensation of chemicals. NBO:GVG Behavior related to the sensation of odors. 2011-04-05T10:48:52Z George Gkoutos behavior_ontology GO:0042048 olfactory behavior Behavior related to the sensation of odors. NBO:GVG 2011-04-05T10:50:50Z George Gkoutos gustatory behavior behavior_ontology 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. taste behavior Behavior related to environmental temperature. 2011-04-05T11:00:51Z George Gkoutos thermosensation behaviour behavior_ontology GO:0040040 thermosensory behavior Behavior related to environmental temperature. NBO:GVG Behavior related to the sensations arising from the skin and from the muscles, tendons, and joints. 2011-04-05T11:01:08Z George Gkoutos behavior_ontology 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. somatic sensation related behavior Behavior related to the sensations arising from the skin and from the muscles, tendons, and joints. OBP:GVG Behavior related to the detection of high environmental temperature. 2011-04-05T11:09:42Z George Gkoutos behavior_ontology hot sensation behavior Behavior related to the detection of high environmental temperature. NBO:GVG Behavior related to the detection of low environmental temperature. 2011-04-05T11:09:56Z George Gkoutos behavior_ontology cold sensation behavior Behavior related to the detection of low environmental temperature. NBO:GVG 2011-04-05T11:11:48Z George Gkoutos behavior_ontology cutaneous sensation behavior 2011-04-05T11:13:27Z George Gkoutos nociception pain behavior_ontology nociceptive behavior 2011-04-05T11:36:23Z George Gkoutos behavior_ontology touch related behavior 2011-04-05T12:38:39Z George Gkoutos chemical nociception behaviour behavior_ontology chemical nociceptive behavior 2011-04-05T12:39:46Z George Gkoutos mechanical nociception behaviour behavior_ontology mechanical nociceptive behavior 2011-04-05T12:41:15Z George Gkoutos thermal nociception behaviour behavior_ontology thermal nociceptive behavior 2011-04-05T12:45:31Z George Gkoutos chemically-elicited antinociception behaviour behavior_ontology chemically-elicited antinociceptive behavior 2011-04-05T02:06:22Z George Gkoutos behavior_ontology pressure related behavior "Movement behavior of the body or its parts." 2011-04-05T02:08:47Z George Gkoutos behavior_ontology kinesthetic behavior "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] 2011-04-05T03:32:44Z George Gkoutos NBO:0000340 behavior_ontology 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] 2011-04-05T03:43:28Z George Gkoutos hand eye coordination behavior_ontology 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. eye-hand coordination The coordination of limb movement. 2011-04-05T03:49:12Z George Gkoutos behavior_ontology limb coordination The coordination of limb movement. NBO:GVG Coordination that results in spatial and temporal planning of reaching and grasping. 2011-04-05T03:57:56Z George Gkoutos intra-limb coordination behavior_ontology intralimb coordination Coordination that results in spatial and temporal planning of reaching and grasping. NBO:GVG Coordination that results in bimanual synchronization and temporal association of the hands. 2011-04-05T03:58:29Z George Gkoutos inter-limb coordination behavior_ontology interlimb coordination Coordination that results in bimanual synchronization and temporal association of the hands. NBO:GVG The coordination of lower limb movement. 2011-04-05T04:05:31Z George Gkoutos behavior_ontology lower limb coordination The coordination of lower limb movement. NBO:GVG The coordination of upper limb movement. 2011-04-05T04:05:44Z George Gkoutos behavior_ontology upper limb coordination The coordination of upper limb movement. NBO:GVG The coordination of large muscle groups and whole body movement. 2011-04-05T04:10:52Z George Gkoutos large muscle coordination whole body coordination behavior_ontology gross motor coordination The coordination of large muscle groups and whole body movement. NBO:GVG Coordination of small muscle movements which occur usually in coordination with the eye. 2011-04-05T04:14:38Z George Gkoutos behavior_ontology fine motor coordination Coordination of small muscle movements which occur usually in coordination with the eye. NBO:GVG 2011-04-05T04:17:46Z George Gkoutos behavior_ontology manual dexterity Coordination involved in writing. 2011-04-05T04:19:34Z George Gkoutos behavior_ontology graphomotor coordination Coordination involved in writing. NBO:GVG The coordination of the whole body movement. 2011-04-05T05:28:29Z George Gkoutos behavior_ontology body coordination The coordination of the whole body movement. NBO:GVG The coordination of the lower body movement. 2011-04-05T05:30:38Z George Gkoutos behavior_ontology upper body coordination The coordination of the lower body movement. NBO:GVG The coordination of the upper body movement. 2011-04-05T05:30:53Z George Gkoutos behavior_ontology lower body coordination The coordination of the upper body movement. NBO:GVG 2011-04-05T05:33:26Z George Gkoutos behavior_ontology bilateral coordination Intentionally or habitually assumed arrangement of the body and its limbs. 2011-04-06T09:30:15Z George Gkoutos behavior_ontology posture Intentionally or habitually assumed arrangement of the body and its limbs. NBO:GVG Intentionally or habitually assumed arrangement of the body. 2011-04-06T09:30:45Z George Gkoutos behavior_ontology body posture Intentionally or habitually assumed arrangement of the body. NBO:GVG Intentionally or habitually assumed arrangement of the limbs. 2011-04-06T09:31:06Z George Gkoutos behavior_ontology limb posture Intentionally or habitually assumed arrangement of the limbs. NBO:GVG Intentionally or habitually assumed arrangement of the body and its limbs in inactivity. 2011-04-06T09:31:29Z George Gkoutos behavior_ontology resting posture Intentionally or habitually assumed arrangement of the body and its limbs in inactivity. NBO:GVG Behavior associated with surface locomotion. 2011-04-06T09:44:37Z George Gkoutos behavior_ontology terrestrial locomotory behavior Behavior associated with surface locomotion. NBO:GVG 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. 2011-04-06T09:47:57Z George Gkoutos saltation behavior_ontology leaping behavior 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. MBP:GVG "The pattern of movement of the limbs of animals, characterized by elements of progression, stability, speed and length over the ground." [MP:0001406] 2011-04-06T10:07:23Z George Gkoutos behavior_ontology gait A behavioral pattern characterized by the distance covered by as many steps as there are legs. 2011-04-06T10:08:59Z George Gkoutos behavior_ontology stride A behavioral pattern characterized by the distance covered by as many steps as there are legs. NBO:GVG Behavior related to the movement resulting by dragging the body close to the ground. 2011-04-06T11:39:16Z George Gkoutos crawl behavior_ontology crawling behavior Behavior related to the movement resulting by dragging the body close to the ground. NBO:GVG "Behavior related to the locomotion of animals in trees." [wikipedia:Arboreal_locomotion] 2011-04-06T11:40:46Z George Gkoutos behavior_ontology arboreal locomotion behavior arm over arm swinging movement through arboreal environment [NBO:AC] 2011-04-06T11:42:31Z George Gkoutos behavior_ontology Arguably the epitome of arboreal locomotion, it involves swinging with the arms from one handhold to another. brachiation Behavior related to the movement of an organism from one location to another through the air. 2011-04-06T11:44:55Z George Gkoutos behavior_ontology aerial locomotion behavior Behavior related to the movement of an organism from one location to another through the air. NBO:GVG 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. 2011-04-06T11:45:51Z George Gkoutos NBO:0000072 fly flying behavior_ontology GO:0007629 flight behavior 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. NBO:GVG Behavior related to the ascending a steep object. 2011-04-06T11:46:00Z George Gkoutos behavior_ontology climbing behavior Behavior related to the ascending a steep object. NBO:GVG 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. 2011-04-06T12:20:11Z George Gkoutos behavior_ontology gliding behavior 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. NBO:GVG Behavior related to the upward thrust produced by the rapid, simultaneous extension of the hind legs with the intend to rise in the air. 2011-04-06T12:25:30Z George Gkoutos hopping behavior_ontology saltation Behavior related to the upward thrust produced by the rapid, simultaneous extension of the hind legs with the intend to rise in the air. NBO:GVG Behavior related to the movement of an organism from one location to another through a liquid medium. 2011-04-06T12:33:07Z George Gkoutos swim swimming behavior_ontology aquatic locomotion Behavior related to the movement of an organism from one location to another through a liquid medium. NBO:GVG Behavior related to the control of the direction of locomotion. 2011-04-06T01:15:21Z George Gkoutos behavior_ontology directional control of locomotion Behavior related to the control of the direction of locomotion. NBO:GVG Behavior related to the ability of an animal to determine and to alter its position in the environment. 2011-04-06T01:16:55Z George Gkoutos behavior_ontology locomotory orientation behavior Behavior related to the ability of an animal to determine and to alter its position in the environment. NBO:GVG Alteration of speed or direction of movement in response to a sensory stimulus. 2011-04-06T01:17:18Z George Gkoutos behavior_ontology GO:0042465 kinesis Alteration of speed or direction of movement in response to a sensory stimulus. NBO:GVG Locomotory orientation in a specific spatial relationship to a stimulus. 2011-04-06T01:17:27Z George Gkoutos behavior_ontology GO:0042330 taxis Locomotory orientation in a specific spatial relationship to a stimulus. NBO:GVG Behavior related to the mechanical alteration of the locomotor pattern through which the animal adjusts its position. 2011-04-06T01:18:17Z George Gkoutos behavior_ontology steering behavior Behavior related to the mechanical alteration of the locomotor pattern through which the animal adjusts its position. NBO:GVG "Locomotory orientation in response to specific chemical concentration gradient." [GO:0006935] 2011-04-06T01:23:34Z George Gkoutos chemotaxis behavior_ontology GO:0006935 chemotactic behavior "Locomotory orientation in response to gravity." [GO:0048062] 2011-04-06T01:27:22Z George Gkoutos geotactic behaviour gravitaxis behavior_ontology GO:0042332 gravitactic behavior "Locomotory orientation away from the source of gravity." [GO:0048060] 2011-04-06T01:32:49Z George Gkoutos negative geotactic behaviour negative gravitaxis behavior_ontology GO:0048060 negative gravitactic behavior "Locomotory orientation towards the source of gravity." [GO:0048061] 2011-04-06T01:34:24Z George Gkoutos positive geotactic behaviour positive gravitaxis behavior_ontology GO:0048061 positive gravitactic behavior "Locomotory orientation in response to touch." [GO:0001966] 2011-04-06T01:45:18Z George Gkoutos stereotaxis behavior_ontology thigmotaxis "Locomotory orientation in response to physical parameters involved in energy generation." [GO:0009453] 2011-04-06T01:47:46Z George Gkoutos behavior_ontology GO:0009453 energy taxis "Locomotory orientation in response to light." [GO:0042331] 2011-04-06T01:48:33Z George Gkoutos phototaxis behavior_ontology GO:0042331 phototactic behavior "Locomotory orientation in response to a temperature gradient." [GO:0043052] 2011-04-06T01:50:19Z George Gkoutos behavior_ontology GO:0043052 thermotaxis Locomotory orientation in response to sound. 2011-04-06T01:58:40Z George Gkoutos behavior_ontology phonotaxis Locomotory orientation in response to sound. NBO:GVG Locomotory orientation in response to mechanical stimulus. 2011-04-06T01:59:20Z George Gkoutos behavior_ontology mechanical stimulus taxis Locomotory orientation in response to mechanical stimulus. NBO:GVG Locomotory orientation in response to pressure. 2011-04-06T02:01:21Z George Gkoutos behavior_ontology barotaxis Locomotory orientation in response to pressure. NBO:GVG Behavior related to movements that occur independent of planning. 2011-04-06T02:35:38Z George Gkoutos behavior_ontology Movevents listed here are involuntary, but may be also generated by free will, like blinking of the eyelids and respiratory movements. involuntary movement behavior Behavior related to movements that occur independent of planning. NBO:GVG Behavior related to involuntary movement in response to a stimulus. 2011-04-06T02:36:55Z George Gkoutos NBO:0000004 reflex behaviour behavior_ontology reflexive behavior Behavior related to involuntary movement in response to a stimulus. NBO:GVG "Reflex actions originating in the central nervous system that are exhibited by normal infants in response to particular stimuli." [wikipedia:Primitive_reflexes] 2011-04-06T02:44:15Z George Gkoutos infant reflex infantile reflex newborn reflex behavior_ontology primitive reflex "An action or movement due to the application of a sudden unexpected stimulus." [wikipedia:Startle_reflex] 2011-04-06T02:55:21Z George Gkoutos alarm reaction behavior_ontology 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] 2011-04-06T03:03:51Z George Gkoutos TLR behavior_ontology 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] 2011-04-06T03:05:52Z George Gkoutos ATNR fencing reflex behavior_ontology 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. 2011-04-06T03:10:14Z George Gkoutos behavior_ontology symmetrical 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. MBP:GVG "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] 2011-04-06T03:11:13Z George Gkoutos spinal galant behavior_ontology 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] 2011-04-06T03:14:17Z George Gkoutos behavior_ontology babkin reflex "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] 2011-04-06T03:15:57Z George Gkoutos behavior_ontology swimming reflex "A reflex elicited when the sole of the foot is stimulated with a blunt instrument." [wikipedia:Plantar_reflex] 2011-04-06T03:18:52Z George Gkoutos behavior_ontology 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] 2011-04-06T03:20:02Z George Gkoutos behavior_ontology palmar grasp reflex "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] 2011-04-06T03:22:48Z George Gkoutos behavior_ontology rooting reflex "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] 2011-04-06T03:25:21Z George Gkoutos behavior_ontology sucking reflex "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] 2011-04-06T03:26:47Z George Gkoutos stepping reflex behavior_ontology walking reflex Behavior related to movements executed with intent. 2011-04-06T03:32:28Z George Gkoutos behavior_ontology voluntary movement behavior Behavior related to movements executed with intent. NBO:GVG "A muscle contraction in response to stretching within the muscle." [wikipedia:Stretch_reflex] 2011-04-06T04:02:17Z George Gkoutos deep tendon reflex behavior_ontology stretch reflex A deep tendon reflex that elicits involuntary contraction of the biceps brachii muscle. 2011-04-06T04:06:11Z George Gkoutos behavior_ontology biceps reflex A deep tendon reflex that elicits involuntary contraction of the biceps brachii muscle. NBO:GVG "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] 2011-04-06T04:07:37Z George Gkoutos supinator reflex behavior_ontology brachioradialis reflex A reflex that elicits involuntary contraction of the extensor digitorum muscle. 2011-04-06T04:09:37Z George Gkoutos BER Braunecker-Effenberg reflex behavior_ontology extensor digitorum reflex A reflex that elicits involuntary contraction of the extensor digitorum muscle. NBO:GVG "A deep tendon reflex that elicits involuntary contraction of the triceps brachii muscle." [wikipedia:Triceps_reflex] 2011-04-06T04:12:22Z George Gkoutos behavior_ontology triceps reflex A deep tendon reflex that elicits extension of the leg resulting from a sharp tap on the patellar tendon. 2011-04-06T04:18:23Z George Gkoutos knee-jerk reflex behavior_ontology patellar reflex A deep tendon reflex that elicits extension of the leg resulting from a sharp tap on the patellar tendon. NBO:GVG "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] 2011-04-06T04:20:42Z George Gkoutos Achilles reflex Achilles tendon reflex ankle reflex triceps surae reflex behavior_ontology ankle jerk reflex A reflex that involves cranial nerves. 2011-04-06T04:28:27Z George Gkoutos behavior_ontology cranial nerve related reflex A reflex that involves cranial nerves. wikipedia: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] 2011-04-06T04:28:58Z George Gkoutos pupillary reflex behavior_ontology 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] 2011-04-06T04:29:55Z George Gkoutos behavior_ontology accommodation reflex 2011-04-06T04:30:58Z George Gkoutos masseter reflex behavior_ontology jaw jerk reflex "An involuntary blinking of the eyelids elicited by stimulation of the cornea." [wikipedia:Corneal_reflex] 2011-04-06T06:08:06Z George Gkoutos GO:0060082 blink reflex blinking behavior_ontology corneal reflex GO:0060082 http://orcid.org/0000-0002-4277-2151 "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] 2011-04-06T06:11:09Z George Gkoutos VOR oculovestibular reflex vestibuloocular reflex behavior_ontology 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] 2011-04-06T06:16:20Z George Gkoutos behavior_ontology physiologic nystagmus "A reflex contraction of the back of the throat, evoked by touching the soft palate." [wikipedia:Gag_reflex] 2011-04-06T06:17:32Z George Gkoutos gag reflex swallowing reflex behavior_ontology pharyngeal reflex Observable characteristic of behavior related to the readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals. 2011-04-07T01:19:38Z George Gkoutos behavior_ontology sleeping behavior phenotype Observable characteristic of behavior related to the readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals. NBO:GVG A NREM parasomnia characterised by Involuntarily grinding of teeth while sleeping. 2011-04-07T01:20:00Z George Gkoutos <new synonym> teeth grinding behavior_ontology HP:0003763 bruxism A NREM parasomnia characterised by Involuntarily grinding of teeth while sleeping. MBP:GVG "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] 2011-04-07T01:22:32Z George Gkoutos DSPS delayed sleep-phase disorder (DSPD) delayed sleep-phase type (DSPT) behavior_ontology delayed sleep phase syndrome Inability to fall asleep and/or remain asleep for a reasonable amount of time. 2011-04-07T01:23:24Z George Gkoutos behavior_ontology insomnia Inability to fall asleep and/or remain asleep for a reasonable amount of time. NBO:GVG A dyssomnia characterised by excessive daytime sleepiness (EDS) in which a person experiences extreme fatigue and possibly falls asleep at inappropriate times. 2011-04-07T01:24:10Z George Gkoutos behavior_ontology MP:0005279 narcolepsy A dyssomnia characterised by excessive daytime sleepiness (EDS) in which a person experiences extreme fatigue and possibly falls asleep at inappropriate times. wikipedia:Narcolepsy A NREM parasomnia characterised by abrupt awakening from sleep with behavior consistent with terror and a temporary inability to regain full consciousness. 2011-04-07T01:25:22Z George Gkoutos Pavor nocturnus night terror behavior_ontology sleep terror A NREM parasomnia characterised by abrupt awakening from sleep with behavior consistent with terror and a temporary inability to regain full consciousness. NBO:GVG "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] 2011-04-07T05:12:21Z George Gkoutos behavior_ontology abdominal reflex "Reflexive contraction of the external anal sphincter upon stroking of the skin around the anus." [wikipedia:Anal_wink] 2011-04-07T05:12:40Z George Gkoutos anal reflex anal wink perineal reflex behavior_ontology anocutaneous reflex "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] 2011-04-07T05:15:36Z George Gkoutos behavior_ontology cremasteric reflex "A reflex in mammals which optimises respiration to allow staying underwater for extended periods of time." [wikipedia:Mammalian_diving_reflex] 2011-04-07T05:16:44Z George Gkoutos behavior_ontology 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] 2011-04-07T05:18:30Z George Gkoutos behavior_ontology visceromotor reflex "A reflex of the abdominal muscles to contract upon mechanical force to the abdomen, and serves as protection." [wikipedia:Muscular_defense] 2011-04-07T05:20:21Z George Gkoutos behavior_ontology muscular defense "A response to activation of sensory neurons whose peripheral terminals are located on the surface of the body." [wikipedia:Scratch_reflex] 2011-04-07T05:21:15Z George Gkoutos NBO:0000021 self-scratching behavior_ontology scratch reflex An action or movement due to the application of a sudden unexpected loud noise. 2011-04-07T05:31:27Z George Gkoutos behavior_ontology acoustic startle reflex An action or movement due to the application of a sudden unexpected loud noise. NBO:GVG A reflex where the body reacts to pain or unpleasant stimuli by trying to move itself away from the source. 2011-04-07T05:35:05Z George Gkoutos flexor withdrawal reflex nociceptive reflex behavior_ontology withdrawal reflex A reflex where the body reacts to pain or unpleasant stimuli by trying to move itself away from the source. NBO:GVG "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] 2011-04-07T05:39:15Z George Gkoutos behavior_ontology 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] 2011-04-07T05:41:07Z George Gkoutos attenuation reflex auditory reflex stapedius reflex behavior_ontology acoustic reflex "A reflex in which joint movement can reflexively cause muscle activation or inhibition." [wikpedia:Arthrokinetic_reflex] 2011-04-07T05:42:50Z George Gkoutos behavior_ontology 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] 2011-04-07T05:45:22Z George Gkoutos behavior_ontology cough reflex "A pouting or pursing of the lips that is elicited by light tapping of the closed lips near the midline." [wikipedia:Snout_reflex] 2011-04-07T05:47:28Z George Gkoutos behavior_ontology snout reflex "A reflex elicited by repetitive tapping on the forehead which result in blinking to the first several taps." [wikipedia:Glabellar_reflex] 2011-04-07T05:48:07Z George Gkoutos glabellar tap sign behavior_ontology glabellar reflex "A skeletal muscle contraction causes the muscle to simultaneously lengthen and relax." [wikipedia:Golgi_tendon_reflex] 2011-04-08T12:01:59Z George Gkoutos inverse myotatic reflex behavior_ontology 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. 2011-04-08T12:05:40Z George Gkoutos behavior_ontology The shivering reflex is triggered to maintain homeostasis. shivering 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. wikipedia:Shivering A reflex in which mucus containing foreign particles or irritants is expelled and the nasal cavity is cleanses. 2011-04-08T12:08:31Z George Gkoutos sneeze sneezing behavior_ontology sternutation A reflex in which mucus containing foreign particles or irritants is expelled and the nasal cavity is cleanses. wikipedia:Sneeze "A contraction of muscles in the gastrointestinal tract in response to distension of the tract following consumption of food and drink." [wikipedia:Vagus_reflex] 2011-04-08T12:10:27Z George Gkoutos behavior_ontology vagovagal reflex 2011-04-08T12:22:02Z George Gkoutos behavior_ontology eye movement 2011-04-08T12:22:13Z George Gkoutos behavior_ontology tail movement Selective tracking that follows a moving object by eye. 2011-04-08T12:25:53Z George Gkoutos behavior_ontology Original definition: Selectively track a moving object (Source: NBO:GVG). visual pursuit Activation of locomotory behavior. 2011-04-08T12:27:51Z George Gkoutos behavior_ontology locomotor activation behavior 2011-04-08T12:28:10Z George Gkoutos behavior_ontology vertical activity Kinesthetic behavior initiated in the absence of specific sensory input. 2011-04-08T12:28:25Z George Gkoutos behavior_ontology spontaneous movement behavior "Behavior related to the activity in which individuals in a group clean or maintain one another's body or appearance." [wikipedia:Social_grooming] 2011-04-08T12:35:02Z George Gkoutos allo-hygiene behavior allogrooming allohygiene behavior_ontology social grooming "Behavior related to the promotion of personal hygiene." [wikipedia:Social_grooming] 2011-04-08T12:35:54Z George Gkoutos NBO:0000058 auto-grooming autohygiene preening self-grooming behavior_ontology personal grooming Behavior related to the state or ability to perceive, to feel, or to be conscious of events, objects or sensory patterns. 2011-04-08T12:50:34Z George Gkoutos behavior_ontology awareness Behavior related to the state or ability to perceive, to feel, or to be conscious of events, objects or sensory patterns. wikipedia:Awareness 2011-04-08T12:52:15Z George Gkoutos behavior_ontology obsolete behavior related to feelings experiencing true The sustained focus of cognitive resources on information while filtering or ignoring extraneous information. Intended to encompass only attention to perceptual stimuli. 2011-04-08T01:02:16Z George Gkoutos behavior_ontology attention behavior The sustained focus of cognitive resources on information while filtering or ignoring extraneous information. Intended to encompass only attention to perceptual stimuli. wikipedia:Attention Behavior involving responding discretely to specific visual, auditory or tactile stimuli. 2011-04-08T01:04:04Z George Gkoutos behavior_ontology focused attention behavior Behavior involving responding discretely to specific visual, auditory or tactile stimuli. wikipedia:Attention Behavior involving maintaining a behavioral or cognitive set in the face of distracting or competing stimuli. 2011-04-08T01:05:54Z George Gkoutos behavior_ontology selective attention behavior Behavior involving maintaining a behavioral or cognitive set in the face of distracting or competing stimuli. wikipedia:Attention Behavior involving mental flexibility that allows individuals to shift their focus of attention and move between tasks having different cognitive requirements. 2011-04-08T01:05:58Z George Gkoutos behavior_ontology alternating attention behavior Behavior involving mental flexibility that allows individuals to shift their focus of attention and move between tasks having different cognitive requirements. wikipedia:Attention Behavior involving maintaining a consistent behavioral response during continuous and repetitive activity. 2011-04-08T01:06:00Z George Gkoutos vigilance behavior_ontology sustained attention behavior Behavior involving maintaining a consistent behavioral response during continuous and repetitive activity. wikipedia:Attention Behavior involving responding simultaneously to multiple tasks or multiple task demands. 2011-04-08T01:08:36Z George Gkoutos behavior_ontology divided attention behavior Behavior involving responding simultaneously to multiple tasks or multiple task demands. wikipedia:Attention "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] 2011-04-08T01:15:31Z George Gkoutos behavior_ontology size constancy behavior "The perception of a color as constant under changing conditions of illumination." [wikipedia:Color_constancy] 2011-04-08T01:16:53Z George Gkoutos behavior_ontology colour constancy behavior The perception of familiar objects as approximately the same shape regardless of their distance or angle of view from the observer. 2011-04-08T01:18:00Z George Gkoutos behavior_ontology shape constancy behavior The perception of familiar objects as approximately the same shape regardless of their distance or angle of view from the observer. NBO:GVG "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] 2011-04-08T01:23:16Z George Gkoutos behavior_ontology perception of motion behavior "Perception related to the identification of objects and their distinction from each other." [:http\://science.jrank.org/pages/5094/Perception.html] 2011-04-08T01:25:53Z George Gkoutos behavior_ontology form perception behavior "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] 2011-04-08T01:29:05Z George Gkoutos behavior_ontology depth perception behavior Perception of the distance of an object. 2011-04-08T01:31:08Z George Gkoutos behavior_ontology distance perception behavior Perception of the distance of an object. NBO:GVG "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] 2011-04-08T01:32:16Z George Gkoutos behavior_ontology perceptual illusion behavior "Behavior related to how the body reacts to a stressor ( a stimulus that causes stress), real or imagined." [wikipedia:Stress_(biological)] 2011-04-08T01:52:36Z George Gkoutos behavior_ontology It refers to the consequence of the failure of an organism to respond adequately to mental, emotional or physical demands, whether actual or imagined. stress related behavior "Behavior related to the identification or realization of a threat or a stressor." [wikipedia:Stress_(biological)] 2011-04-08T01:55:58Z George Gkoutos behavior_ontology behavioral alarm 2011-04-08T02:00:36Z George Gkoutos behavior_ontology predator avoidance behavior Behavior related to the depletion of the body resources for coping to stress. 2011-04-08T02:06:24Z George Gkoutos behavior_ontology behavioral exhaustion Behavior related to the depletion of the body resources for coping to stress. NBO:GVG 2011-04-08T02:18:40Z George Gkoutos behavior_ontology rhythmic behavior phenotype 2011-04-08T02:19:42Z George Gkoutos pathological circadian behaviour behavior_ontology circadian behavior phenotype 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. 2011-04-08T02:20:42Z George Gkoutos behavior_ontology dyssomnia 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. wikipedia:Dyssomnia 2011-04-08T02:21:57Z George Gkoutos behavior_ontology intrinsic sleep disorder A dyssomnia characterized by excessive amounts of sleepiness. 2011-04-08T02:26:26Z George Gkoutos behavior_ontology hypersomnia A dyssomnia characterized by excessive amounts of sleepiness. wikipedia:Hypersomnia "A dyssomnia where the patient moves limbs involuntarily during sleep, and has symptoms or problems related to the movement." [wikipedia:Periodic_limb_movement_disorder] 2011-04-08T02:27:28Z George Gkoutos PLMD nocturnal myoclonus behavior_ontology 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] 2011-04-08T02:28:45Z George Gkoutos RLS Wittmaack Ekbom syndrome behavior_ontology restless legs syndrome "A sleep breathing disorder characterized by abnormal pauses in breathing or instances of abnormally low breathing, during sleep." [wikipedia:Sleep_apnea] 2011-04-08T02:30:29Z George Gkoutos sleep apnoea behavior_ontology sleep apnea "A dyssomnia characterized by a mistakenly perception of one's sleep as wakefulness." [wikipedia:Sleep_state_misperception] 2011-04-08T02:31:33Z George Gkoutos SSM paradoxical insomnia pseudo-insomnia sleep hypochondriasis subjective insomnia subjective sleepiness behavior_ontology sleep state misperception 2011-04-08T02:35:59Z George Gkoutos behavior_ontology extrinsic sleep disorder A dyssomnia associated with alcohol intake. 2011-04-08T02:36:22Z George Gkoutos behavior_ontology alcohol-dependent sleep disorder A dyssomnia associated with alcohol intake. NBO:GVG A insomnia associated with food allergies. 2011-04-08T02:37:51Z George Gkoutos behavior_ontology food allergy insomnia A insomnia associated with food allergies. NBO:GVG "A pathological circadian behavior primarily related to the timing of sleep." [wikipedia:Circadian_rhythm_sleep_disorder] 2011-04-08T02:38:58Z George Gkoutos behavior_ontology 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] 2011-04-08T02:54:21Z George Gkoutos behavior_ontology extrinsic circadian rhythm sleep disorder 2011-04-08T02:54:52Z George Gkoutos behavior_ontology 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] 2011-04-08T02:55:50Z George Gkoutos behavior_ontology jet lag 2011-04-08T02:57:20Z George Gkoutos SWSD behavior_ontology shift work sleep disorder "A circadian rhythm sleep disorder characterized by difficulty staying awake in the evening and staying asleep in the morning." [wikipedia:Advanced_sleep_phase_syndrome] 2011-04-08T03:00:14Z George Gkoutos ASPS ASPT advanced sleep-phase type behavior_ontology 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] 2011-04-08T03:11:40Z George Gkoutos circadian rhythm sleep disorder, free running type circadian rhythm sleep disorder, nonentrained type free running disorder (FRD) hypernychthemeral syndrome non-24 non-24-hour circadian rhythm disorder non-24-hour sleep-wake disorder behavior_ontology non-24-hour sleep-wake syndrome "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] 2011-04-08T03:16:00Z George Gkoutos behavior_ontology 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. 2011-04-08T03:20:06Z George Gkoutos behavior_ontology parasomnia 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. wikipedia:Parasomnia An intrinsic sleep disorder characterised by breathing abnormalities. 2011-04-08T03:27:40Z George Gkoutos SBD behavior_ontology sleep breathing disorder An intrinsic sleep disorder characterised by breathing abnormalities. NBO:GVG A sleeping behavior characterised by vibration of respiratory structures and the resulting sound, due to obstructed air movement during breathing while sleeping. 2011-04-08T03:28:23Z George Gkoutos behavior_ontology snoring A sleeping behavior characterised by vibration of respiratory structures and the resulting sound, due to obstructed air movement during breathing while sleeping. wikipedia:Snoring "A sleep breathing disorder characterized by airway resistance to breathing during sleep." [wikipedia:Upper_airway_resistance_syndrome] 2011-04-08T03:30:24Z George Gkoutos behavior_ontology upper airway resistance syndrome A hypersomnia characterized by recurrent episodes. 2011-04-08T03:32:17Z George Gkoutos behavior_ontology recurrent hypersomnia A hypersomnia characterized by recurrent episodes. NBO:GVG A hypersomnia that occurs as a result of a traumatic event involving the central nervous system. 2011-04-08T03:32:25Z George Gkoutos behavior_ontology posttraumatic hypersomnia A hypersomnia that occurs as a result of a traumatic event involving the central nervous system. NBO:GVG A type of parasomnia that occurs during NREM sleep. 2011-04-08T03:37:10Z George Gkoutos behavior_ontology NREM parasomnia A type of parasomnia that occurs during NREM sleep. NBO:GVG 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. 2011-04-09T09:32:07Z George Gkoutos somnambulism behavior_ontology sleepwalking 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. wikipedia:Sleepwalking A NREM parasomnia characterised by involuntary urination while asleep after the age at which bladder control usually occurs. 2011-04-09T09:39:54Z George Gkoutos bedwetting behavior_ontology nocturnal enuresis A NREM parasomnia characterised by involuntary urination while asleep after the age at which bladder control usually occurs. wikipedia:Bedwetting A NREM parasomnia characterised by talking during sleep. 2011-04-09T10:02:28Z George Gkoutos sleep-talking behavior_ontology somniloquy A NREM parasomnia characterised by talking during sleep. NBO:GVG "A REM parasomnia characterised by the lack of muscle atonia during sleep." [wikipedia:REM_Sleep_Behavior_Disorder] 2011-04-09T10:06:44Z George Gkoutos RBD behavior_ontology REM sleep behavior disorder A type of parasomnia that occurs during REM sleep. 2011-04-09T10:07:11Z George Gkoutos behavior_ontology REM parasomnia A type of parasomnia that occurs during REM sleep. NBO:GVG A RBD that occurs mostly as a result of a side-effect in prescribed medication- usually antidepressants. 2011-04-09T10:10:12Z George Gkoutos behavior_ontology acute RBD A RBD that occurs mostly as a result of a side-effect in prescribed medication- usually antidepressants. wikipedia:Parasomnia Idiopathic or associated with neurological disorders REM sleep behavior disorder. 2011-04-09T10:11:32Z George Gkoutos behavior_ontology chronic RBD Idiopathic or associated with neurological disorders REM sleep behavior disorder. wikipedia:Parasomnia A REM parasomnia consisting of breath holding and expiratory groaning during sleep that is distinct from both somniloquy and obstructive sleep apnea. 2011-04-09T10:13:44Z George Gkoutos behavior_ontology catathrenia A REM parasomnia consisting of breath holding and expiratory groaning during sleep that is distinct from both somniloquy and obstructive sleep apnea. wikipedia:Catathrenia "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] 2011-04-09T10:14:54Z George Gkoutos RISP behavior_ontology recurrent isolated sleep paralysis "A sleep paralaysis characterised by the absence of narcolepsy." [wikipedia:Sleep_paralysis] 2011-04-09T10:20:09Z George Gkoutos ISP behavior_ontology isolated 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] 2011-04-09T10:24:27Z George Gkoutos behavior_ontology sleep paralysis "A sleep paralysis which upon falling asleep the person remains aware while the body shuts down for REM sleep." [wikipedia:Sleep_paralysis] 2011-04-09T10:25:40Z George Gkoutos predormital sleep paralysis behavior_ontology hypnagogic sleep paralysis "A sleep paralysis which upon awakening, the person becomes aware before the REM cycle is complete,." [wikipedia:Sleep_paralysis] 2011-04-09T10:28:53Z George Gkoutos postdormital sleep paralysis behavior_ontology hypnopompic sleep paralysis Behavior related to the ascending stairs. 2011-04-09T10:51:13Z George Gkoutos behavior_ontology climbing stairs Behavior related to the ascending stairs. NBO:GVG A dyssomnia characterised by fear of sleep. 2011-04-09T11:20:26Z George Gkoutos somniphobia behavior_ontology hypnophobia A dyssomnia characterised by fear of sleep. NBO:GVG 2011-04-09T12:28:31Z George Gkoutos NBO:0000523 DD-NOS depressive disorder not otherwise specified behavior_ontology HP:0000716 depressive disorder "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] 2011-04-10T12:55:14Z George Gkoutos AD behavior_ontology 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] 2011-04-10T12:57:29Z George Gkoutos behavior_ontology 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] 2011-04-10T12:58:44Z George Gkoutos PMD behavior_ontology psychotic major depression A major depressive disorder characterized by psychological and motorological disturbances. 2011-04-10T01:01:38Z George Gkoutos behavior_ontology catatonic depression A major depressive disorder characterized by psychological and motorological disturbances. wikipedia:Catatonia "A major depressive disorder characterized by a intense, sustained and sometimes disabling depression experienced by women after giving birth." [wikipedia:Postpartum_depression] 2011-04-10T01:03:17Z George Gkoutos PDD postnatal depression behavior_ontology 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] 2011-04-10T01:10:46Z George Gkoutos winter blues winter depression behavior_ontology seasonal affective disorder A depressive disorder characterized by chronic, different mood disturbance. 2011-04-10T01:13:55Z George Gkoutos behavior_ontology For humans: where a person reports a low mood almost daily over a span of at least two years. dysthymia A depressive disorder characterized by chronic, different mood disturbance. wikipedia:Dysthymia "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] 2011-04-10T01:17:54Z George Gkoutos RBD behavior_ontology 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] 2011-04-10T01:19:53Z George Gkoutos minor depression behavior_ontology 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] 2011-04-10T01:25:04Z George Gkoutos behavior_ontology bipolar I "A bipolar disorder characterised by recurrent intermittent hypomanic and depressive episodes." [wikipedia:Mood_disorder] 2011-04-10T01:26:32Z George Gkoutos behavior_ontology bipolar II A bipolar disorder characterised by recurrent hypomanic and dysthymic episodes, but no full manic episodes or full major depressive episodes. 2011-04-10T01:27:37Z George Gkoutos behavior_ontology cyclothymia A bipolar disorder characterised by recurrent hypomanic and dysthymic episodes, but no full manic episodes or full major depressive episodes. wikipedia:Cyclothymia "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] 2011-04-10T01:28:33Z George Gkoutos BD-NOS behavior_ontology bipolar disorder not otherwise specified 2011-04-10T01:33:58Z George Gkoutos behavior_ontology substance induced mood disorder 2011-04-10T01:34:12Z George Gkoutos behavior_ontology alcohol induced mood disorder 2011-04-10T01:34:25Z George Gkoutos behavior_ontology benzodiazepine induced mood disorder 2011-04-10T01:34:41Z George Gkoutos behavior_ontology Interferon-alpha induced mood disorder "A pathological anxiety which results from a traumatic experience." [wikipedia:Post-traumatic_stress_disorder] 2011-04-10T01:42:56Z George Gkoutos PTSD post-traumatic stress disorder behavior_ontology post-traumatic stress "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] 2011-04-10T01:44:22Z George Gkoutos SepAD behavior_ontology separation anxiety Any process in which an organism modulates its heart rate at different values with a regularity of approximately 24 hours. 2011-04-10T02:18:47Z George Gkoutos behavior_ontology GO:0003053 circadian regulation of heart rate Any process in which an organism modulates its heart rate at different values with a regularity of approximately 24 hours. GOC:rl "Any process in which an organism modulates its blood pressure at different values with a regularity of approximately 24 hours." [GO:GO\:0003052] 2011-04-10T02:21:01Z George Gkoutos behavior_ontology 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. 2011-04-10T02:22:58Z George Gkoutos circadian thermoregulation behavior_ontology circadian temperature homeostasis Any homeostatic process in which an organism modulates its internal body temperature at different values with a regularity of approximately 24 hours. GOC:dbh Observable characteristic of feeding behavior that relates to eating. 2011-04-10T10:39:39Z George Gkoutos eating disorder behavior_ontology eating behavior phenotype Observable characteristic of feeding behavior that relates to eating. NBO:GVG Observable characteristic of feeding behavior that relates to drinking. 2011-04-10T10:40:49Z George Gkoutos drinking disorder pathological drinking behaviour behavior_ontology drinking behavior phenotype Observable characteristic of feeding behavior that relates to drinking. NBO:GVG A pathological drinking behavior characterised by an excessive desire to drink. 2011-04-10T10:41:10Z George Gkoutos behavior_ontology 'participates in' some ('regulation of drinking behavior' and (has_quality some ('increased frequency' and towards some 'liquid consumption' and owl:qualifier some chronic))) MP:0002119 dipsosis A pathological drinking behavior characterised by an excessive desire to drink. NBO:GVG A pathological drinking behavior characterised by large intake of fluids by mouth, usually due to excessive thirst that is relatively prolonged. 2011-04-10T10:41:10Z George Gkoutos behavior_ontology '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') HP:0001959 MP:0001426 polydipsia A pathological drinking behavior characterised by large intake of fluids by mouth, usually due to excessive thirst that is relatively prolonged. NBO:GVG A pathological drinking behavior characterised by an excessive relative temporal desire to drink. 2011-04-10T10:41:10Z George Gkoutos behavior_ontology 'participates in' some ('regulation of drinking behavior' and (has_quality some ('increased frequency' and (towards some 'liquid consumption') and (owl:qualifier some 'temporally extended')))) MP:0005111 hyperdipsia A pathological drinking behavior characterised by an excessive relative temporal desire to drink. NBO:GVG A pathological feeding behavior characterised by failure to eat. 2011-04-10T10:41:10Z George Gkoutos behavior_ontology MP:0001438 aphagia A pathological feeding behavior characterised by failure to eat. NBO:GVG The act of moving food from the mouth cavity to the esophagus through coordinated muscular movements [NBO:AC] 2011-04-10T10:39:39Z George Gkoutos swallow behavior_ontology swallowing A pathological eating behavior characterised by an abnormally large intake of food by mouth, usually due to excessive hunger that is relatively prolonged. 2011-04-10T10:41:10Z George Gkoutos hyperphagia behavior_ontology HP:0000724 MP:0001433 polyphagia A pathological eating behavior characterised by an abnormally large intake of food by mouth, usually due to excessive hunger that is relatively prolonged. NBO:GVG Lack of ability to enjoy a sense of pleasure. 2011-04-10T10:41:10Z George Gkoutos behavior_ontology MP:0009710 anhedonia Lack of ability to enjoy a sense of pleasure. NBO:GVG Behaviour related to the male activity which primary purpose is the sexual reproduction. 2011-04-10T10:41:10Z George Gkoutos behavior_ontology male sexual activity Behaviour related to the male activity which primary purpose is the sexual reproduction. NBO:GVG Behaviour related to the female activity which primary purpose is the sexual reproduction. 2011-04-10T10:41:10Z George Gkoutos behavior_ontology female sexual activity Behaviour related to the female activity which primary purpose is the sexual reproduction. NBO:GVG "Ability to correctly remember something that has been encountered before." [wikipedia:Recognition_memory] 2011-04-14T01:53:29Z George Gkoutos behavior_ontology 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] 2011-04-14T01:56:14Z George Gkoutos behavior_ontology 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. 2011-04-14T02:02:11Z George Gkoutos behavior_ontology long term object recognition memory 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. NBO:GVG 2011-04-14T02:03:00Z George Gkoutos behavior_ontology short term object recognition memory 2011-04-14T02:09:28Z George Gkoutos behavior_ontology visual short term memory 2011-04-14T02:10:17Z George Gkoutos behavior_ontology spatial working memory "A type of memory responsible for recording information about one's environment and its spatial orientation." [wikipedia:Spatial_memory] 2011-04-14T02:14:26Z George Gkoutos behavior_ontology 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] 2011-04-14T02:17:28Z George Gkoutos behavior_ontology short term spatial memory 2011-04-14T02:19:43Z George Gkoutos behavior_ontology long term spatial memory Behavior related to the activity in which a mother cleans or maintains the body or the appearance of her offsprings. 2011-04-14T07:58:09Z George Gkoutos behavior_ontology maternal grooming Behavior related to the activity in which a mother cleans or maintains the body or the appearance of her offsprings. NBO:GVG Behavior relating to the plucking of fur/hair or whiskers/vibrissae. 2011-04-14T08:03:48Z George Gkoutos behavior_ontology barbering behavior Behavior relating to the plucking of fur/hair or whiskers/vibrissae. NBO:GVG Behavior related to the barbering of other individuals of a cohort. 2011-04-14T08:04:13Z George Gkoutos NBO:0000083 whisker trimming behavior_ontology MP:0001446 hetero-barbering Behavior related to the barbering of other individuals of a cohort. NBO:GVG Behavior related to the barbering of oneself. 2011-04-14T08:05:32Z George Gkoutos behavior_ontology self-barbering Behavior related to the barbering of oneself. NBO:GVG A pathological behavior characterized by muscular rigidity and fixation of posture regardless of external stimuli, as well as decreased sensitivity to pain. 2011-04-14T08:14:28Z George Gkoutos behavior_ontology MP:0002822 catalepsy A pathological behavior characterized by muscular rigidity and fixation of posture regardless of external stimuli, as well as decreased sensitivity to pain. wikipedia:Catalepsy Observable characteristic of behavior that occurs predominantly or only, in individuals that are part of a group. 2011-04-14T08:24:37Z George Gkoutos pathological social behaviour behavior_ontology social behavior phenotype Observable characteristic of behavior that occurs predominantly or only, in individuals that are part of a group. NBO:GVG 2011-04-14T08:24:50Z George Gkoutos behavior_ontology MP:0001361 social withdrawal 2011-04-14T08:25:50Z George Gkoutos behavior_ontology social withdrawal in childhood A pathological behavior associated with repetitive or ritualistic movement, posture, or utterance. 2011-04-14T08:28:29Z George Gkoutos stereotypic behaviour stereotypy behavior_ontology HP:0000733 MP:0001408 stereotypic behavior A pathological behavior associated with repetitive or ritualistic movement, posture, or utterance. wikipedia:Stereotypy Observable characteristic of behavior related to the movement of the body's muscles, tendons, and joints. 2011-04-14T08:31:34Z George Gkoutos behavior_ontology kinesthetic behavior phenotype Observable characteristic of behavior related to the movement of the body's muscles, tendons, and joints. NBO:GVG Exhibiting abnormal exhaustion due to mental or physical exertion. 2011-04-14T08:32:15Z George Gkoutos behavior_ontology MP:0002899 fatigue Exhibiting abnormal exhaustion due to mental or physical exertion. NBO:GVG Movement of the head in the vertical plane. [NBO:GVG] 2011-04-14T08:39:38Z George Gkoutos head nodding nod head behavior_ontology head bobbing Movement of the head in multiple directions. 2011-04-14T08:43:33Z George Gkoutos behavior_ontology multidirectional head movement Movement of the head in multiple directions. NBO:GVG "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] 2011-04-14T09:01:45Z George Gkoutos behavior_ontology MP:0002571 senility 2011-04-14T09:04:45Z George Gkoutos behavior_ontology MP:0002573 behavioral despair "A reflex allows the eye to follow objects in motion when the head remains stationary." [wikipedia:Optokinetic_reflex] 2011-04-14T09:20:48Z George Gkoutos behavior_ontology 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] 2011-04-14T10:15:17Z George Gkoutos horripilation piloerection behavior_ontology pilomotor reflex A reflex that elucidates a characteristic ear twitch in response to an auditory stimulus. 2011-04-14T10:19:59Z George Gkoutos Preyer's reflex behavior_ontology pinna reflex A reflex that elucidates a characteristic ear twitch in response to an auditory stimulus. NBO:GVG A reflex that maintains body position and equilibrium either during rest or during movement. 2011-04-14T10:24:14Z George Gkoutos behavior_ontology postural reflex A reflex that maintains body position and equilibrium either during rest or during movement. NBO:GVG A reflex process in which an animal immediately tries to turn over after being placed in a supine position. 2011-04-14T10:28:56Z George Gkoutos righting response behavior_ontology righting reflex A reflex process in which an animal immediately tries to turn over after being placed in a supine position. NBO:GVG A pathological behavior characterised by pronounced startle responses to tactile or acoustic stimuli and hypertonia. 2011-04-14T10:37:34Z George Gkoutos behavior_ontology hyperekplexia A pathological behavior characterised by pronounced startle responses to tactile or acoustic stimuli and hypertonia. wikipedia:Hyperekplexia "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] 2011-04-14T10:42:28Z George Gkoutos TNR cervicospinal reflex behavior_ontology tonic neck reflex A reflex which results from activation of afferents from the vestibular organs and uses neck movements to stabilize the head position in space. 2011-04-14T10:44:18Z George Gkoutos VCR behavior_ontology vestibulocollic reflex A reflex which results from activation of afferents from the vestibular organs and uses neck movements to stabilize the head position in space. JAX: A reflex that originates with vestibular stimulation and control body posture. 2011-04-14T10:47:03Z George Gkoutos behavior_ontology vestibulospinal reflex A reflex that originates with vestibular stimulation and control body posture. NBO:GVG "Change position in response to stimulation of the whiskers." [JAX:<new dbxref>] 2011-04-14T10:52:19Z George Gkoutos vibrissa reflex behavior_ontology vibrissae reflex A mouse reflex that elicidated the clasping of front and/or hind feet almost immediately upon being lifted by tail. 2011-04-14T10:55:22Z George Gkoutos hindlimb extension reflex limb clasping limb grasping behavior_ontology clutching reflex A mouse reflex that elicidated the clasping of front and/or hind feet almost immediately upon being lifted by tail. EUROPHENOME: A form of tetanic spasm in which the head and feet are drawn forward and the spine arches backward. 2011-04-14T11:05:57Z George Gkoutos behavior_ontology MP:0009354 emprosthotonos A form of tetanic spasm in which the head and feet are drawn forward and the spine arches backward. JAX: A form of tetanic spasm in which the head, neck and spine are bent backward and the body is bowed forward. 2011-04-14T11:08:01Z George Gkoutos behavior_ontology HP:0002179 MP:0002880 opisthotonus A form of tetanic spasm in which the head, neck and spine are bent backward and the body is bowed forward. JAX: A sudden, involuntary contraction of a muscle or group of muscles associated with strychnine poisoning and tetanus. 2011-04-14T11:09:10Z George Gkoutos behavior_ontology tetanic spasm A sudden, involuntary contraction of a muscle or group of muscles associated with strychnine poisoning and tetanus. NBO:GVG A sudden, involuntary contraction of a muscle or group of muscles. 2011-04-14T11:10:55Z George Gkoutos behavior_ontology spasm A sudden, involuntary contraction of a muscle or group of muscles. NBO:GVG An involuntary rhythmical, oscillatory movement of a body part. 2011-04-14T11:13:39Z George Gkoutos quivering shivering trembling behavior_ontology HP:0001337 MP:0000745 tremor An involuntary rhythmical, oscillatory movement of a body part. NBO:GVG Inability to coordinate voluntary muscular movements. 2011-04-14T11:25:59Z George Gkoutos behavior_ontology HP:0001251 MP:0001393 ataxia Inability to coordinate voluntary muscular movements. NBO:GVG 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. 2011-04-14T11:32:30Z George Gkoutos behavior_ontology motor coordination phenotype 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. NBO:GVG Lack of coordination of movement typified by the undershoot or overshoot of intended position with the hand, arm, leg, or eye. 2011-04-14T11:33:13Z George Gkoutos behavior_ontology MP:0003314 dysmetria Lack of coordination of movement typified by the undershoot or overshoot of intended position with the hand, arm, leg, or eye. wikipedia:Dysmetria Overshooting the intended position. 2011-04-14T11:34:23Z George Gkoutos behavior_ontology hypermetria Overshooting the intended position. wikipedia:Dysmetria Undershooting the intended position. 2011-04-14T11:34:31Z George Gkoutos behavior_ontology hypometria Undershooting the intended position. wikipedia:Dysmetria Observable characteristic of behavior related with the Intentionally or habitually assumed arrangement of the body and its limbs. 2011-04-14T11:37:02Z George Gkoutos behavior_ontology posture phenotype Observable characteristic of behavior related with the Intentionally or habitually assumed arrangement of the body and its limbs. NBO:GVG "Posture distinguished by a faltering gait while walking and/or a swaying motion of the trunk or head while resting." [JAX:<new dbxref>] 2011-04-14T11:37:27Z George Gkoutos behavior_ontology MP:0009514 titubation Loss of power of voluntary movement in the muscles of the hindlimb through injury or disease of it or its nerve supply. 2011-04-14T01:20:30Z George Gkoutos behavior_ontology MP:0000755 hindlimb paralysis Loss of power of voluntary movement in the muscles of the hindlimb through injury or disease of it or its nerve supply. JAX: A locomotory disorder in which sustained muscle contractions cause twisting and repetitive movements or abnormal postures. 2011-04-14T01:24:20Z George Gkoutos behavior_ontology HP:0001332 MP:0005323 dystonia A locomotory disorder in which sustained muscle contractions cause twisting and repetitive movements or abnormal postures. wikipedia:Dystonia A type of memory that allows one to store and manage information about one's environment and its spatial orientation lasting hours to months. 2011-04-14T01:43:30Z George Gkoutos behavior_ontology long-term spatial memory A type of memory that allows one to store and manage information about one's environment and its spatial orientation lasting hours to months. NBO:GVG "Agitation characterised by a series of unintentional and purposeless motions that stem from mental tension and anxiety of an individual." [wikipedia:Psychomotor_agitation] 2011-04-14T03:03:58Z George Gkoutos behavior_ontology psychomotor agitation behavior 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. 2011-04-14T03:07:16Z George Gkoutos behavior_ontology emotional behavior phenotype 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. NBO:GVG "Exhibiting indifference, or suppression of emotions such as concern, excitement, motivation and passion." [wikipedia:Indifference_(emotion)] 2011-04-14T03:07:51Z George Gkoutos impassivity perfunctoriness behavior_ontology HP:0000741 apathy A belief that is either mistaken or not substantiated that is held with vehemence. 2011-04-14T03:20:48Z George Gkoutos behavior_ontology HP:0000746 delusion A belief that is either mistaken or not substantiated that is held with vehemence. wikipedia:Delusion "A social behavior characterised by conscious or unconscious constraint of a behavior that might be considered objectionable in a social setting." [wikipedia:Social_inhibition] 2011-04-14T03:33:25Z George Gkoutos behavior_ontology 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] 2011-04-14T03:34:29Z George Gkoutos behavior_ontology sexual inhibition Loss of information already encoded and stored in an individual's long term memory. 2011-04-14T03:42:46Z George Gkoutos pathological forgetting retention loss behavior_ontology HP:0000747 forgetfulness Loss of information already encoded and stored in an individual's long term memory. wikipedia:Forgetting Behaviour related to cognitive processes. 2011-04-14T03:51:13Z George Gkoutos behavior_ontology cognitive behavior Behaviour related to cognitive processes. NBO:JH Perception in the absence of a stimulus. 2011-04-14T03:52:31Z George Gkoutos behavior_ontology HP:0000738 hallucination Perception in the absence of a stimulus. wikipedia:Hallucination A form of hallucination that involves perceiving images without visual stimulus. 2011-04-14T03:54:02Z George Gkoutos paracusia behavior_ontology HP:0008765 visual hallucination A form of hallucination that involves perceiving images without visual stimulus. NBO:GVG "A form of hallucination that involves perceiving sounds without auditory stimulus." [wikipedia:Auditory_hallucination] 2011-04-14T03:56:24Z George Gkoutos behavior_ontology HP:0002367 auditory hallucination A form of hallucination that involves perceiving odors without odor stimulus. 2011-04-14T03:58:15Z George Gkoutos phantosmia behavior_ontology olfactory hallucination A form of hallucination that involves perceiving odors without odor stimulus. NBO:GVG A social behavior related to the activity of conveying information. 2011-04-14T04:39:42Z George Gkoutos communicating signal exchange behavior_ontology communication behavior A social behavior related to the activity of conveying information. wikipedia:Communication "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] 2011-04-14T04:40:59Z George Gkoutos non-verbal communication behaviour nonverbal communication behaviour behavior_ontology nonverbal communication behavior "Communication behavior related to the conveyance of ideas and information through creation of visual representations." [wikipedia:Visual_communication] 2011-04-14T04:42:57Z George Gkoutos behavior_ontology visual communication behavior "Communication behavior related to the process of conveying meaning in the form of word messages." [wikipedia:Oral_communication#Oral_communication] 2011-04-14T04:44:04Z George Gkoutos behavior_ontology oral communication behavior "A nonverbal communication behavior that is characterised by the meeting the eyes between two individuals." [wikipedia:Eye_contact] 2011-04-14T04:46:09Z George Gkoutos behavior_ontology eye contact 2011-04-14T04:51:05Z George Gkoutos behavior_ontology laughing behavior The behavior in which an organism sheds tears, often accompanied by non-verbal vocalizations and in response to external or internal stimuli. 2011-04-14T04:52:56Z George Gkoutos crying behaviour behavior_ontology GO:0060273 crying behavior The behavior in which an organism sheds tears, often accompanied by non-verbal vocalizations and in response to external or internal stimuli. NBO:GVG Behavior stemming from understanding of a specific cause and effect in a specific context. 2011-04-14T04:57:19Z George Gkoutos behavior_ontology behavior stemming from insight Behavior stemming from understanding of a specific cause and effect in a specific context. wikipedia:Insight An emotional behavior that arises from the perceived resistance to the fulfillment of individual will. 2011-04-14T05:00:59Z George Gkoutos behavior_ontology frustration behavior An emotional behavior that arises from the perceived resistance to the fulfillment of individual will. wikipedia:Frustration "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] 2011-04-14T05:06:03Z George Gkoutos behavior_ontology HP:0002300 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] 2011-04-14T05:18:30Z George Gkoutos behavior_ontology HP:0008758 stereotypic motor behavior Stereotypic behavior characterised by a tendency to repeat vocalizations. 2011-04-14T05:20:29Z George Gkoutos behavior_ontology HP:0010529 echolalia Stereotypic behavior characterised by a tendency to repeat vocalizations. NBO:GVG Play behavior associated with the manipulation of objects. 2011-04-19T10:51:54Z George Gkoutos behavior_ontology Object play is important in developing skills important in adulthood, especially hunting. object play Play behavior associated with the manipulation of objects. NBO:GVG "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] 2011-04-19T10:52:50Z George Gkoutos love play behavior_ontology sexual play "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] 2011-04-19T10:53:55Z George Gkoutos behavior_ontology 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 fight Play behavior that is associated with the pursuit of an individual. 2011-04-19T10:54:09Z George Gkoutos behavior_ontology play chasing Play behavior that is associated with the pursuit of an individual. NBO:GVG Play behavior associated with the exhibition of parenting behavior by non-parents. 2011-04-19T11:03:02Z George Gkoutos behavior_ontology nursing play Play behavior associated with the exhibition of parenting behavior by non-parents. NBO:GVG "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] 2011-04-19T11:07:20Z George Gkoutos behavior_ontology 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. imitative play Harassment of and-or attack of a presumed predator or intruder by multiple individuals at once [NBO:SMAC] 2011-04-19T01:44:21Z George Gkoutos mobbing behavior_ontology mobbing behavior "Behavior associated with signals made by the mobbing species while harassing a predator." [wikipedia:Mobbing_(animal_behavior)] 2011-04-19T01:46:33Z George Gkoutos behavior_ontology mobbing calling Aggressive behavior related to the defence of a fixed area against intruders, typically conspecifics. 2011-04-19T02:02:11Z George Gkoutos territorial aggression territorial aggressive behaviour behavior_ontology GO:0002124 territorial aggressive behavior Aggressive behavior related to the defence of a fixed area against intruders, typically conspecifics. GOC:hjd 2011-04-19T02:05:35Z George Gkoutos behavior_ontology irritable aggressive behavior "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] 2011-04-19T03:36:00Z George Gkoutos behavior_ontology avoidance behavior Behavior related to the activity seen in animals exposed to potential danger in which they exhibit the tendency to act defensively. 2011-04-19T03:49:55Z George Gkoutos defense defensive behaviour behavior_ontology protective behavior Behavior related to the activity seen in animals exposed to potential danger in which they exhibit the tendency to act defensively. NBO:SD The actions or reactions of a male, for the purpose of attracting a sexual partner. 2011-04-21T08:40:33Z George Gkoutos male courtship behaviour behavior_ontology GO:0008049 male courtship behavior The actions or reactions of a male, for the purpose of attracting a sexual partner. GOC:bf The actions or reactions of a female, for the purpose of attracting a sexual partner. 2011-04-21T08:42:23Z George Gkoutos female courtship behaviour behavior_ontology GO:0008050 female courtship behavior The actions or reactions of a female, for the purpose of attracting a sexual partner. GOC:bf Any process which modulates the physical craving for water over long term water deprivation. 2011-04-21T09:06:28Z George Gkoutos behavior_ontology long term thirst regulation Any process which modulates the physical craving for water over long term water deprivation. NBO:GVG Any process which modulates the physical craving for water over short term water deprivation. 2011-04-21T09:06:40Z George Gkoutos behavior_ontology short term thirst regulation Any process which modulates the physical craving for water over short term water deprivation. NBO:GVG 2011-05-06T03:56:31Z George Gkoutos behavior_ontology discrimination learning Two or more unprovoked recurrent seizures. 2011-05-27T11:42:33Z George Gkoutos unprovoked seizure behavior_ontology HP:0001275 epilepsy Two or more unprovoked recurrent seizures. NBO:GVG Observable characteristic of behavior related to movements that occur independent of planning. 2011-05-27T11:56:52Z George Gkoutos behavior_ontology involuntary movement behavior phenotype Observable characteristic of behavior related to movements that occur independent of planning. NBO:GVG Observable characteristic of behavior related to movements executed with intent. 2011-05-27T11:57:12Z George Gkoutos behavior_ontology voluntary movement behavior phenotype Observable characteristic of behavior related to movements executed with intent. NBO:GVG A rapid and repeated body muscle contract that results in an uncontrolled shaking of the body. 2011-05-27T11:59:40Z George Gkoutos fit behavior_ontology convulsion A rapid and repeated body muscle contract that results in an uncontrolled shaking of the body. NBO:GVG "A seizure which affect only a part of the brain at onset." [wikipedia:http\://en.wikipedia.org/wiki/Focal_seizures] 2011-05-27T12:49:09Z George Gkoutos focal seizure localized seizure behavior_ontology HP:0007359 Partial seizures begin with an electrical discharge in one limited area of the brain. partial seizure "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] 2011-05-27T12:51:40Z George Gkoutos behavior_ontology HP:0002349 Depending on the area of cerebral cortex involved, symptoms may be motor, cognitive, sensory, autonomic, or affective. Consciousness is not impaired. simple partial seizure "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] 2011-05-27T12:59:01Z George Gkoutos psychomotor seizure temporal lobe seizure behavior_ontology HP:0002384 MP:0002195 complex partial seizure 2011-05-27T01:51:38Z George Gkoutos behavior_ontology being conscious "A type of focal epilepsy characterized by recurrent seizures." [NBO:http\://en.wikipedia.org/wiki/Temporal_lobe_epilepsy] 2011-05-27T02:42:59Z George Gkoutos psychomotor epilepsy behavior_ontology temporal lobe epilepsy A simple partial seizure affecting the kinesthetic behavior. 2011-05-27T02:50:59Z George Gkoutos focal clonic seizure motor seizure behavior_ontology HP:0002266 simple partial seizure with motor signs A simple partial seizure affecting the kinesthetic behavior. NBO:GVG A simple partial seizure affecting any of the five senses -- vision, touch, smell, taste, and hearing. 2011-05-27T02:51:16Z George Gkoutos Jacksonian sensory seizure sensory seizure behavior_ontology 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 any of the five senses -- vision, touch, smell, taste, and hearing. NBO:GVG A simple partial seizure affecting the part of the nervous system that automatically controls bodily functions. 2011-05-27T02:51:31Z George Gkoutos abdominal epilepsy autonomic seizure behavior_ontology 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 part of the nervous system that automatically controls bodily functions. NBO:GVG A simple partial seizure affecting the emotional behavior. 2011-05-27T02:51:48Z George Gkoutos psychic seizure simple partial seizures of temporal lobe origin temporal lobe auras behavior_ontology 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 A simple partial seizure affecting the emotional behavior. NBO:GVG Observable characteristic of behavior related any of the five senses -- vision, touch, smell, taste, and hearing. 2011-05-27T03:06:17Z George Gkoutos behavior_ontology sensation behavior phenotype Observable characteristic of behavior related any of the five senses -- vision, touch, smell, taste, and hearing. NBO:GVG A phenotype manifested by a behavior related to the sensations arising from the skin and from the muscles, tendons, and joints. 2011-05-27T03:20:39Z George Gkoutos behavior_ontology somatic sensation related behavior phenotype A phenotype manifested by a behavior related to the sensations arising from the skin and from the muscles, tendons, and joints. NBO:GVG 2011-05-27T03:21:20Z George Gkoutos behavior_ontology cutaneous sensation behavior phenotype Observable characteristic of behavior related to the actions or reactions of an organism in response to a sound. 2011-05-27T03:22:16Z George Gkoutos behavior_ontology auditory behavior phenotype Observable characteristic of behavior related to the actions or reactions of an organism in response to a sound. NBO:GVG A phenotype manifested by a behavior related to the actions or reactions of an organism in response to a visual stimulus. 2011-05-27T03:22:59Z George Gkoutos behavior_ontology visual behavior phenotype A phenotype manifested by a behavior related to the actions or reactions of an organism in response to a visual stimulus. NBO:GVG Observable characteristic of behavior related to the sensation of chemicals. 2011-05-27T03:26:33Z George Gkoutos behavior_ontology chemosensory behavior phenotype Observable characteristic of behavior related to the sensation of chemicals. NBO:GVG Observable characteristic of behavior related to the sensation of odors. 2011-05-27T03:28:54Z George Gkoutos behavior_ontology olfactory behavior phenotype Observable characteristic of behavior related to the sensation of odors. NBO:GVG A seizure which affect the whole of the brain at onset. 2011-05-27T03:46:46Z George Gkoutos primarily generalized seizure behavior_ontology HP:0002197 Primary generalized seizures begin with a widespread electrical discharge that involves both sides of the brain at once. generalized seizure A seizure which affect the whole of the brain at onset. NBO:GVG 2011-05-27T03:49:54Z George Gkoutos behavior_ontology HP:0007334 partial seizure evolving to secondarily generalized seizure 2011-05-27T03:50:07Z George Gkoutos behavior_ontology simple partial seizure evolving to generalized seizure 2011-05-27T03:50:26Z George Gkoutos behavior_ontology complex partial seizure evolving to generalized seizure 2011-05-27T03:50:49Z George Gkoutos behavior_ontology simple partial seizure evolving to complex partial seizure evolving to generalized seizure 2011-05-27T03:51:50Z George Gkoutos behavior_ontology simple partial onset, followed by impairment of consciousness 2011-05-27T03:52:02Z George Gkoutos behavior_ontology 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] 2011-05-27T03:54:48Z George Gkoutos petit mal seizure behavior_ontology HP:0002121 MP:0003216 absence seizures "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] 2011-05-27T03:57:35Z George Gkoutos akinetic seizure drop attack drop seizure behavior_ontology HP:0010819 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. 2011-05-27T04:52:23Z George Gkoutos myoclonus behavior_ontology HP:0001336 HP:0002123 MP:0000243 Symmetric jerking of the extremities. myoclonic 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. NBO:GVG A type of seizure that is characterised by rhythmic symmetric alternating contraction and relaxation of a muscle or a group of muscles. 2011-05-27T04:54:59Z George Gkoutos behavior_ontology MP:0003996 Rapid, repetitive motor activity. clonic seizure A type of seizure that is characterised by rhythmic symmetric alternating contraction and relaxation of a muscle or a group of muscles. NBO:GVG A type of epilepsy characterised by myoclonic seizures usually involving the neck, shoulders, and upper arms. 2011-05-27T04:55:32Z George Gkoutos Janz syndrome behavior_ontology juvenile myoclonic epilepsy A type of epilepsy characterised by myoclonic seizures usually involving the neck, shoulders, and upper arms. NBO:GVG A type of epilepsy characterised by multiple different types of seizures, particularly including tonic (stiffening) and atonic (drop) types of seizures. 2011-05-27T04:56:28Z George Gkoutos behavior_ontology Lennox-Gastaut syndrome A type of epilepsy characterised by multiple different types of seizures, particularly including tonic (stiffening) and atonic (drop) types of seizures. NBO:GVG A type of seizure generated by sudden sensor stimulation caused by the environment. 2011-05-28T11:07:41Z George Gkoutos environmental epilepsy reflex epilepsy behavior_ontology MP:0009358 reflex seizure A type of seizure generated by sudden sensor stimulation caused by the environment. NBO:GVG A type of generalized seizure characterised by a combination of tonic stiffening (extensions) followed by clonic flexion motions. 2011-05-27T05:03:11Z George Gkoutos gran mal seizure grand mal seizure behavior_ontology HP:0002069 MP:0003997 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. tonic clonic seizure A type of generalized seizure characterised by a combination of tonic stiffening (extensions) followed by clonic flexion motions. NBO:GVG A type of seizure characterised by muscle rigidity. 2011-05-27T05:09:15Z George Gkoutos behavior_ontology HP:0010818 MP:0002826 tonic seizure A type of seizure characterised by muscle rigidity. NBO:GVG "A type of seizure associated with a significant rise in body temperature." [wikpedia:http\://en.wikipedia.org/wiki/Febrile_seizure] 2011-05-27T05:13:26Z George Gkoutos febrile convulsion fever fit behavior_ontology HP:0002373 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] 2011-05-27T05:16:07Z George Gkoutos behavior_ontology simple 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] 2011-05-27T05:19:54Z George Gkoutos behavior_ontology complex 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] 2011-05-27T05:24:49Z George Gkoutos benign (childhood) epilepsy with centrotemporal (EEG) spikes behavior_ontology benign rolandic epilepsy "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] 2011-05-27T05:30:25Z George Gkoutos MTLE behavior_ontology medial 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] 2011-05-27T05:31:27Z George Gkoutos LTLE behavior_ontology lateral temporal lobe epilepsy 2011-05-27T05:32:59Z George Gkoutos pyknolepsy behavior_ontology childhood absence epilepsy 2011-05-27T05:39:40Z George Gkoutos behavior_ontology continuous seizure "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] 2011-05-27T05:47:13Z George Gkoutos non-epileptic seizure behavior_ontology provoked 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] 2011-05-27T05:50:08Z George Gkoutos PNES non-epileptic attack disorder behavior_ontology psychogenic non-epileptic seizure A type of epilepsy that is characterised by myoclonic seizures. 2011-05-27T05:53:42Z George Gkoutos behavior_ontology myoclonic epilepsy A type of epilepsy that is characterised by myoclonic seizures. NBO:GVG "A myoclonic epilepsy characterised by a combination of myoclonic and tonic-clonic seizures." [wikipedia:http\://en.wikipedia.org/wiki/Progressive_myoclonic_epilepsy] 2011-05-27T05:55:29Z George Gkoutos behavior_ontology 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] 2011-05-27T05:59:47Z George Gkoutos behavior_ontology HP:0002133 status epilepticus 2011-05-27T06:42:06Z George Gkoutos behavior_ontology non-convulsive status epilepticus 2011-05-27T06:42:29Z George Gkoutos behavior_ontology 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] 2011-05-27T07:20:21Z George Gkoutos behavior_ontology complex partial status epilepticus 2011-05-27T07:21:27Z George Gkoutos behavior_ontology absence 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] 2011-05-28T10:08:42Z George Gkoutos behavior_ontology subtle status epilepticus "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] 2011-05-28T10:10:13Z George Gkoutos behavior_ontology simple partial status epilepticus "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] 2011-05-28T10:14:48Z George Gkoutos behavior_ontology frontal lobe epilepsy A type of epilepsy characterised by seizure, usually tonic clonic, that occur only during sleep. 2011-05-28T10:17:46Z George Gkoutos behavior_ontology nocturnal epilepsy A type of epilepsy characterised by seizure, usually tonic clonic, that occur only during sleep. NBO:GVG "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] 2011-05-28T11:11:25Z George Gkoutos photosensitive epilepsy behavior_ontology photosensitive seizure A type of seizure induced by exposure to an auditory stimulus. 2011-05-28T11:12:23Z George Gkoutos NBO:0000725 auditory stimulation induced seizure behavior_ontology MP:0001496 audiogenic seizure A type of seizure induced by exposure to an auditory stimulus. NBO:GVG An absence seizure induced by hyperventilation. 2011-05-28T11:59:14Z George Gkoutos behavior_ontology typical absence seizure An absence seizure induced by hyperventilation. NBO:GVG An absence seizure not induced by hyperventilation. 2011-05-28T11:59:31Z George Gkoutos behavior_ontology HP:0007270 atypical absence seizure An absence seizure not induced by hyperventilation. NBO:GVG A generalized seizure that was initiated as a partial seizure. 2011-05-28T12:08:24Z George Gkoutos behavior_ontology HP:0002434 secondary generalized seizure A generalized seizure that was initiated as a partial seizure. NBO:GVG A generalized seizure that was initiated as a partial seizure but very rapidly spread to both hemispheres. 2011-05-28T12:11:05Z George Gkoutos behavior_ontology rapid secondary generalization A generalized seizure that was initiated as a partial seizure but very rapidly spread to both hemispheres. NBO:GVG Purposeless repetitive motor activities that often occur during a seizure. 2011-05-28T12:14:35Z George Gkoutos behavior_ontology Automatisms may occur during complex partial or absence seizures. automatism Purposeless repetitive motor activities that often occur during a seizure. NBO:GVG An automatism characterised by involuntary oral activity such as lip smacking and swallowing. 2011-05-28T12:15:48Z George Gkoutos behavior_ontology oral automatism An automatism characterised by involuntary oral activity such as lip smacking and swallowing. NBO:GVG An automatism characterised by involuntary movement of the limbs or body such as fumbling, picking and rubbing. 2011-05-28T12:17:42Z George Gkoutos behavior_ontology gestural automatism An automatism characterised by involuntary movement of the limbs or body such as fumbling, picking and rubbing. NBO:GVG An automatism characterised by stereotyped series of motor actions usually involving the limbs bilaterally such as swimming \nmovements, kicking movements and bicycling movements. 2011-05-28T12:20:03Z George Gkoutos behavior_ontology complex motor automatism An automatism characterised by stereotyped series of motor actions usually involving the limbs bilaterally such as swimming \nmovements, kicking movements and bicycling movements. NBO:GVG A type of seizure induced by the administration of a drug. 2011-05-28T12:32:11Z George Gkoutos behavior_ontology drug induced seizure A type of seizure induced by the administration of a drug. NBO:GVG A type of seizure induced by accidental or intentional ingestion or application of a drug in quantities greater than recommended. 2011-05-28T12:34:37Z George Gkoutos behavior_ontology drug overdose induced seizure A type of seizure induced by accidental or intentional ingestion or application of a drug in quantities greater than recommended. NBO:GVG A type of seizure induced by termination of drug administration. 2011-05-28T12:35:22Z George Gkoutos behavior_ontology drug withdrawal induced seizure A type of seizure induced by termination of drug administration. NBO:GVG A type of seizure induced by lower than normal level of blood glucose levels. 2011-05-28T12:35:56Z George Gkoutos behavior_ontology HP:0002173 hypoglycemia induced seizure A type of seizure induced by lower than normal level of blood glucose levels. GVG:NBO A type of seizure induced by the administration of cocaine. 2011-05-28T12:36:15Z George Gkoutos behavior_ontology cocaine overdose induced seizure A type of seizure induced by the administration of cocaine. NBO:GVG A type of seizure induced by the administration of isoniazide. 2011-05-28T12:36:46Z George Gkoutos behavior_ontology isoniazide overdose induced seizure A type of seizure induced by the administration of isoniazide. NBO:GVG A type of seizure induced by the administration of amphetamine. 2011-05-28T12:37:01Z George Gkoutos behavior_ontology amphetamine overdose induced seizure A type of seizure induced by the administration of amphetamine. NBO:GVG A type of seizure induced by the administration of antidepressant. 2011-05-28T01:14:12Z George Gkoutos behavior_ontology antidepressant overdose induced seizure A type of seizure induced by the administration of antidepressant. NBO:GVG A type of seizure induced by the administration of theophylline. 2011-05-28T01:15:33Z George Gkoutos behavior_ontology theophylline overdose induced seizure A type of seizure induced by the administration of theophylline. NBO:GVG A type of seizure induced by the administration of penicillin. 2011-05-28T01:16:56Z George Gkoutos behavior_ontology penicillin overdose induced seizure A type of seizure induced by the administration of penicillin. NBO:GVG A type of seizure induced by termination of alcohol administration. 2011-05-28T01:19:06Z George Gkoutos behavior_ontology alcohol withdrawal induced seizure A type of seizure induced by termination of alcohol administration. NBO:GVG A type of seizure induced by termination of benzodiazepine administration. 2011-05-28T01:22:57Z George Gkoutos behavior_ontology benzodiazepine withdrawal induced seizure A type of seizure induced by termination of benzodiazepine administration. NBO:GVG A type of seizure induced by termination of barbiturates administration. 2011-05-28T01:24:25Z George Gkoutos behavior_ontology barbiturates withdrawal induced seizure A type of seizure induced by termination of barbiturates administration. NBO:GVG A type of seizure induced by termination of heroin administration. 2011-05-28T01:26:05Z George Gkoutos behavior_ontology heroin withdrawal induced seizure A type of seizure induced by termination of heroin administration. NBO:GVG A type of seizure induced by lower than normal level of blood magnesium levels. 2011-05-28T01:34:40Z George Gkoutos behavior_ontology hypomagnesemia induced seizure A type of seizure induced by lower than normal level of blood magnesium levels. NBO:GVG A type of seizure induced by exposure to an electrical stimulus. 2011-05-28T01:42:36Z George Gkoutos behavior_ontology electrical stimulation induced seizure A type of seizure induced by exposure to an electrical stimulus. NBO:GVG A type of seizure induced by the administration of a brain trauma. 2011-05-28T03:39:02Z George Gkoutos behavior_ontology trauma induced seizure A type of seizure induced by the administration of a brain trauma. NBO:GVG A type of seizure induced by kindling, a repeated administration of seizure invoking stimulus which eventually results changes in the brain. 2011-05-28T03:46:52Z George Gkoutos behavior_ontology kindling induced seizure A type of seizure induced by kindling, a repeated administration of seizure invoking stimulus which eventually results changes in the brain. NBO:GVG A type of seizure induced by kindling, a repeated administration of electrical stimulus which eventually results changes in the brain. 2011-05-28T03:50:30Z George Gkoutos behavior_ontology electrical kindling induced seizure A type of seizure induced by kindling, a repeated administration of electrical stimulus which eventually results changes in the brain. NBO:GVG A type of seizure induced by kindling, a repeated administration of chemical stimulus which eventually results changes in the brain. 2011-05-28T03:51:25Z George Gkoutos behavior_ontology chemical kindling induced seizure A type of seizure induced by kindling, a repeated administration of chemical stimulus which eventually results changes in the brain. NBO:GVG A type of seizure induced by kindling, a repeated administration of auditory stimulus which eventually results changes in the brain. 2011-05-28T03:52:15Z George Gkoutos behavior_ontology auditory kindling induced seizure A type of seizure induced by kindling, a repeated administration of auditory stimulus which eventually results changes in the brain. NBO:GVG A simple partial seizure affecting the kinesthetic behavior of one side of the body. 2011-05-28T05:51:10Z George Gkoutos unilateral clonic seizure behavior_ontology HP:0006813 hemiclonic seizure A simple partial seizure affecting the kinesthetic behavior of one side of the body. NBO:GVG A simple partial seizure affecting the kinesthetic behavior of left side of the body. 2011-05-28T06:01:58Z George Gkoutos behavior_ontology left side clonic seizure A simple partial seizure affecting the kinesthetic behavior of left side of the body. NBO:GVG A simple partial seizure affecting the kinesthetic behavior of right side of the body. 2011-05-28T06:03:17Z George Gkoutos behavior_ontology right side clonic seizure A simple partial seizure affecting the kinesthetic behavior of right side of the body. NBO:GVG A type of epileptic seizures occurring in infants and characterised by clusters of myoclonic spasms. 2011-05-28T06:47:31Z George Gkoutos Generalized Flexion Epilepsy Infantile Epileptic Encephalopathy Infantile Myoclonic Encephalopathy Massive Myoclonia Salaam spasms West syndrome jackknife convulsions behavior_ontology HP:0002391 HP:0011097 infantile spasm A type of epileptic seizures occurring in infants and characterised by clusters of myoclonic spasms. NBO:GVG A type of seizure induced by lower than normal level of blood calcium levels. 2011-05-28T08:04:53Z George Gkoutos behavior_ontology HP:0002199 hypocalcemia induced seizure A type of seizure induced by lower than normal level of blood calcium levels. NBO:GVG A generalized tonic clonic seizure that was initiated as a partial seizure. 2011-05-28T08:28:12Z George Gkoutos behavior_ontology HP:0002602 secondary generalized tonic clonic seizure A generalized tonic clonic seizure that was initiated as a partial seizure. NBO:GVG A type of seizure induced by exposure to a light stimulus. 2011-05-28T08:34:10Z George Gkoutos behavior_ontology HP:0001327 photostimulation induced seizure A type of seizure induced by exposure to a light stimulus. NBO:GVG A type of epilepsy that is characterised a sudden burst of energy, usually in the form of laughing. 2011-05-28T11:12:42Z George Gkoutos gelastic seizure behavior_ontology HP:0010821 gelastic epilepsy A type of epilepsy that is characterised a sudden burst of energy, usually in the form of laughing. NBO:GVG "A type of epilepsy that is characterised a sudden paroxysmal crying." [NBO:<new dbxref>, NBO:GVG] 2011-05-28T11:18:45Z George Gkoutos dacrystic seizure behavior_ontology HP:0010820 dacrystic epilepsy 2012-02-16T01:16:13Z gkoutos behavior_ontology aggressive behavior by intent 2012-02-16T01:16:31Z gkoutos behavior_ontology aggressive behavior by means Agressive behavior towards oneself. 2012-02-16T01:16:55Z gkoutos behavior_ontology autoaggressive behavior Agressive behavior towards oneself. NBO:GVG An aggressive behavior towards other members of the society. 2012-02-16T02:27:08Z gkoutos behavior_ontology social aggression behavior An aggressive behavior towards other members of the society. NBO:RH 2012-03-16T04:51:23Z gkoutos behavior_ontology perception behavior phenotype 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. 2012-03-16T05:13:17Z gkoutos behavior_ontology language communication behavior 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. NBO:GVG 2012-03-16T05:57:42Z gkoutos behavior_ontology spatial perception 2012-03-17T09:51:17Z gkoutos behavior_ontology jaw movement The act of displacing part or all of the tongue from its current position [NBO:SMAC] 2012-03-17T09:52:25Z gkoutos behavior_ontology tongue movement 2012-03-17T09:53:29Z gkoutos behavior_ontology blinking 2012-03-17T09:54:30Z gkoutos behavior_ontology eyelid movement 2012-03-16T05:23:06Z gkoutos behavior_ontology perception behavior by means 2012-03-17T03:59:12Z gkoutos behavior_ontology electrical nociceptive behavior Observable characteristic of behavior related to all sleep stages in the circadian sleep/wake cycle other than REM sleep. 2012-03-19T10:59:20Z gkoutos behavior_ontology non-rapid eye movement sleep behavior phenotype Observable characteristic of behavior related to all sleep stages in the circadian sleep/wake cycle other than REM sleep. NBO:GVG 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. 2012-03-19T11:08:01Z gkoutos behavior_ontology rapid eye movement sleep 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. NBO:GVG Observable characteristic of behavior related to the actions or interactions of an organism that are associated with reproduction. 2012-03-19T02:08:56Z gkoutos behavior_ontology reproductive behavior phenotype Observable characteristic of behavior related to the actions or interactions of an organism that are associated with reproduction. NBO:GVG Observable characteristic of behavior related to the interactions between organisms for the purpose of mating. 2012-03-19T02:10:16Z gkoutos behavior_ontology mating behavior phenotype Observable characteristic of behavior related to the interactions between organisms for the purpose of mating. NBO:GVG Observable characteristic of behavior related to the specific actions or reactions of an organism following mating. 2012-03-19T02:10:27Z gkoutos behavior_ontology post-mating behavior phenotype Observable characteristic of behavior related to the specific actions or reactions of an organism following mating. NBO:GVG Observable characteristic of behavior related to the activity which primary purpose is the sexual reproduction. 2012-03-19T02:10:54Z gkoutos behavior_ontology sexual activity phenotype Observable characteristic of behavior related to the activity which primary purpose is the sexual reproduction. NBO:GVG Observable characteristic related to the behavioral interactions between organisms for the purpose of attracting sexual partners. 2012-03-19T02:13:54Z gkoutos behavior_ontology courtship behavior phenotype Observable characteristic related to the behavioral interactions between organisms for the purpose of attracting sexual partners. NBO:GVG Observable characteristic of behavior related to the actions or reactions of a female, for the purpose of attracting a sexual partner. 2012-03-19T02:16:31Z gkoutos behavior_ontology female courtship behavior phenotype Observable characteristic of behavior related to the actions or reactions of a female, for the purpose of attracting a sexual partner. NBO:GVG Observable characteristic of behavior related to the actions or reactions of a male, for the purpose of attracting a sexual partner. 2012-03-19T02:16:49Z gkoutos behavior_ontology male courtship behavior phenotype Observable characteristic of behavior related to the actions or reactions of a male, for the purpose of attracting a sexual partner. NBO:GVG Observable characteristic of behavior related to the act of sexual union between male and female, involving the transfer of sperm. 2012-03-19T02:22:41Z gkoutos behavior_ontology copulation phenotype Observable characteristic of behavior related to the act of sexual union between male and female, involving the transfer of sperm. NBO:GVG Observable characteristic of behavior related to the female activity which primary purpose is the sexual reproduction. 2012-03-19T02:22:53Z gkoutos behavior_ontology female sexual activity phenotype Observable characteristic of behavior related to the female activity which primary purpose is the sexual reproduction. NBO:GVG Observable characteristic of behavior related to the male activity which primary purpose is the sexual reproduction. 2012-03-19T02:23:03Z gkoutos behavior_ontology male sexual activity phenotype Observable characteristic of behavior related to the male activity which primary purpose is the sexual reproduction. NBO:GVG Observable characteristic of behaviour related to the acquisition and processing of information and/or the storage and retrieval of this information over time. 2012-03-19T02:33:56Z gkoutos behavior_ontology learning and/or memory behavior phenotype Observable characteristic of behaviour related to the acquisition and processing of information and/or the storage and retrieval of this information over time. NBO:GVG 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. 2012-03-19T02:34:12Z gkoutos behavior_ontology learning 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. NBO:GVG Observable characteristic of behaviour related to the ability of an organism's ability to store, retain, and recall information and experiences. 2012-03-19T02:34:26Z gkoutos behavior_ontology memory behavior phenotype Observable characteristic of behaviour related to the ability of an organism's ability to store, retain, and recall information and experiences. NBO:GVG 2012-03-19T03:46:31Z gkoutos behavior_ontology emission behavior phenotype 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. 2012-03-19T03:46:55Z gkoutos behavior_ontology behavioral control of excretion phenotype 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. NBO:GVG Observable characteristic of behaviour related to the expulsion of feces from the rectum. 2012-03-19T03:47:09Z gkoutos behavior_ontology behavioral control of defecation phenotype Observable characteristic of behaviour related to the expulsion of feces from the rectum. NBO:GVG 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. 2012-03-19T03:48:16Z gkoutos behavior_ontology behavioral control of urination 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. NBO:GVG 2012-03-20T05:24:59Z gkoutos behavior_ontology behavioral control of production of sound phenotype 2012-03-20T05:25:03Z gkoutos behavior_ontology 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. 2012-03-20T05:28:58Z gkoutos behavior_ontology behavioral control of lacrimation phenotype Observable characteristic of behaviour related to the regulated release of the aqueous layer of the tear film from the lacrimal glands. NBO:GVG Observable characteristic of behaviour in which an organism sheds tears, often accompanied by non-verbal vocalizations and in response to external or internal stimuli. 2012-03-20T05:30:38Z gkoutos behavior_ontology crying behavior 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. NBO:GVG Observable characteristic of behaviour associated with signals made by the mobbing species while harassing a predator. 2012-03-20T05:32:31Z gkoutos behavior_ontology mobbing calling phenotype Observable characteristic of behaviour associated with signals made by the mobbing species while harassing a predator. NBO:GVG Observable characteristic of behaviour in which an organism produces sounds by a mechanism involving its respiratory system. 2012-03-20T05:34:04Z gkoutos behavior_ontology vocalization behavior phenotype Observable characteristic of behaviour in which an organism produces sounds by a mechanism involving its respiratory system. NBO:GVG 2012-03-23T10:05:56Z gkoutos behavior_ontology emotional conditioning 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. George Gkoutos behavioral response to radiation Behavior as a result of an electromagnetic radiation stimulus. NBO:GVG Behavior as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. George Gkoutos behavioral response to light Behavior as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light. NBO:GVG Behavior as a result of a chemical stimulus. George Gkoutos behavioral response to chemical stimulus Behavior as a result of a chemical stimulus. NBO:GVG Behavior as a result of a xenobiotic compound (compound foreign to living organisms) stimulus. George Gkoutos behavioral response to xenobiotics Behavior as a result of a xenobiotic compound (compound foreign to living organisms) stimulus. NBOC:GVG Behavior as a result of sensitivity to an addictive substance intake. George Gkoutos behavioral response to addictive substance Behavior as a result of sensitivity to an addictive substance intake. NBOC:GVG Behavior as a result of sensitivity to cocaine alcohol. behavioral response to alcohol Behavior as a result of sensitivity to cocaine alcohol. NBOC:GVG "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] George Gkoutos 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. George Gkoutos regulation of alcohol consumption 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. NBOC:GVG Behavior related to the intake of substances. George Gkoutos ingest consumption behavior Behavior related to the intake of substances. NBOC:GVG Behavior related to the intake of addictive substances. George Gkoutos consumption of an addictive substance Behavior related to the intake of addictive substances. NBOC:GVG Behavior related to the intake of cocaine. George Gkoutos cocaine consumption Behavior related to the intake of cocaine. NBOC:GVG Behavior related to the intake of morphine. George Gkoutos morphine consumption Behavior related to the intake of morphine. NBOC:GVG Behavior as a result of sensitivity to cocaine intake. GO:0048148 behavioral response to cocaine Behavior as a result of sensitivity to cocaine intake. NBOC:GVG Behavior as a result of sensitivity to morphine George Gkoutos behavioral response to morphine Behavior as a result of sensitivity to morphine NBOC:GVG Behavior as a result of sensitivity to nicotine intake. George Gkoutos GO:0035095 behavioral response to nicotine Behavior as a result of sensitivity to nicotine intake. NBOC:GVG Behavior related to the intake of nicotine. George Gkoutos nicotine consumption Behavior related to the intake of nicotine. NBOC:GVG 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. George Gkoutos regulation of cocaine 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. NBOC:GVG 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. George Gkoutos regulation of consumption behavior 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. NBOC:GVG 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. George Gkoutos regulation of consumption of an addictive substance 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. NBOC:GVG 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. George Gkoutos regulation of nicotine consumption 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. NBOC:GVG 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. George Gkoutos regulation of morphine 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. NBOC:GVG Behavior as a result of sensitivity to an anasthetic intake. George Gkoutos behavioral response to anesthetic Behavior as a result of sensitivity to an anasthetic intake. NBOC:GVG Maternal behavior related to the nursing offspring. nursing behavior Maternal behavior related to the nursing offspring. NBOC:GVG Any process that modulates the frequency, rate or extent of consumption of food or liquid George Gkoutos regulation of feeding behavior Any process that modulates the frequency, rate or extent of consumption of food or liquid NBOC:GVG 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. George Gkoutos regulation of water consumption 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. NBOC:GVG 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. George Gkoutos regulation of saccharin 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. NBOC:GVG A pathological drinking behavior characterised by a lack of desire to drink. George Gkoutos MP:0001428 adipsia A pathological drinking behavior characterised by a lack of desire to drink. NBO:GVG Increase in core body termperature in response to stress or anticipatory anxiety. George Gkoutos stress-induced hypothermia Increase in core body termperature in response to stress or anticipatory anxiety. NBOC:GVG 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. George Gkoutos regulation of sexual activity 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. NBOC:GVG A regulation of drinking behavior process associated with the preference over the type of liquids that are consumed. George Gkoutos regulation of drinking preference behavior A regulation of drinking behavior process associated with the preference over the type of liquids that are consumed. NBO:GVG A regulation of drinking behavior process associated with the preference over alchohol consumption. George Gkoutos regulation of alcohol preference behavior A regulation of drinking behavior process associated with the preference over alchohol consumption. NBO:GVG A regulation of drinking behavior process associated with the preference over the type of food that is consumed. George Gkoutos regulation of eating preference behavior A regulation of drinking behavior process associated with the preference over the type of food that is consumed. NBO:GVG A regulation of drinking behavior process associated with the preference over saccharing consumption. George Gkoutos regulation of saccharin preference behavior A regulation of drinking behavior process associated with the preference over saccharing consumption. NBO:GVG A regulation of consumption of an addictive sustance behavior process associated with the preference over the type of addictive sustance that is consumed. George Gkoutos regulation of addictive substance consumption preference A regulation of consumption of an addictive sustance behavior process associated with the preference over the type of addictive sustance that is consumed. NBO:GVG A regulation of consumption of an addictive sustance behavior process associated with the preference over cocaine consumption. George Gkoutos regulation of cocaine consumption preference A regulation of consumption of an addictive sustance behavior process associated with the preference over cocaine consumption. NBO:GVG A regulation of sexual activity process associated with the preference over a males or females. regulation of mating preference A regulation of sexual activity process associated with the preference over a males or females. NBO:GVG 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] GO:0060006 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] GO:0060007 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. George Gkoutos regulation of behavioral response to chemical stimulus Any process that modulates the frequency, rate or extent of behavioral response to chemical stimulus. NBOC:GVG Any process that modulates the frequency, rate or extent of behavioral response to addictive substance. George Gkoutos regulation of behavioral response to addictive substance Any process that modulates the frequency, rate or extent of behavioral response to addictive substance. https://orcid.org/0000-0002-4277-2151 NBOC:GVG Any process that modulates the frequency, rate or extent of withdrawal response. George Gkoutos regulation of withdrawal response Any process that modulates the frequency, rate or extent of withdrawal response. NBOC:GVG 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. George Gkoutos regulation of addiction response Any process that modulates the frequency, rate or extent of addiction response. https://orcid.org/0000-0002-4277-2151 NBOC:GVG rotation behavior Deactiviation of locomotory behavior. locomotor inactivation behavior A predator behavior involving actively stalking prey over a distance. http://orcid.org/0000-0002-2908-3327 2019-03-11T13:51:02Z Nicolas Matentzoglu 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. http://orcid.org/0000-0002-2908-3327 2019-03-11T13:51:02Z Nicolas Matentzoglu ambush behavior An avoidance behavior engaged in by prey that reduces the success of a predator without the prey actually attacking the predator. http://orcid.org/0000-0002-2908-3327 2019-03-11T13:51:02Z Nicolas Matentzoglu predator avoidance behavior A predator behavior involving subduing prey using a structure or modification of the environment created by the predator for that purpose. http://orcid.org/0000-0002-2908-3327 2019-03-11T13:51:02Z Nicolas Matentzoglu trapping behavior Feeding behavior during which a living entity acquires food and energy by actively searching for food resources. http://orcid.org/0000-0002-2908-3327 2019-08-04T13:51:02Z https://orcid.org/0000-0002-7356-1779 active foraging behavior OBSOLETE. Feeding behavior during which a living entity acquires food and energy by actively searching for food resources. http://orcid.org/0000-0002-2908-3327 2019-08-04T13:51:02Z https://orcid.org/0000-0002-7356-1779 A duplicate of NBO:0015003 obsolete active foraging behavior true A duplicate of NBO:0015003 0000-0002-4277-2151 Consumption behavior that involves burning a substance and inhaling the particulate and gas suspension emitted. http://orcid.org/0000-0002-2908-3327 2019-09-06T10:51:02Z https://orcid.org/0000-0002-7356-1779 smoking behavior Consumption behavior that involves burning a substance and inhaling the particulate and gas suspension emitted. 0000-0002-4277-2151 https://en.wikipedia.org/wiki/Smoking Smoking behavior that involves burning a substance such as tobacco and tasting or inhaling the smoke through a pipe. http://orcid.org/0000-0002-2908-3327 2019-09-06T10:51:02Z https://orcid.org/0000-0002-7356-1779 pipe smoking behavior Smoking behavior that involves burning a substance such as tobacco wrapped in paper and inhaling the smoke. http://orcid.org/0000-0002-2908-3327 2019-09-06T10:51:02Z https://orcid.org/0000-0002-7356-1779 cigarette smoking behavior Smoking behavior that involves burning a substance such as tobacco wrapped in tobacco leaf and inhaling the smoke. http://orcid.org/0000-0002-2908-3327 2019-09-06T10:51:02Z https://orcid.org/0000-0002-7356-1779 cigar smoking behavior Consumption behavior that involves inhaling a material (such as finely ground tobacco leaves) through the nose. http://orcid.org/0000-0002-2908-3327 2019-09-06T10:51:02Z https://orcid.org/0000-0002-7356-1779 snuffing behavior Consumption of specific compounds that facilitate processing of food items. Luke Slater aiding digestion Assessment of cues and signals from encountered individual to determine reproductive condition. Luke Slater reproductive status assessment Postures or signals that alert other animals to presence or approach of a predator. Luke Slater warn other prey Behavior in which one animal causes the death of another. Luke Slater killing kill Signal or behavior that reveals presence of the signaller directed to multiple receivers and not limited to particular receivers. Luke Slater broadcast advertisement Threat that will not be acted upon. Luke Slater bluff Agonistic behavior involving direct physical contact including (but not limited to) biting, kicking, grabbing. Luke Slater contact aggression Perform behaviors that may induce one or more other animals to share food with the performer. Luke Slater beg food Surveillance for presence or approach of predators. Luke Slater vigilance Active pursuit of fleeing prey. Luke Slater chase prey Behaviors in which predator forces potential prey to emerge from cover. Luke Slater flush prey Behavior associated with deposition of material by male following ejaculation to block access to female's reproductive tract during her future matings. Luke Slater insert genital plug Deposition of eggs either into the medium, or onto a substrate. Luke Slater facilitating oviposition One member of a recently mating pair prevents the other from subsequent matings with other individuals. Luke Slater mate guarding Currently reside in constructed or existing structure that provides reduced predator and/or environmental risk. Luke Slater occupy refuge Forcible alteration of behavior of one animal by another. Luke Slater coercion Facilitating release or transfer of gametes. Luke Slater gamete release function Caching or hoarding of food for later use and for protection from competitors, or use of specific substrates for cultivation. Luke Slater 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. Luke Slater pair affirmation Performance of behaviors that demonstrate physical condition of performer to a detected predator. Luke Slater display condition (to predator) Emission of signals in such a way as to prevent effective use of signals emitted by other parties. Luke Slater jamming Active search for possible mates. Luke Slater 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. Luke Slater resource advertisement Sensory assessment of a resource (usually using olfaction or taste), for suitability of subsequent usage. Luke Slater 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. Luke Slater assessment behavior Locomotion to a resource guided by visual or olfactory cues created by a prior finder and/or user of that resource. Luke Slater trail following to resource Behavior by one animals soliciting food provision by a potential mate. Luke Slater courtship begging Consumption of one member of a mating pair, usually the male, usually after the mating. Luke Slater sexual cannibalism Process of retaining developing eggs in the mouth cavity. Luke Slater mouth brooding Construction of a structure in which builder can benefit from reduced predation risk and/or environmental stress. Luke Slater create refuge Behavior that signifies hostility and predicts an increased probability of attack. Luke Slater threat Use of specialized male organs to remove sperm already deposited in female's reproductive tract. Luke Slater sperm scraping Behavior in which one animal causes bodily damage to another. Luke Slater injuring injure Carrying or manipulation of infants or equivalent items to reduce chances of aggression on carrier by other animals. Luke Slater agonistic buffering Use of behavioral tactics or chemical weapons to deter predation. Example: flashing eye spots (behavioral tactic) or expulsion of noxious liquid (chemical). Luke Slater deploy defense Insertion of sperm not in a spermatophore into female body. Luke Slater insemination Building of a trap, web, net, or other structure to help ensnare potential food items. Luke Slater construct capturing device Behaviors that reduce detectability of performer against background. Luke Slater enhance crypsis Chasing of one animal by another during an agonistic conflict. Luke Slater agonistic chase The identification, avoidance, or neutralization of toxic substances in food. Luke Slater dealing with toxins Removal of food resource from previously-stored supply of food. Luke Slater recovery from cache Alarm behavior triggered by agonistic actions or postures. 0000-0002-4277-2151 Luke Slater agonistic alarm Signals emitted by an animal trapped or captured by a presumed predator. Luke Slater distress signaling Behaviors that serve to reduce body temperature as by moving to shade or panting. Luke Slater cooling behaviour Approach to prey in manner designed to avoid early detection by prey. Luke Slater stalk prey Behaviors that reveal a hidden food resource, such as digging, cracking, or breaking. Luke Slater food exposure Behaviors in which animals solicit or allow other animals to utilize a resource they currently control. Luke Slater share food Release of gametes one or both sexes into the ambient medium. Luke Slater spawning Halting or diminution of activity to minimize detection by predator. Luke Slater reduce activity Obtaining food that has been procured by other conspecifics or heterospecifics. Luke Slater social acquisition of food Increasing intensity of directed agonistic behavior. Luke Slater escalation Movement directed to the detection of new resources. Luke Slater nutrient locating Become immobile and reduce other evidence of living state. Luke Slater feign death Spawning in which male and female are clasped or attached to ensure close proximity of released gametes Luke Slater mating amplexus Behaviors directed towards presumed predators to redirect their attention away from a location of importance to the performer. Luke Slater misdirect predator Behavior that serves to exlude an animal from a group. Luke Slater exclusion Conspicuous orientation towards and/or approach to detected predator. Luke Slater inspect predator Perform physically violent acts on a presumed predator. Luke Slater attack predator Display behavior by the winner of a prior agonistic contest. Luke Slater triumph Performance of a behavior that indicates the performer's willingness to mate or bond Luke Slater mating solicitation Creation of or modification of a structure or area that is used in attraction of mates. Luke Slater build display structure Behaviors, anatomical structures, or signals that imitate aposematic animals, plants, or inanimate objects that are undesirable to predators of performer. Luke Slater mimicry enhancement Erratic movements or similar behaviors that would confuse a predator. Luke Slater promote confusion Behavior that serves to demonstrate non-aggressive intent by one member of a courting or potentially mating pair to the other. Luke Slater mating appeasement Any of several behaviors directed towards one animal unwilling to mate by another eager to do so. Luke Slater 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. Luke Slater displacement behavior Provision of food to a potential mate Luke Slater courtship feeding Deposition of spermatophore either on substrate or in body of female. Luke Slater spermatophore deposition Depart [from] current location of predator. Luke Slater flee Active searching of potential mate Luke Slater hunt for mate Actions resulting in establishment or use of one locale for reproductive activity. Luke Slater breeding site selection Behaviors that appear to signifiy lack of hostility and to reduce chances of attack. Luke Slater appeasement General category of behaviors including sampling of medium to detect presence of possible mates, and sampling of encountered individuals to determine mate suitability. Luke Slater mate sampling Behaviors related to acquisition and utilization of external resources. Luke Slater nutrient acquisition Removal of food items from location by use of appendage or tool. Luke Slater food extraction Conspicuous postures or signals (often coloration) that potential predators learn to associate with strong defense mechanisms of performer Luke Slater aposematism Postures or signals that can communicate to predator that it has been detected by performer. Luke Slater (predator) detection notification Behavior that precedes and facilitates attaining food. Luke Slater nutrient preparation Suite of behaviors involved in securing a prey item once it has been located. Luke Slater capturing behaviour Behaviors that result in ending flight of prey with successful predation. Luke Slater capturing prey The act of putting a food resource in a location in which it can be stored or protected until a future time. Luke Slater caching behavior Behaviors that prepare food for consumption, such as nut-cracking or peeling. Luke Slater food processing Uninvited taking of food from another animal. Luke Slater scrounge Behavior associated with locating and acquiring food that has been killed or procured by another animal. Luke Slater 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. Luke Slater sexual interference Behavior associated with refusing courtship or solicitation behaviors by avoidance, retreat, or other active repulsion of suitor. Luke Slater mate rejection A behavior associated with the gathering of organisms together in some locality. [Wikipedia:Aggregation_(ethology)] https://orcid.org/0000-0002-9611-1279 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] https://orcid.org/0000-0002-9611-1279 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] https://orcid.org/0000-0002-9611-1279 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] https://orcid.org/0000-0002-9611-1279 escape reaction 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] https://orcid.org/0000-0002-9611-1279 surface breathing A behavior involving avoidance of or escape from approaching visual stimuli, threats, or objects which are on a collision course. [PMID:23364572] https://orcid.org/0000-0002-9611-1279 visually guided collision avoidance behavior Any habitual use of the tobacco plant leaf and its products. 2020-01-27T20:46:57Z 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. 2020-01-27T20:51:17Z spit tobacco consumption tobacco chewing behavior The inhalation and exhalation of tobacco smoke. 2020-01-27T20:51:34Z tobacco smoking behavior The inhalation and exhalation of tobacco aerosol, referred to as vapor, which is produced by an e-cigarette or other device. 2020-01-27T20:51:58Z tobacco vaping behavior 2020-01-27T21:03:19Z cannabis consumption The inhalation and exhalation of marijuana smoke. 2020-01-27T21:04:14Z marijuana smoking behavior pot smoking behavior weed smoking behavior cannabis smoking behavior The inhalation and exhalation of cannabis aerosol, referred to as vapor, which is produced by an e-cigarette or other device. 2020-01-27T21:04:28Z marijuana vaping behavior pot vaping behavior weed vaping behavior cannabis vaping behavior The consuming of cannabis through eating or applying the oil sublingually. 2020-01-27T21:04:49Z marijuana oil consumption cannabis oil consumption A feeding behavior during which an animal ingests biomass produced by a plant or other primary producer 2017-09-14T19:12:10+09:00 http://orcid.org/0000-0002-1816-4260 http://orcid.org/0000-0002-4366-3088 https://en.wikipedia.org/wiki/Grazing behavior_ontology grazing behaviour 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. http://orcid.org/0000-0002-3528-5267 2020-02-05T20:14:32Z Sofia Robb inchworm-like locomotion inchworming behavior_ontology inchworming behavior Behavior related to the repeating or looping movement of the whole organism along a circular or round path. http://orcid.org/0000-0002-3528-5267 2020-02-05T20:14:32Z Sofia Robb circling circling locomotion behavior_ontology circling behavior Protective behavior that sheds or discards an animal's body part. 2023-04-23 behavior_ontology 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. autotomy Protective behavior that sheds or discards an animal's body part. DOI:10.1093/beheco/arl010 Rhythmic behavior that involves cue-initiated, persistent, direct, focused movement between habitats. 2023-04-22T14:17:43Z behavior_ontology Movement ecology Dingle H. Migration: the biology of life on the move. Oxford University Press, USA; 2014. migration Rhythmic behavior that involves cue-initiated, persistent, direct, focused movement between habitats. ISBN:0199640394 Migration that involves regular movement up and down in the water column. 2023-04-22T14:41:53Z behavior_ontology 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. diel vertical migration Migration that involves regular movement up and down in the water column. DOI:10.1111/brv.12715 Migration that involves regular movement laterally between distant ranges in seasonal cycles. 2023-05-01T14:41:27Z behavior_ontology geographical migration Migration that involves regular movement laterally between distant ranges in seasonal cycles. DOI:10.1146/annurev-ecolsys-012021-031035 Display that involves taking all four legs off the ground simultaneously and holding the legs stiff and straight. 2023-04-24T19:52:42Z pronking behavior_ontology Caro TM. The functions of stotting: a review of the hypotheses. Animal Behaviour. 1986 Jun 1;34(3):649-62. stotting Display that involves taking all four legs off the ground simultaneously and holding the legs stiff and straight. DOI:10.1016/S0003-3472(86)80051-3 root Muridae Rattus Sedentaria Canalipalpata Xenoturbellida Xenoturbella Teleostomi Euteleostomi Chromadorea Ecdysozoa Lophotrochozoa Neoteleostei Eurypterygia Ctenosquamata Acanthomorphata Euacanthomorphacea Xenacoelomorpha cellular organisms Archelosauria Toxicofera Episquamata Unidentata Bifurcata Dipnotetrapodomorpha Boreoeutheria Acoelomorpha Osteoglossocephalai Euteleosteomorpha Percomorphaceae Eupercaria Xenoturbellidae Actinopteri Clupeocephala Otophysi Cypriniphysae Otomorpha Myomorpha Pancrustacea Mandibulata Homininae Rhabditina Rhabditomorpha Xenopus <subgenus> Spiralia Danionidae Danioninae Eukaryota Pipoidea Cyprinoidei Tetraodontiformes Tetraodontoidei Tetraodontidae Takifugu Takifugu rubripes Euarchontoglires Glires Simiiformes Hominoidea Sophophora melanogaster group melanogaster subgroup Teleostei Tetradontoidea Ostariophysi Tetrapoda Amniota Theria <mammals> Sauria Opisthokonta Metazoa Bilateria Protostomia Neoptera Endopterygota Deuterostomia Muroidea Haplorrhini Murinae Mammalia Siboglinidae Neopterygii Batrachia Dinosauria Saurischia Theropoda Coelurosauria Muscomorpha Schizophora Acalyptratae Ephydroidea Drosophilinae Drosophilini Cyclorrhapha Eremoneura Insecta Rhabditoidea Peloderinae Porifera Eumetazoa Cnidaria Platyhelminthes Nematoda Rhabditida Caenorhabditis Caenorhabditis elegans Rhabditidae Annelida Polychaeta Sabellida Arthropoda Hexapoda Diptera Brachycera Drosophilidae Drosophila <flies,genus> Drosophila melanogaster Pterygota <insects> Chordata Tunicata Vertebrata <vertebrates> Gnathostomata <vertebrates> Chondrichthyes Holocephali Chimaeriformes Dipnomorpha Actinopterygii Cypriniformes Danio Danio rerio Sarcopterygii Amphibia Anura Pipidae Xenopus <genus> Xenopus laevis Xenopodinae Sauropsida Archosauria Lepidosauria Sphenodontia Sphenodontidae Sphenodon Squamata Dicondylia Serpentes Aves Palaeognathae Struthioniformes Struthionidae Struthio Struthio camelus Neognathae Panarthropoda Columbiformes Columbidae Craniata <chordates> Prototheria Monotremata Tachyglossidae Eutheria Primates Catarrhini Hominidae Homo Homo sapiens Rodentia characteristic quality https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 We should name the inverse in COB and avoid the confusing inverse(..) construct color For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). composition distance frequency morphology 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. shape TODO: define this or obsolete it and move children somewhere else. qualitative deviation (from_normal) 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. amount size 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 mass closure structure temperature texture rate behavioral quality coordination maturity increased distance decreased distance increased frequency decreased frequency branched flat circular normal 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. absent present increased amount increased duration decreased duration increased size decreased size closed uncoordinated decreased rate increased rate elliptic opacity opaque transparent viscosity viscous physical quality elasticity elastic larval See comments of relational quality of a physical entity. process quality 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. physical object quality optical quality increased temperature decreased temperature duration temporally extended decreased depth quality of a gas quality of a liquid has number of lacking processual parts decreased mass increased mass extra or missing processual parts contractility increased contractility decreased contractility curvature depth increased depth This refers to the disposition of the bearer. contractile increased viscosity decreased viscosity 1-D extent disposition liquid configuration chronic cylindrical saccular cellularity multicellular organismal quality decreased amount lacks parts or has fewer parts of type 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. lacks all parts of type 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. has fewer parts of 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. has extra parts of type 2-D shape Use this term or an is_a child of this term when the entire shape of the object is known. convex 3-D shape branchiness structure, cavities dendritic physical quality of a process hollow altered number of laminar quality of a substance Becoming flat but not necessarily completely flat. flattened grooved 3-D shape increased elasticity decreased elasticity tubular increased quality decreased quality decreased process quality decreased object quality increased process quality increased object quality superelliptic temporal distribution quality offset quality tendency increased tendency decreased tendency Acinus is Latin for berry. acinar collagenous distensible disconnected distensibility rate of occurence increased rate of occurrence decreased rate of occurrence 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 http://www.jbiomedsem.com/content/4/1/43 system processual entity chemosensory organ islet of Langerhans http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png submucosal submucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png peripheral nervous system http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png somatic nervous system has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest) sympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png 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 zone of skin http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg 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. non-material anatomical boundary create a separate class for distributed pancreas, eg cyclostomes? endocrine pancreas exocrine pancreas compound eye https://github.com/obophenotype/uberon/issues/457 camera-type eye sense organ http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png 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) tubular tube appendicular this is currently a subtype of organism subdivision - which would exclude feathers appendage lamina propria https://upload.wikimedia.org/wikipedia/commons/f/fb/GI_Organization.svg lamina propria of trachea head serous membrane http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg 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. ganglionic ganglion simple eye vessel ureteral ureteric in humans, consists of adventitial, muscular and mucoa layers ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg urethral 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. urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. duct large intestine anatomical wall anatomical structure 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 organ 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 organ subunit currently defined in a very broad sense, may be replaced by more specific classes in the future organ part respiratory tract fully formed stage https://github.com/obophenotype/uberon/issues/566 embryo stage Uberon includes clade-specific subclasses, e.g. nematod larva larval stage death stage proximo-distal subdivision of respiratory tract regional part of nervous system subdivision of skeletal system 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 external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png 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 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 ectoderm/mesoderm/endoderm-derived structure mesonephric 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] mesonephros http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png TODO check developmental relationships metanephric 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 metanephros TODO check mesonephric tubule ureteric bud morula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png zona pellucida http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png 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] inner cell mass https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg trophoblastic 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] trophoblast https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg bilaminar disc http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) post-embryonic stage https://github.com/obophenotype/uberon/issues/344 membrane organ cardiac neural crest lung vasculature life cycle https://github.com/obophenotype/uberon/issues/532 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 life cycle stage zygote stage cleavage stage consider adding a preceding stage 'morula stage' as part of cleavage blastula stage http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png gastrula stage neurula stage https://github.com/obophenotype/uberon/issues/343 organogenesis stage https://github.com/obophenotype/uberon/issues/533 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 lung connective tissue 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] lung epithelium respiratory tube clarify successors - include bronchi? lung bud http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png neuron projection bundle 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. neural nucleus cranial nerve nucleus http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png anterior region of body posterior region of body membranous layer requires alignment with EHDAA2 and complete developmental relationships anal canal https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png This class is probably too inclusive intestinal 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. intestine orifice adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca cloacal Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs cloaca this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. embryonic cloaca primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png oral some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives mouth https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg oral opening oral cavity proximal-distal subdivision of colon 1 1 pair of lungs respiration organ excreta This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. blood haemolymphatic fluid TODO - add layer relations. 'tendon sheath' GAT in FMA. tendon sheath 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 blastula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png defined generically to encompass both vertebrates and invertebrates body wall colonic mucosa duodenal mucosa gastric gland pancreatic juice We model the digestive tract as consisting of two parts: the wall and the lumen. gut wall Note that some sources treat 'intestinal gland' as synonymous with crypts intestinal gland mucosal mucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html] ophthalmic nerve parenchymal parenchyma pharyngeal mucosa Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm) blastocyst https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg mandibular nerve http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png maxillary nerve http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png tongue muscle http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png tracheal mucosa consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 musculature of body lens cortex lens nucleus colonic epithelium serous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png bronchial mucosa mucous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png artery wall secretion of exocrine gland cavernous artery organism substance anatomical space material anatomical entity immaterial anatomical entity anatomical system TODO - split body and mc organism? body continues after death stage organismal multicellular organism 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 compound organ component female reproductive system http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency organism subdivision acellular anatomical structure anatomical cluster see also conceptus extraembryonic component in EHDAA2. extraembryonic structure changed label and definition to reflect CARO2 tissue multi-tissue structure epithelial 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? epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg needs to be synchronized with CL - there is no distinct cuboidal cell in CL simple cuboidal epithelium http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png simple columnar epithelium http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png multilaminar epithelium simple squamous epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg atypical epithelium 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 cavitated compound organ consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable unilaminar epithelium mucoid mucous mucus 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 thoracic segment of trunk 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 abdominal celiac abdomen embryonic embryo https://github.com/obophenotype/uberon/issues/503 https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg 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] germ layer ectodermal ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png endodermal endoderm http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png mesodermal mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png 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 stomodeal 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. stomodeum http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. proctodeal proctodeum https://github.com/obophenotype/uberon/issues/685 stomach https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg aortic 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 aorta https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg cardiac 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 heart endocrine endocrine system requires review for applicability to invertebrate structures, e.g. synganglion brain TODO - merge with cell layer? laminar lamina http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png this term should be ceded to the arthropod anatomy ontology head sensillum corneal 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 cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg This class excludes compound eye corneal lenses. The lens is avascular and nourished by diffusion from the aqueous and vitreous humors. lens of camera-type eye retinal 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 retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png 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) ocular optic 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, eye ommatidial ommatidium 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. cervical neck https://upload.wikimedia.org/wikipedia/commons/9/99/Female_neck.jpg skeletal joint 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 pons http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png consider splitting genitalia from reproductive system reproductive system http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg gonadal gonad ovarian ovary http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png epidermal 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). skin epidermis respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg 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 respiratory airway digestive digestive system 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 renal system the cardiovascular system and the lymphatic system are parts of the circulatory system circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg adipose 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. adipose tissue musculature http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png nervous neural nervous system http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png central nervous system nervous nerve sensory nerve note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs sensory system http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png gustatory gustatory system consider splitting class 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)] yolk sac http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png 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 foregut http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png Consider generalizing to deuterostome pharynx chordate pharynx esophageal esophagus http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg 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 midgut http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg 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 hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png primordium neural tube http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png rectal 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 rectum http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif anatomical entity in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue ventral pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of back not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO external carotid artery https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] superficial cervical artery posterior vena cava http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png ileocecal junction pericardial cavity endocardium of ventricle epicardium of ventricle myocardium of ventricle TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of head TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of trunk kidney excreta from some taxa (e.g. in aves) may not be liquid urine 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 synovial fluid wall of esophagus 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 lobe of liver right lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png left lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit cardiac muscle tissue TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. skeletal muscle tissue https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg 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. smooth muscle tissue https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg dorsal 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 dorsum http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG superior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png common iliac vein https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png right renal vein left renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png todo - add developmental relationships for other taxa hepatic vein http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png ovarian vein http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg cystic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png TODO - abstract this such that it legitimately covers all vertebrates colonic 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] colon sigmoid colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg we include this as zone of stomach even though it is not distinguished by gland type body of stomach http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg pyloric antrum http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg We follow Kardong in defining stomach regions by glands pyloric pylorus http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg wall of stomach wall of small intestine wall of large intestine mesentery of small intestine portal lobule hepatic acinus 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] biliary tree common bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png 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 common hepatic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg right hepatic duct left hepatic duct visceral peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png peritoneal cavity renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability. renal artery http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png 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] right renal artery http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png 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] left renal artery ovarian artery http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png currently defined in a generic fashion. hepatic artery http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png splenic artery https://github.com/obophenotype/uberon/issues/268 http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png mucosa of stomach https://upload.wikimedia.org/wikipedia/commons/1/1c/Normal_gastric_mucosa_intermed_mag.jpg submucosa of stomach TODO - check serosa/peritoneum serosa of stomach pyloric sphincter mucosa of small intestine submucosa of small intestine duodenum, 1st part serosa, 2nd - 4th adventitia serosa of small intestine mucosa of large intestine submucosa of large intestine TODO - check serosa/peritoneum serosa of large intestine currently defined as equivalent to any submucosal gland in the duodenum. duodenal gland 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 intestinal villus http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg inferior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right ureter https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left ureter In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg 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] cortex of kidney https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg nephron tubule collecting duct of renal tubule lamina propria of small intestine intestinal mucosa TODO - check serosa/peritoneum serosa of intestine anal 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 anus http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif interlobular bile duct adventitia of ureter lamina propria of ureter vesical 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] urinary bladder https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg wall of urinary bladder mucosa of urinary bladder TODO - check serosa/peritoneum serosa of urinary bladder Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue lamina propria of urinary bladder we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different wall of intestine pancreatic acinus pancreatic 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 pancreas https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png peritoneal fluid 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 pelvic girdle region epithelium of stomach intestinal epithelium epithelium of large intestine 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. portal triad https://upload.wikimedia.org/wikipedia/commons/6/62/Portal_triad.JPG liver parenchyma 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) intralobular bile duct kidney terms require review for cross-vertebrate compatibility and developmental relationships. nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP] superior vesical artery https://upload.wikimedia.org/wikipedia/commons/0/02/Internal_iliac_branches.PNG internal iliac vein http://upload.wikimedia.org/wikipedia/commons/c/cb/Internaliliacv.png muscle of pelvis female urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png urethral gland anal region https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png parietal peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png skin of pelvis skin of abdomen skin of neck skin of thorax skin of limb this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). pectoral girdle region skeletal skeletal system https://github.com/obophenotype/uberon/wiki/The-skeletal-system TODO - find a home for: FMA:24139 ! skeleton of upper limb forelimb skeleton TOOD - find a home for: FMA:24140 hindlimb skeleton subdivision of head facial face http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg skin of lip bone element articular capsule http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png ascending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg muscle of pelvic girdle Do not confuse with aortic arch birds have right aortic arch, mammals left. arch of aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg results from fusion of left and right dorsal aortae descending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg thoracic aorta http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates abdominal aorta http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png brachiocephalic artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg 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 common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg internal carotid artery http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO) subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg 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 right subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg 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 digestive tract lower urinary tract lower respiratory tract http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg muscle of larynx genioglossus muscle http://upload.wikimedia.org/wikipedia/commons/7/7e/Genioglossus.png hyoglossus muscle http://upload.wikimedia.org/wikipedia/commons/7/7e/Hyoglossus.png extrinsic muscle of tongue intrinsic muscle of tongue 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 left subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg 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). anterior vena cava http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png internal jugular vein http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png bronchial vein ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png revisit this, see issue #331 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 muscle of iris 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 constricts iris sphincter pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png 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 dilatator pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png lingual artery https://upload.wikimedia.org/wikipedia/commons/3/3c/Lingual_artery.PNG facial artery http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png maxillary artery http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png ophthalmic artery http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png lacrimal artery http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png muscular muscle organ 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. arterial Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system. artery TODO - check with MA - vein vs venous blood vessel venous vein http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg 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] hepatic portal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png dorsal aorta in Kardong celiac artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png trigeminal nerve https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png glossopharyngeal nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves hypoglossal nerve http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png TODO - add class 'pulmonary artery tree organ' right pulmonary artery http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png TODO - add class 'pulmonary artery tree organ' left pulmonary artery http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png facial vein http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks) trigeminal ganglion http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png occipital bone http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process temporal bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg hyoid bone http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png glossopharyngeal ganglion neurocranial 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 neurocranium 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). jaw skeleton See notes for jaw w.r.t skeletal element vs subdivision of head lower jaw region http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png cranial ganglion 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. glossal lingual 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 tongue http://upload.wikimedia.org/wikipedia/commons/a/a6/Tongue.agr.jpg cranial synchondrosis papilla of tongue 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) taste bud http://upload.wikimedia.org/wikipedia/commons/5/5a/Gray1018.png See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship TOODO check cavity of pharynx laryngeal larynx http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg laryngeal cartilage TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal lacrimal apparatus http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png vagus nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png anterior chamber of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus uveal uvea http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png iridial 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] iris 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 corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png scleral 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. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg 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. skeletal muscle of trunk ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg 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 choroidal optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png ciliary epithelium iris stroma http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png spinal nerve https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg layer of retina 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 cranial nerve http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg sensory ganglion anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former epithelium of lens synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens capsule of lens http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png autonomic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png sympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, they are situated in the upper, outer portion of each orbit Innervation is highly complex and species-specific lacrimal gland http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png mucosa of larynx secretion of lacrimal gland labial lip http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg lower lip http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg cortical cortex developmental relationships need revised mesencephalic midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG 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) rhombomere 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]. metencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg medulla oblongata http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg epithelium of trachea epithelium of small intestine endothelium of capillary endothelium of arteriole endothelium of artery endothelium of venule endothelium of vein '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 midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png regional part of spinal cord cartilage of bronchus submucosa of bronchus 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] terminal bronchiole epithelium blood plasma 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 elimination of cholesterol 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 bile gastric juice submucosa of esophagus lamina propria of esophagus serosa of esophagus TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar epithelium of esophagus parenchyma of pancreas venule https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg arteriole https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg 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. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg 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 capillary https://github.com/obophenotype/uberon/issues/2186 http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg corneal endothelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png endothelial 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) endothelium fecal feces hyaline cartilage tissue http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg 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] pulmonary artery https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png 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] kidney capsule https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg pulmonary vein https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png portal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png accessory XI nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png gray matter https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg rhombencephalic hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg epithelium of gall bladder epithelium of bronchus striated muscle tissue Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. bronchial artery http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png pontine raphe nucleus pulmonary 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] lung https://github.com/obophenotype/uberon/issues/701 see also: vascular system. Consider merging? vascular vasculature http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg embryonic structure epithelium of bronchiole truncus arteriosus 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 endocardial cushion http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png 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 sinus venosus http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png Consider adding a layer-of-skin grouping class for all skin layers dermal dermis http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg hypodermal subcutaneous subcutaneus hypodermis http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg viscus https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with the pulmonary arteries heart right ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg cardiac atrium cardiac ventricle https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with aorta heart left ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg interatrial septum http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. postcranial axial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton appendicular skeleton https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg brain dura mater spinal dura mater interventricular septum http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png mesenteric mesentery http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png consider 'integumentary system' for invertebrates skin of body http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg 'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations' cardiac septum trunk limb Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm forelimb crural hindlimb http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png visual system vestibulo-auditory system http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg lienal splenic 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 spleen https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg hepatic 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]. liver https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg small intestine http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg 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) gallbladder https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg artery smooth muscle tissue smooth muscle of esophagus renal kidney duodenal duodenum http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right ovary https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left ovary pronephric 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 pronephros 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. superior olivary complex http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png TODO - check ZFA/pons. also GO says part of dorsorostral pons locus ceruleus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png superior salivatory nucleus http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 endocardium http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png endocardium of atrium https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right lung http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left lung http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png bronchial 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 bronchus http://upload.wikimedia.org/wikipedia/commons/1/18/Respiratory_system_complete_numbered.svg bronchiolar bronchiole https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png terminal bronchiole https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png subcutaneous adipose tissue hemolymphoid system 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. integumental integumentary integument vasculature of head vasculature of trunk submucosa of trachea vasculature of eye musculoskeletal musculoskeletal system fibrous joint cartilaginous joint WP considers epiphyseal plates as subtypes of this consider adding link to hyaline cartilage synchondrosis http://upload.wikimedia.org/wikipedia/commons/7/76/Gray297.png consider adding fibrocartilage class symphysis http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray298.png synovial joint In many species, the diaphragm separates thoracic and abdominal cavities thoracic cavity http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg TODO - add superclass to unify with VNC? spinal cord http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg 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) chondrocranial covers the brain dorsally in chondrichthyans chondrocranium 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 olfactory organ 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. reticular formation http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png biliary system http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png dorsal mesentery http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png '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). brainstem http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png myocardium of atrium nucleus of brain gray matter of spinal cord check the FMA placement here; ncit placement of body cavity here probably not correct In mammals it forms the peritoneal, pleural, and pericardial cavities coelemic cavity lumen muscle of back epithelium of urethra lamina propria of urethra notochordal 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] notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png 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 somitic 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] somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png exocrine system pulmonary trunk https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png lamina propria of bronchus 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. neural crest http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png distinction between abdomen muscle and abdomen musculature abdomen musculature descending thoracic aorta neurectodermal we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here neurectoderm 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] 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 myocardial myocardium http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg EHDAA2 divides the system from the tissue conducting system of heart pelvic pelvic region of trunk serous pericardium TODO - in ZFA is_a epithelium peritoneal peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium] fibrous pericardium meningeal 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). meninx https://upload.wikimedia.org/wikipedia/commons/4/48/Illu_meninges.jpg 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] dura mater http://upload.wikimedia.org/wikipedia/commons/8/8e/Meninges-en.svg 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 exocrine gland endocrine gland http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png 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) cranial muscle muscle of neck muscle of abdomen connective tissue 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. muscle tissue hematopoietic hematopoietic system bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png immune system pericardial sac http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png pericardial pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png parietal serous pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png pericardial fluid autonomic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png integumental system abdominal segment of trunk 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] cartilage tissue http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg check FMA, use plural for now as general class not there skin gland 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] hepatobiliary system consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) oral epithelium visceral serous pericardium the formal definition is very inclusive, and includes sesamoids limb bone cannot find singular in FMA, using Set class choroidal blood vessel intersomitic artery spinal artery vesical vein http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png intestine secretion esophagus mucosa see https://github.com/obophenotype/uberon/issues/27 bone tissue iris epithelium placement in this class to be inferred endochondral bone https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg intramembranous bone elastic tissue http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png May be composed of smooth muscle and elastic tissue tunica media https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg 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 tunica intima https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg glandular gland http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png 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 epiblast (generic) http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png this term should be ceded to the arthropod anatomy ontology arthropod sensillum 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 pharyngeal arch http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png Do not merge with neurogenic placode 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 cranial placode TODO discriminate between stages and organisms larval larva anatomical cavity organ cavity lumen of central nervous system regional part of brain hypoglossal nucleus http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png trigeminal nucleus gustatory epithelium involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum] pontine tegmentum https://upload.wikimedia.org/wikipedia/commons/9/9c/Brainstem_Abducens.png septal general anatomical term in FMA septum consider adding class for organizer. Consider adding separate class for isthmus as a structure midbrain-hindbrain boundary 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) periderm pre-chordal neural plate chordal neural plate presomitic mesoderm 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] pronephric duct blood island TODO - check; developmental relationship to anterior hypoblast in ZFA? prechordal plate intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png 2 pharyngeal arch 2 http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode dorsolateral placode axial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png 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...' trigeminal placode complex eye primordium optic cup lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png 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. mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png posterior neural tube paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png epibranchial placode TODO - add grouping class for the anterior end of the neural tube at all stages anterior neural tube lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png trunk neural crest should probably be merged with heart rudiment. heart primordium sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png cranial neural crest female organism consider obsoleting. See issue/1305 surface structure 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 compound organ the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense mesenchymal mesenchyme http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007 dermatocranium 3 pharyngeal arch 3 4 pharyngeal arch 4 6 pharyngeal arch 6 Disappears early in development in tetrapods pharyngeal arch artery 1 pharyngeal arch artery 2 pharyngeal arch artery 3 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 proximal right subclavian pharyngeal arch artery 4 pharyngeal arch artery 6 tracheal 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. trachea http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg cranial cranium in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton skull reproductive organ female reproductive organ gustatory organ ovary septum 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"] metanephric mesenchyme epithelium of lower jaw yolk sac endoderm TODO - check endoderm of foregut TODO - check endoderm of midgut TODO - check endoderm of hindgut skeletal muscle tissue of eye skeleton of lower jaw endothelium of trachea TODO - check primitive vs developed mesentery of stomach mesentery of heart mesentery of oesophagus mesentery of midgut consider changing genus to subdivision of meninx meninx of midbrain consider changing genus to subdivision of meninx meninx of hindbrain meninx of spinal cord gland of foregut pharyngeal gland gland of integumental system mesoderm blood island TODO - change mesenchyme relationships to precursor_of eye mesenchyme mesenchyme of ovary mesenchyme of yolk sac mesenchyme of lower jaw submucosa of anal canal submucosa of rectum submucosa of colon submucosa of duodenum serosa of rectum serosa of colon 1st part serosa, 2nd - 4th adventitia serosa of duodenum ganglion of peripheral nervous system ganglion of central nervous system mucosa of anal canal mucosa of oral region mucosa of rectum lies on top of lamina propria epithelium of mucosa pharyngeal epithelium epithelium of midgut epithelium of hindgut epithelium of rectum 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. epithelium of tongue epithelium of right lung epithelium of left lung pelvic appendage bud ectoderm pectoral appendage bud ectoderm cardiac muscle of right atrium cardiac muscle of left atrium cardiac muscle of right ventricle cardiac muscle of left ventricle cardiac muscle tissue of interventricular septum skeletal muscle tissue of pharynx Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle smooth muscle of eye smooth muscle of trachea mesothelium of pericardial cavity mesentery of urinary system mesentery of hindgut mesentery of rectum mesentery of colon mesentery of duodenum cartilage of respiratory system gland of digestive tract gland of tongue pelvic appendage bud mesenchyme pectoral appendage bud mesenchyme TODO - develops_from mesenchyme of tongue dermis adipose tissue abdomen nerve neck nerve 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 iris nerve nerve of trunk region limb nerve forelimb nerve hindlimb nerve consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve thoracic cavity nerve pelvis nerve Different sources vary regarding which bones are craniofacial; e.g. hyoid bone head bone neck bone test whether 'facial bone' is an exact synonym facial bone trunk bone hindlimb bone ureteric segment of renal artery respiratory system artery artery of lower lip thoracic cavity artery meningeal artery ureteric vein respiratory system venous blood vessel vein of lower lip http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png thoracic cavity vein respiratory system capillary endothelium respiratory system venule respiratory system arteriole head blood vessel abdomen blood vessel heart blood vessel brain blood vessel follow up on tracker item corneal blood vessel retina blood vessel neck blood vessel respiratory system blood vessel trachea blood vessel only in MA - supertype of artery, arteriole, aorta. arterial blood vessel iris blood vessel lung blood vessel trunk blood vessel limb blood vessel forelimb blood vessel hindlimb blood vessel kidney blood vessel thoracic cavity blood vessel pelvis blood vessel respiratory system capillary kidney capillary brain gray matter TODO - check free limb vs pectoral complex forelimb skin TODO - check free limb vs pelvic complex hindlimb skin right lung bronchiole left lung bronchiole right lung terminal bronchiole left lung terminal bronchiole brain meninx midbrain dura mater hindbrain dura mater head connective tissue abdomen connective tissue neck connective tissue respiratory system connective tissue trachea connective tissue lower respiratory tract connective tissue larynx connective tissue dermis connective tissue trunk connective tissue limb connective tissue forelimb connective tissue hindlimb connective tissue bronchus connective tissue thoracic cavity connective tissue pelvis connective tissue neck cartilage lower respiratory tract cartilage check whether to classify as part of splanchoncranium in mammals the rings are incomplete, in avians the rings are complete. trachea cartilage http://upload.wikimedia.org/wikipedia/commons/5/56/Gray952.png eye skin gland aorta elastic tissue heart elastic tissue respiratory system elastic tissue cardiovascular system elastic tissue blood vessel elastic tissue lung elastic tissue bronchus elastic tissue trachea elastic tissue aorta tunica media aorta tunica intima respiratory system arterial blood vessel kidney arterial blood vessel Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses limb joint limb muscle forelimb muscle hindlimb muscle abdominal cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg cranial suture Design pattern notes: check whether this fits the foramen design pattern foramen magnum http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png abdominal wall http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct extrahepatic bile duct includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts intrahepatic bile duct brachiocephalic vein http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png cavernous sinus splenic vein http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png neural tissue All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers splanchnic nerve recurrent laryngeal nerve lingual nerve 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) mouth mucosa nerve of thoracic segment nerve of abdominal segment thoracic segment bone abdominal segment bone urethra muscle tissue thoracic segment muscle respiratory system muscle merge muscle and muscle layer? esophagus muscle abdominal segment muscle thoracic segment blood vessel abdominal segment blood vessel abdominal segment skin thoracic segment connective tissue abdominal segment connective tissue forelimb joint hindlimb joint neural tube lumen gonadal vein http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png mesencephalic neural crest rhombencephalon neural crest spinal cord neural crest spinal cord neural plate gonad mesenchyme forelimb mesenchyme hindlimb mesenchyme presumptive ganglion future coelemic cavity lumen 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 intraembryonic coelom stromal stroma 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 liver primordium axial muscle skeletal muscle tissue of trunk retinal neural layer contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers epithelial tube endothelial tube check this kidney mesenchyme Compare to: vein venous blood vessel revisit after standardizing terms 'primordium', 'anlagen', 'bud' pancreas primordium http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png pancreatic epithelial bud http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png dorsal pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png 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. ventral pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png digestive system duct digestive tract epithelium cartilage element of chondrocranium cranial cartilage reproductive gland somatosensory system anterior stroma of cornea posterior stroma of cornea cutaneous elastic tissue valvular valve embryonic-extraembryonic boundary Not to be confused with 'dermatome segment of skin'. dermatome http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png 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] germinal neuroepithelium biliary ductule consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure neural tube ventricular layer neural tube mantle layer neural tube marginal layer neural tube basal plate vena cava http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png 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 orbital region renal collecting system http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png 2 anatomical conduit 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] pharyngeal pouch vasculature of iris Grouping term for query purposes endoderm-derived structure Grouping term for query purposes mesoderm-derived structure Grouping term for query purposes ectoderm-derived structure genitourinary urogenital genitourinary system 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] optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png salivatory nucleus TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO cardiogenic plate primary heart field heart tube outflow tract septum 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] outflow tract cardiac vein 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 cardiac chamber propepicardial Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA] proepicardium 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. septum transversum TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 external genitalia consider splitting out lymph organ, compare with lymph node hemopoietic organ aorta smooth muscle tissue endodermal part of digestive tract cortical collecting duct 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] nephrogenic mesenchyme 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 renal vesicle nephron epithelium back nerve urethra smooth muscle layer large intestine smooth muscle intestine smooth muscle stomach smooth muscle respiratory system smooth muscle gastrointestinal system smooth muscle kidney pelvis smooth muscle urinary bladder smooth muscle anal region smooth muscle lower respiratory tract smooth muscle see notes for muscle of iris. iris smooth muscle arteriole smooth muscle 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. blood vessel smooth muscle spleen smooth muscle small intestine smooth muscle gallbladder smooth muscle bronchus smooth muscle outflow tract smooth muscle this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern bone of dorsum review as part of general integumentary system review - part of skin, or more generally, integumental system skin muscle back blood vessel outflow tract myocardium back connective tissue outflow tract pericardium cartilaginous joint suture eye muscle skeletal skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system dermomyotome heart rudiment 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] cardiac skeleton http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png respiratory system blood vessel smooth muscle primitive streak http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png distinction between trophectoderm and trophoblast unclear/inconsistent in many sources trophectodermal trophectoderm developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm limb bud optic eminence 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 apical ectodermal ridge http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg 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] paired limb/fin bud 1 pharyngeal arch 1 http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png add specific artery derivatives Do not confuse with arch of aorta. 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 pharyngeal arch artery http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png vitelline blood vessel 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) Descemet's membrane https://github.com/obophenotype/uberon/issues/15 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 anterior limiting lamina of cornea vitelline vasculature bone of free limb or fin skeleton of limb neurula embryo note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs entire sense organ system 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 skeletal musculature of head https://github.com/obophenotype/mouse-anatomy-ontology/issues/4 https://github.com/obophenotype/uberon/issues/1405 define generically to encompass both vertebrates and invertebrates musculature of body wall musculature of thorax musculature of neck musculature of back musculature of pelvic girdle musculature of pectoral girdle 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 musculature of face currently defined by location rather than attachment musculature of larynx currently defined by location rather than attachment musculature of trunk currently defined by location rather than attachment musculature of limb currently defined by location rather than attachment musculature of upper limb currently defined by location rather than attachment musculature of lower limb cardiac muscle tissue of atrium cardiac muscle tissue of interatrial septum cardiac muscle tissue of cardiac septum Note placement of MA class based on parthood relationship cardiac muscle tissue of myocardium smooth muscle tissue of bronchiole smooth muscle tissue of terminal bronchiole vasculature of muscle organ vasculature of musculoskeletal system we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. cardiovascular system blood vasculature https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left kidney https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right kidney https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left eye https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right eye systemic arterial system arterial system systemic artery systemic venous system venous system sphincter muscle blood vessel endothelium 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] liver lobule aorta wall aorta tunica adventitia interventricular septum membranous part interventricular septum muscular part vestibular system 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' raphe nuclei http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png costo-cervical trunk http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png arterial system smooth muscle venous system smooth muscle vena cava endothelium outflow tract endothelium arterial system endothelium venous system endothelium respiratory system blood vessel endothelium TODO - check relationship to bulbus arteriosus bulbus cordis http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png this class is the union of the classes limb, pectoral fin and pelvic fin. paired limb/fin pelvic appendage pectoral appendage jugular vein http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png 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 conceptus nematode larval stage https://github.com/obophenotype/uberon/issues/567 We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted neuromere 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) segmental subdivision of nervous system segmental subdivision of hindbrain gastrula metanephric collecting duct 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. dentary 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 skeletal tissue dermal skeletal element gland of anal canal cartilaginous neurocranium intramembranous bone tissue skeletal element here cranium = skull - mandible cranial bone Do not manually classify under here - bones are automatically classified bone of lower jaw articular system respiratory system submucosa larynx submucosa respiratory system lamina propria gastrointestinal system lamina propria gallbladder lamina propria gastrointestinal system serosa gallbladder serosa heart ventricle wall TODO - split respiratory tract mucosa from respiratory system mucosa respiratory system mucosa The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 gastrointestinal system mucosa larynx mucous gland See comments for 'skin mucus' skin mucous gland secretion of endocrine pancreas secretion of exocrine pancreas esophagus secretion pancreas secretion blood vessel layer https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg respiratory tract epithelium respiratory system epithelium gastrointestinal system epithelium See https://github.com/obophenotype/uberon/issues/1305 nephron tubule epithelium lower respiratory tract epithelium composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0] larynx epithelium lacrimal gland epithelium kidney epithelium bile duct epithelium extrahepatic bile duct epithelium intrahepatic bile duct epithelium urethra skeletal muscle tissue respiratory system skeletal muscle Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal esophagus skeletal muscle anal region skeletal muscle 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 lip skeletal muscle hepatic duct smooth muscle respiratory system arterial endothelium respiratory system venous endothelium aorta endothelium consider merging with 'endothelium' cardiovascular system endothelium gastrointestinal system mesentery skeletal muscle connective tissue Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands eye gland vasculature of retina splanchnic layer of lateral plate mesoderm TODO - check relationship to LPM splanchnopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png 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 somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png part_of or develops_from urogenital ridge? nephrogenic cord 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] urogenital fold WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. chordamesoderm lung mesenchyme urogenital sinus epithelium for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II) neuron projection bundle connecting eye with brain articulation ectodermal part of digestive tract lower digestive tract upper digestive tract 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 epithelium of gonad 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 epithelium of female gonad biliary bud http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg duodenal papilla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png sphincter of hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png anal sphincter urethral sphincter intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. subdivision of digestive tract organ component layer submucosa of pharynx submucosa of cystic duct submucosa of sigmoid colon submucosa of body of stomach submucosa of pyloric antrum submucosa of pylorus submucosa of biliary tree submucosa of common bile duct submucosa of common hepatic duct submucosa of right hepatic duct submucosa of left hepatic duct submucosa of urinary bladder submucosa of bronchiole mucosa of ureter mucosa of cystic duct mucosa of sigmoid colon mucosa of body of stomach mucosa of pyloric antrum mucosa of pylorus mucosa of biliary tree mucosa of common bile duct mucosa of common hepatic duct mucosa of right hepatic duct mucosa of left hepatic duct mucosa of right ureter mucosa of left ureter mucosa of renal pelvis mucosa of female urethra mucosa of tongue mucosa of lower lip mucosa of gallbladder mucosa of bronchiole mucosa of terminal bronchiole 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 external female genitalia immune organ hemolymphoid system gland neural groove neural fold neural rod hindbrain-spinal cord boundary metanephric ureteric bud ureter ureteric bud tube lumen 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. ectodermal placode 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 muscle structure right horn of sinus venosus class added for consistency with GO - consider merging with kidney mesenchyme. kidney rudiment mesonephric epithelium metanephric tubule metanephric epithelium metanephric smooth muscle tissue metanephric nephron metanephric cortex mesenchyme metanephric cortical collecting duct metanephric nephron epithelium metanephric capsule metanephric nephron tubule metanephric renal vesicle epithelial bud reproductive structure epithelial fold parenchyma of central nervous system multi cell part structure 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 hepatic duct abdomen element abdominal segment element dorsal region element trunk region element thoracic cavity element pelvic region element thoracic segment organ thoracic vein larynx submucosa gland right atrium valve optic eminence surface ectoderm liver right lobe parenchyma liver left lobe parenchyma optic eminence ectoderm basal plate metencephalon TODO - split? interventricular septum endocardium bulbus cordis myocardium metanephric renal pelvis check this stomatodeum gland yolk sac cavity head mesenchyme trunk mesenchyme renal cortex artery renal cortex vein 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 myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg embryonic tissue extraembryonic tissue pronephric nephron pronephric nephron tubule endocardial endothelium pulmonary artery endothelium mesonephric collecting duct mesonephric smooth muscle tissue mesonephric nephron mesonephric mesenchyme mesonephric nephron epithelium mesonephric renal vesicle oral lamina propria outflow tract of ventricle merge with LVOT? outflow tract aortic component merge with RVOT? outflow tract pulmonary component vagus X ganglion photoreceptor array directing or focusing light onto light receptors transparent eye structure 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 carotid artery segment female reproductive gland 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) forelimb bud Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick. hindlimb bud at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future pectoral appendage bud at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future pelvic appendage bud pectoral appendage apical ectodermal ridge pelvic appendage apical ectodermal ridge developing anatomical structure presumptive neural retina lens vesicle corneal primordium vagal neural crest aortic sac common hepatic artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png jugular foramen http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left vitelline vein https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right vitelline vein sulcus limitans of neural tube the MA placement should be checked venous dural sinus https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.gif vitelline vein http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png glossopharyngeal neural crest neural tube lateral wall 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). non-neural ectoderm primitive heart tube rhombomere lateral wall todo - compare ZFA and EHDAA2 representation trigeminal neural crest this is a very broad grouping class gonad primordium in humans this includes somites 1-4 head somite lung primordium trunk somite dorsal mesogastrium extrahepatic part of hepatic duct iliac vein left dorsal aorta 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 lens anterior epithelium includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries mesenteric artery In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein mesenteric vein right dorsal aorta stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)] extraembryonic membrane https://github.com/obophenotype/uberon/wiki/Modeling-extraembryonic-membranes pyloric region epithelium anterior chamber epithelium lens vesicle epithelium 2nd arch ectoderm 3rd arch ectoderm 4th arch ectoderm 2nd arch endoderm 3rd arch endoderm 4th arch endoderm peritoneal cavity mesothelium right lung endothelium left lung endothelium midgut dorsal mesentery lens vesicle cavity 2nd arch mesenchyme 3rd arch mesenchyme 4th arch mesenchyme optic eminence mesenchyme foregut duodenum mesentery midgut duodenum mesentery hindbrain venous system 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 pronephric mesoderm 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]. olfactory system chemosensory system extraembryonic mesoderm pectoral appendage field pelvic appendage field 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. paired limb/fin field 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) limb field 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 tunica adventitia of blood vessel https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg tunica intima of artery adventitia http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg bone foramen http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png caudal part of nephrogenic cord rostral part of nephrogenic cord acellular membrane 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. basement membrane of epithelium TODO - check ridge vs cord vs nephrogenic cord vs blastema nephric ridge section of aorta dorsal aorta http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png portal system developing mesenchymal condensation cartilaginous condensation pre-muscle condensation pre-cartilage condensation check develops_from mandibular prominence hyoid arch skeleton TODO - check occipital region See notes for serous membrane serous sac endo-epithelium zone of bone organ axial skeleton plus cranial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg outflow tract of atrium outflow part of right ventricle outflow part of left ventricle outflow part of right atrium outflow part of left atrium heart layer TODO - change relation from part_of coronary vessel atrioventricular septum Development notes:; the vitelline arteries give rise to the celiac artery, superior mesenteric artery, and inferior mesenteric artery in the adult[MP:0010664] vitelline artery http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. integumentary adnexa posterior surface of head mesonephric capsule aortico-pulmonary spiral septum http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png buccopharyngeal membrane http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png common atrial chamber foregut-midgut junction future brain future spinal cord gallbladder primordium the collection consisting of the two lateral swellings and the medial swelling lingual swellings mouth-foregut junction TODO - check ordering; awaiting confirmation from JB notochordal plate 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. notochordal process 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] future cardiac ventricle spleen primordium 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 future trigeminal ganglion chamber of eyeball ocular refraction ocular refractive media bodily fluid brainstem nucleus 2 Grouping for anterior and posterior communicating artery inferred from artery superior vesical vein skin secretion female reproductive gland secretion respiratory system fluid/secretion kidney vasculature renal duct excretory tube currently this is an extremely generic class, encompassing both protostomes and deuterostomes. 2023-04-20 branchial pharyngeal pharynx tunica media of pulmonary trunk female urethral meatus left ventricle myocardium right ventricle myocardium pectinate line http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png vestibular organ presumptive endoderm presumptive blood Consider merging with anlage presumptive structure presumptive ectoderm presumptive mesoderm 2 this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints mandibular symphysis http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png check if it is valid to group ZFA class here. venous sinus 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. muscular coat carotid canal http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png venous valve surface of epithelium hypoglossal canal 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] median lingual swelling http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png paired lateral lingual swelling http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343 corneo-scleral junction http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png consider splitting epithelium from epithelial tissue glandular epithelium areolar connective tissue lumen of trachea uterus or analog Surface groove is modelled as immaterial - see https://github.com/obophenotype/uberon/issues/2667 for discussion surface groove https://github.com/obophenotype/uberon/issues/2667 muscular coat of ureter this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. terminal part of digestive tract vasculature of organ vasculature of liver merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme head mesenchyme from mesoderm mandibular process mesenchyme lumen of digestive tract lip epithelium squamous epithelium stratified squamous epithelium non-keratinized epithelium of tongue tongue squamous epithelium esophagus squamous epithelium stomach squamous epithelium 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. stomach glandular epithelium digestive system gland glandular columnar epithelium stomach glandular region mucosa sensory epithelium ovary stroma vascular cord coronary capillary 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. anatomical surface consider FBbt:00005541 ! cardiogenic mesoderm review EHDAA2 placement cardiogenic splanchnic mesoderm cleaving embryo presumptive gut mechanosensory system mandibular neural crest hyoid neural crest 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 Gene notes: Bmp, Nkx, Gata primary circulatory organ pharyngeal pouch 1 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. pharyngeal pouch 2 pharyngeal pouch 3 trunk ganglion neural keel lumen of midgut lumen of hindgut lumen of anal canal lumen of colon inferior petrosal sinus lamina propria of mucosa of colon mesothelium of serous pericardium tracheobronchial tree brachiocephalic vasculature mesenchyme derived from head neural crest mesenchyme derived from trunk neural crest relationship to Meckel's cartilage to be added 1st arch mandibular component tunica media of artery tunica adventitia of artery tunica adventitia of vein tunica intima of vein tunica media of vein nuclear complex of neuraxis 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. nucleus of superior olivary complex trachea pre-cartilage rings currently defined by location rather than attachment pectoral appendage musculature currently defined by location rather than attachment pelvic appendage musculature currently defined by location rather than attachment appendage musculature pectoral appendage skeleton pelvic appendage skeleton TODO - unify naming conventions presumptive hindbrain presumptive sinus venosus presumptive endocardium presumptive midbrain hindbrain boundary presumptive segmental plate consider merging presumptive neural plate presumptive paraxial mesoderm presumptive pronephric mesoderm pectoral appendage blood vessel appendage blood vessel pectoral appendage vasculature pharyngeal vasculature appendage vasculature TODO - check In mice many lobules lack islets, in contrast to other mammals including humans pancreatic lobule this class groups together accessory (dorsal) and main (ventral) pancreatic ducts pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png surface of tongue this grouping class exists primarily to align with GO - see GO:0008544. outer epithelium 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. enveloping layer of ectoderm paired limb/fin cartilage pectoral appendage cartilage tissue pelvic appendage cartilage tissue this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species nucleus of midbrain tegmentum lumen of epithelial sac matrix-based tissue epithelial sac epithelial tube open at both ends arborizing epithelial duct system epithelial vesicle smooth muscle sphincter dense mesenchyme tissue this class will be an important part of the NC reorganization migrating mesenchyme population 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] ciliated columnar epithelium ciliated epithelium layer of synovial tissue synovial cavity of joint pigment epithelium of eye nucleus of medulla oblongata trigeminal nuclear complex http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx future meninx ectomeninx 2 anatomical junction 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 esophageal sphincter uriniferous tubule kidney field anlage relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' early pharyngeal endoderm gustatory pore https://upload.wikimedia.org/wikipedia/commons/0/0e/Taste_bud.svg bone of reproductive organ epidermis gland transudative characteristically low in protein and cellular content (unless there has been secondary concentration) transudate secretion of serous gland consider merging with vasculature vascular system adipose tissue of abdominal region craniocervical region this encompasses non-skeletal tissue appendage girdle region peritoneal mesentery girdle bone/zone pectoral girdle bone 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 pelvic girdle bone/zone pectoral girdle skeleton http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png membrane bone cartilage element 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). regular connective tissue dense regular connective tissue bone of craniocervical region irregular bone joint of girdle surface of cartilage 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] pneumatized bone muscle of pectoral girdle pelvic cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg craniocervical region musculature 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. heart endothelium microvascular endothelium https://github.com/obophenotype/uberon/issues/2186 intestinal villus of duodenum duodenal epithelium tracheobronchial epithelium 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. inner cell mass derived epiblast Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing pharyngeal arch system embryonic head a reasoner should automatically classify all the vertebrate ontology brain classes here neural tube derived brain https://github.com/obophenotype/uberon/issues/338 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. hepatic diverticulum http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png liver bud stomach muscularis externa pyloric canal https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg check relationship to pylorus vs antrum pyloric gastric gland http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this hypodermis skeletal muscle layer pulmonary vascular system 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 splanchnocranium http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg post-hyoid pharyngeal arch other AOs are not yet in sync with this classification dermal bone 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 perichordal bone lung parenchyma respiratory primordium forelimb bone renal parenchyma submucosal esophageal gland http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg vasculature of brain periurethral tissue vesical artery pudendal vein left pulmonary vein right pulmonary vein typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] indifferent gonad Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion petrosal placode Epibranchial ganglia orchestrate the development of the cranial neurogenic crest epibranchial ganglion right atrium endocardium craniocervical region vein consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) entire embryonic mesenchyme pharyngeal region of foregut indifferent external genitalia 2 we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA craniofacial suture 2 facial suture limb epidermis pronephric duct or mesonephric duct nephric duct dorsum of tongue ectoderm of buccopharyngeal membrane endoderm of buccopharyngeal membrane associated mesenchyme of foregut-midgut junction mesentery of foregut-midgut junction pharyngeal arch mesenchymal region epithelium of foregut-midgut junction mesenchyme of hindgut mesenchyme of trachea anal membrane endodermal component lateral lingual swelling epithelium endoderm of foregut-midgut junction intestinal submucosa subdivision of trunk spinal cord sulcus limitans medulla oblongata sulcus limitans metencephalon sulcus limitans myelencephalon sulcus limitans midbrain mantle layer spinal cord mantle layer 1st arch mandibular mesenchyme left lung associated mesenchyme right lung associated mesenchyme TODO - developmental relationships for lines midbrain hindbrain boundary neural plate TODO - unify naming conventions presumptive midbrain A major contributor to neurocranium [PMID:16313393] head paraxial mesoderm trunk paraxial mesoderm trachea non-cartilage connective tissue nephron tubule basement membrane bronchus basement membrane trachea basement membrane artery of lip midbrain nucleus hindbrain nucleus gut mesentery https://github.com/obophenotype/uberon/issues/509 embryonic cloacal lumen rectal lumen dorsal pancreas ventral pancreas endocardium of right ventricle endocardium of left ventricle stomodeal lumen entire pharyngeal arch endoderm limb mesenchyme decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts cardiac mesenchyme pancreas mesenchyme abdominal ganglion this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules renal tubule acinar glandular acinus http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png urogenital sinus lumen embryonic cloacal epithelium nematode larva digestive tract diverticulum sac 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 zone of stomach http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish. nephrogenic zone anterior lateral plate mesoderm 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 medullary ray interlobar artery https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png interlobar vein https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png in mouse has left ventricular identity[PMID:22855565] secondary heart field facial mesenchyme todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland) lobule anatomical lobe todo - add has_part relationships. renal lobe https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png 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 renal lobule wall of ureter ureter smooth muscle optic neural crest post-embryonic organism https://github.com/obophenotype/uberon/issues/667 Includes: trigeminal, otic, lateral line and epibranchial placodes. neurogenic placode in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this epithelium of pancreatic duct ureteropelvic junction ureterovesical junction multicellular anatomical structure May be obsoleted. aggregate regional part of brain 6th arch mesenchyme This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates food storage organ 1st arch mesenchyme entire pharyngeal arch associated mesenchyme oral gland check surface terms develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN:1607950324 mucosa of dorsum of tongue future tongue hypoglossal cord TODO - coordinate with CL, add cuboidal cell cuboidal epithelium future common hepatic duct check development future dermis future hindbrain meninx future metencephalon future myelencephalon future superior salivatory nucleus conducting tissue of heart neuroendocrine gland skin mucus lumen of blood vessel female urethral gland requires review protuberance right atrium venous valve aortic system genital artery hepatic portal system 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) bona-fide anatomical boundary check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton laryngeal apparatus laryngeal pre-cartilage condensation Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6? laryngeal associated mesenchyme future cardiac atrium See notes for camera-type eye eyeball of camera-type eye 1st arch mandibular mesenchyme from neural crest 2nd arch mesenchyme from neural crest 3rd arch mesenchyme from neural crest 4th arch mesenchyme from neural crest 6th arch mesenchyme from neural crest mesenchyme from rhombencephalic neural crest 1st arch mesenchyme from 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). hyoid apparatus zone of hyoid bone midbrain basal plate we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed midbrain neural tube layer of sclera scleral endothelium substantia propria of sclera 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 scleral mesenchyme extraembryonic epithelium non-keratinized stratified squamous epithelium immature eye Grouping term for query purposes neural crest-derived structure Grouping term for query purposes structure with developmental contribution from neural crest germ layer / neural crest skeletal element of eye region 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 cranial skeletal system limb bud mesenchyme paired limb/fin bud mesenchyme extraembryonic membrane mesenchyme 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 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from head mesenchyme endoskeleton endochondral element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO dermal skeleton pulmonary lobule ecto-epithelium consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen') pancreas dorsal primordium Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen') pancreas ventral primordium the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives mesenchyme from somatopleure mesenchyme from splanchnopleure lumen of urethra ocular surface region urethral opening ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png 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 flat bone 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 columnar epithelium pseudostratified ciliated columnar epithelium replacement element microcirculatory vessel cavity of bone organ pneumatic cavity of bone metanephros induced blastemal cells primitive nephron metanephros cortex primitive mesonephric nephron primitive metanephric nephron nephron progenitor mesonephric nephron progenitor 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] appendage girdle complex pectoral complex pelvic complex note the distinction between this and skeleton of limb limb skeleton subdivision girdle skeleton bone of appendage girdle complex considering adding pectoral and pelvic complex skeleton classes bone of pectoral complex bone of pelvic complex meningeal In some primitive organisms, the meningeal cluster includes only the primitive meninx meningeal cluster limb cartilage element limb bone pre-cartilage condensation forelimb cartilage element forelimb bone pre-cartilage condensation hindlimb cartilage element hindlimb pre-cartilage condensation pelvic complex muscle the MA class belongs here, based on its current child classes pectoral complex muscle subdivision of skeleton craniocervical muscle pharyngeal arch cartilage skeleton of right pelvic girdle skeleton of left pelvic girdle https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right pelvic girdle region https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left pelvic girdle region lacrimal nerve synovial joint of pelvic girdle synovial joint of pectoral girdle laryngeal joint nonsynovial joint axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. synovial limb joint upper urinary tract submucosal gland facial skeleton http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg primary subdivision of skull primary subdivision of cranial skeletal system neurocranium bone gastrointestinal sphincter lamina propria of large intestine ophthalmic vein http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png superior ophthalmic vein http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png muscle layer of large intestine muscle layer of small intestine central nervous system cell part cluster organ system subdivision intra-ocular muscle 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 appendicular skeletal system https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton 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] dorsal trunk compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' embryonic skin basal layer extrinsic tongue pre-muscle mass cranial blood vasculature lumen of gastrointestinal system lumen of esophagus mesonephric duct lumen paired limb/fin skeleton consider obsoleting, coordinate with VSAO cell condensation jaw region http://eol.org/collections/11578 future lower lip oral epithelium from ectoderm jaw muscle 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 embryonic cardiovascular system The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP] left recurrent laryngeal nerve https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg right recurrent laryngeal nerve lower jaw opening vagus nerve nucleus nucleus of spinal cord nerve of head region non-neurogenic ectodermal placode atrioventricular region irregular connective tissue dense irregular connective tissue 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. dense connective tissue fibrous connective tissue loose connective tissue acinus of lacrimal gland acinus of exocrine gland collection of collagen fibrils aorta collagen fibril pulmonary collagen fibril bone collagen fibril tendon collagen fibril corneal stroma collagen fibril muscle layer of esophagus anterior uvea The Epimysium also protects muscles from friction against other muscles and bones epimysium yolk sac blood island 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 stomach glandular region left hepatic vein right hepatic vein 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. coelomic coelom myocoele replacement bone stomach primordium head or neck skin urethral meatus abdominal aorta artery columnar epithelium meso-epithelium 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 embryonic cloacal fold mucosa of urethra embryonic facial prominence cervical artery deep cervical artery transverse cervical artery Do not manually classify under here - bones are automatically classified bone of jaw internal anal region muscle layer of intestine Contains nerves, blood vessels, lymphatics and lymph nodes subserosa muscle layer of urinary bladder respiratory system arterial smooth muscle respiratory system venous 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 layer of microvilli striated border microvillus layer tunica fibrosa of eyeball cloacal lumen cloacal vent includes the cloacal lumen, in species where this is present lumen of terminal part of digestive tract extraembryonic cavity enclosed anatomical space external anal region skeleton of pectoral complex skeleton of pelvic complex cloacal gland cloacal mucosa cloacal epithelium submucosa of cloaca serosa of cloaca cloacal villus muscle layer of cloaca muscle layer of duodenum muscle layer of colon muscle layer of anal canal adventitia of esophagus gastroduodenal junction mucosa of gastroduodenal junction 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 vein of abdomen vein of lip systemic vein 1st arch mandibular endoderm foregut-midgut junction gland ovarian cortex serous acinus embryonic urethral groove cranial cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg lung endothelium the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938). cloacal sphincter space surrounding organism subdivision of tube stomach lumen epithelium of intestinal villus foramen of skull 2 anatomical conduit space brain endothelium colon endothelium exocrine pancreas epithelium axial musculature main body axis body proper notochordal canal Distinct feature of coelocanths notochordal fluid integumentary system layer arterial blood venous blood capillary blood digestive system element Groupings may vary - typically pulmonary vessels and aorta and vena cavae great vessel of heart mesenchyme derived from neural crest 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 kidney collecting duct epithelium gustatory papilla of tongue this class may be merged with 'respiratory system muscle'; check intercostals respiratory muscle renal venous blood vessel tongue taste bud gustatory epithelium of tongue visceral abdominal adipose tissue subcutaneous abdominal adipose tissue thoracic skeleton anal membrane ectodermal component median lingual swelling epithelium primitive renal collecting duct system interlobular duct mucous acinus intralobular duct interlobar duct midbrain neuromere spinal neuromere cloacal muscle lingual septum currently defined by location rather than attachment musculature of pelvic complex currently defined by location rather than attachment musculature of pectoral complex pectoral appendage muscle pelvic appendage muscle skeletal muscle organ primordial vasculature intersomitic vessel forelimb endochondral element hindlimb endochondral element limb endochondral element consider merging into myocardial compact layer subepicardial layer of epicardium epicardial fat 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] gland of ocular region 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 lateral gland of orbital region multi-unit eye somite border somite boundary epithelium non-connected functional system glandular system This class is primarily to implement taxon constraints. It may be removed in the future. lateral structure circulatory organ pancreas left lobe pancreas right lobe respiratory system basement membrane heart plus pericardium urethra mesenchymal layer ureteral valve proper hepatic artery left hepatic artery right hepatic artery choledocho-duodenal junction anal canal epithelium smooth muscle layer in fatty layer of subcutaneous tissue liver blood vessel eye epithelium foregut epithelium duodenum lamina propria pulmonary capillary liver stroma auditory system cavity of right ventricle lumen of duodenum cavity of left atrium cavity of left ventricle epithelium of female urethra cavity of right atrium pharyngeal ectoderm central nervous system gray matter layer phlegm respiratory system mucus pit lamina of gray matter of spinal cord future central nervous system future nervous system epithelium of terminal part of digestive tract muscle tissue of terminal part of digestive tract entire extraembryonic component transitional anatomical structure paired venous dural sinus dorsal body wall developing mesenchymal structure abdominal viscera muscle layer of rectum rectum smooth muscle tissue left renal pelvis right renal pelvis fibrocollagenous connective tissue