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 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 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 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 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 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 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 X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes true 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 true 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 inverse of directly develops from developmental precursor of directly develops into true 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 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 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 inverse of has developmental contribution from developmentally contributes to 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 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 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 inverse of has input input of 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 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 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 developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y has potential to developmentally induce 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 A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. 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) 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 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 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 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 inverse of branching part of has branching part 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 p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 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 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 has-input qualifier has number of atomic nuclei BFO:0000001 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]) BFO:0000002 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] BFO:0000003 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] BFO:0000004 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] BFO:0000006 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] BFO:0000015 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] BFO:0000016 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] BFO:0000017 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] BFO:0000019 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] BFO:0000020 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] BFO:0000023 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] BFO:0000034 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] BFO:0000040 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] BFO:0000141 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 CHEBI:10545 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 CHEBI:131604 Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. Mycoplasma genitalium metabolite CHEBI:131927 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 CHEBI:132153 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 CHEBI:134179 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 CHEBI:137982 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 CHEBI:138000 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 CHEBI:138103 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 CHEBI:138675 Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). gas molecular entity CHEBI:13941 -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 CHEBI:142163 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 CHEBI:15339 A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. acceptor CHEBI:15377 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 CHEBI:15734 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 CHEBI:15841 A peptide containing ten or more amino acid residues. C4H6N2O3R2(C2H2NOR)n polypeptide CHEBI:16134 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 CHEBI:16189 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 CHEBI:16234 -1 HO InChI=1S/H2O/h1H2/p-1 XLYOFNOQVPJJNP-UHFFFAOYSA-M 17.00734 17.00329 [O-][H] hydroxide CHEBI:16236 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 CHEBI:16336 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 CHEBI:16541 A naturally occurring polypeptide synthesized at the ribosome. protein polypeptide chain CHEBI:16646 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 CHEBI:16670 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 CHEBI:167559 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 CHEBI:16990 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 CHEBI:17089 A compound in which a carbohydrate component is covalently bound to a protein component. glycoprotein CHEBI:17303 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 CHEBI:176497 Any compound that supports healthy aging, slows the biological aging process, or extends lifespan. geroprotector CHEBI:17688 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 CHEBI:17790 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 CHEBI:17891 A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. donor CHEBI:18059 '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 CHEBI:18085 Any polysaccharide containing a substantial proportion of aminomonosaccharide residues. glycosaminoglycan CHEBI:18154 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 CHEBI:18723 A racemate composed of equimolar amounts of (R)- and (S)-nicotine. nicotine CHEBI:22221 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 CHEBI:22314 alkali metal atom CHEBI:22315 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 CHEBI:22506 aminoglycan CHEBI:22563 A monoatomic or polyatomic species having one or more elementary charges of the electron. anion CHEBI:22586 A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. antioxidant CHEBI:22695 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 CHEBI:22712 Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. benzenes CHEBI:22723 Any aromatic carboxylic acid that consists of benzene in which at least a single hydrogen has been substituted by a carboxy group. benzoic acids CHEBI:22868 A sodium salt of the conjugate of any bile acid with either glycine or taurine. bile salt CHEBI:22917 An insecticide compound naturally occurring in plants. phytogenic insecticide CHEBI:23004 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 CHEBI:23019 0 CO 28.01010 27.99491 O=C(*)* carbonyl group CHEBI:23357 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 CHEBI:23367 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity CHEBI:23888 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 CHEBI:23906 monoatomic cation CHEBI:23924 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 CHEBI:23982 Any primary alcohol based on an ethanol skeleton. ethanols CHEBI:24431 A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity CHEBI:24432 A role played by the molecular entity or part thereof within a biological context. biological role CHEBI:24433 A defined linked collection of atoms or a single atom within a molecular entity. group CHEBI:24532 A cyclic compound having as ring members atoms of carbon and at least of one other element. organic heterocyclic compound CHEBI:24651 Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). hydroxides CHEBI:24782 imide CHEBI:24833 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 CHEBI:24834 inorganic anion CHEBI:24835 A molecular entity that contains no carbon. inorganic molecular entity CHEBI:24836 inorganic oxide CHEBI:24852 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 CHEBI:24866 A salt is an assembly of cations and anions. salt CHEBI:24867 monoatomic ion CHEBI:24868 organic salt CHEBI:24870 A molecular entity having a net electric charge. ion CHEBI:24921 Any alkaloid that has a structure based on an isoquinoline nucleus. They are derived from the amino acids like tyrosine and phenylalanine. isoquinoline alkaloid CHEBI:25046 linear tetrapyrrole CHEBI:25212 Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. metabolite CHEBI:25213 metal cation CHEBI:25248 Any carboxylic ester resulting from the formal condensation of a carboxy group with methanol. 0 C2H3O2R 59.044 59.01330 COC([*])=O methyl ester CHEBI:25367 Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule CHEBI:25414 +1 0.00000 [*+] monoatomic monocation CHEBI:25418 An isoquinoline alkaloid based on a morphinan skeleton and its substituted derivatives. morphinane alkaloid CHEBI:25555 0 N 14.007 14.00307 nitrogen atom CHEBI:25585 nonmetal atom CHEBI:25693 organic heteromonocyclic compound CHEBI:25696 Any organic ion with a net negative charge. organic anion CHEBI:25697 Any organic ion with a net positive charge. organic cation CHEBI:25699 organic ion CHEBI:25704 Compounds of the general formula SO3HOR where R is an organyl group organic sulfate CHEBI:2571 An alcohol derived from an aliphatic compound. 0 HOR 17.007 17.00274 O* aliphatic alcohol CHEBI:25741 An oxide is a chemical compound of oxygen with other chemical elements. oxide CHEBI:25805 0 O InChI=1S/O QVGXLLKOCUKJST-UHFFFAOYSA-N 15.99940 15.99491 [O] oxygen atom CHEBI:25806 oxygen molecular entity CHEBI:25944 Strictly, a substance intended to kill pests. In common usage, any substance used for controlling, preventing, or destroying animal, microbiological or plant pests. pesticide CHEBI:26416 pyridine alkaloid CHEBI:26421 Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives. pyridines CHEBI:26456 pyrrolidine alkaloid CHEBI:26708 0 Na InChI=1S/Na KEAYESYHFKHZAL-UHFFFAOYSA-N 22.98977 22.98977 [Na] sodium atom CHEBI:26712 sodium molecular entity CHEBI:26714 Any alkali metal salt having sodium(1+) as the cation. sodium salt CHEBI:26819 An ester of an alcohol and sulfuric acid. 0 O4SR2 96.06300 95.95173 [*]OS(=O)(=O)O[*] sulfuric ester CHEBI:26820 Salts and esters of sulfuric acid sulfates CHEBI:26833 0 S InChI=1S/S NINIDFKCEFEMDL-UHFFFAOYSA-N 32.06600 31.97207 [S] sulfur atom CHEBI:26835 sulfur molecular entity CHEBI:26836 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 CHEBI:26932 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 CHEBI:27171 organic heterobicyclic compound CHEBI:27207 A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid. univalent carboacyl group CHEBI:27369 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 CHEBI:27594 0 C InChI=1S/C OKTJSMMVPCPJKN-UHFFFAOYSA-N 12.01070 12.00000 [C] carbon atom CHEBI:27958 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 CHEBI:28616 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 CHEBI:28938 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 CHEBI:28965 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 CHEBI:29067 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 CHEBI:29101 A monoatomic monocation obtained from sodium. +1 Na InChI=1S/Na/q+1 FKNQFGJONOIPTF-UHFFFAOYSA-N 22.98977 22.98922 [Na+] sodium(1+) CHEBI:29337 -1 H2N InChI=1S/H2N/h1H2/q-1 HYGWNUKOUCZBND-UHFFFAOYSA-N 16.02262 16.01927 [H][N-][H] azanide CHEBI:29340 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-) CHEBI:29412 +1 H3O InChI=1S/H2O/h1H2/p+1 XLYOFNOQVPJJNP-UHFFFAOYSA-O 19.02322 19.01784 [H][O+]([H])[H] oxonium CHEBI:30879 A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. 0 HOR 17.007 17.00274 O[*] alcohol CHEBI:32111 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 CHEBI:32988 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 CHEBI:33232 Intended use of the molecular entity or part thereof by humans. application CHEBI:33233 A particle not known to have substructure. fundamental particle CHEBI:33238 A monoatomic entity is a molecular entity consisting of a single atom. monoatomic entity CHEBI:33241 oxoacid derivative CHEBI:33242 inorganic hydride CHEBI:33245 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 CHEBI:33246 Any substituent group which does not contain carbon. inorganic group CHEBI:33247 Any substituent group or skeleton containing carbon. organic group CHEBI:33249 Any organic substituent group, regardless of functional type, having one free valence at a carbon atom. organyl group CHEBI:33250 A chemical entity constituting the smallest component of an element having the chemical properties of the element. atom uncharged atom CHEBI:33252 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 CHEBI:33253 Heavy nuclear particle: proton or neutron. nucleon CHEBI:33256 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 CHEBI:33257 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 CHEBI:33259 A molecular entity all atoms of which have the same atomic number. elemental molecular entity CHEBI:33261 An organosulfur compound is a compound containing at least one carbon-sulfur bond. organosulfur compound CHEBI:33273 An anion consisting of more than one atom. polyatomic anion CHEBI:33281 A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. antimicrobial agent CHEBI:33284 A nutrient is a food component that an organism uses to survive and grow. nutrient CHEBI:33285 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 CHEBI:33290 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 CHEBI:33292 An energy-rich substance that can be transformed with release of usable energy. fuel CHEBI:33296 A molecular entity containing one or more atoms of an alkali metal. alkali metal molecular entity CHEBI:33300 Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogen CHEBI:33302 A p-block molecular entity containing any pnictogen. pnictogen molecular entity CHEBI:33303 Any p-block element belonging to the group 16 family of the periodic table. chalcogen CHEBI:33304 Any p-block molecular entity containing a chalcogen. chalcogen molecular entity CHEBI:33306 carbon group element atom CHEBI:33308 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 CHEBI:33318 An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group element atom CHEBI:33402 sulfur oxoacid CHEBI:33424 sulfur oxoacid derivative CHEBI:33482 sulfur oxoanion CHEBI:33484 chalcogen oxoacid CHEBI:33485 chalcogen oxoanion CHEBI:33504 alkali metal cation CHEBI:33521 An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. metal atom CHEBI:33558 An amino-acid anion obtained by deprotonation of any alpha-amino acid. alpha-amino-acid anion CHEBI:33559 s-block element atom CHEBI:33560 Any main group element atom belonging to the p-block of the periodic table. p-block element atom CHEBI:33575 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 CHEBI:33579 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 CHEBI:33582 carbon group molecular entity CHEBI:33595 Any molecule that consists of a series of atoms joined together to form a ring. cyclic compound CHEBI:33597 A cyclic compound having as ring members atoms of the same element only. homocyclic compound CHEBI:33598 A homocyclic compound in which all of the ring members are carbon atoms. carbocyclic compound CHEBI:33608 hydrogen molecular entity CHEBI:33635 polycyclic compound CHEBI:33636 A molecule that features two fused rings. bicyclic compound CHEBI:33655 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 CHEBI:33659 organic aromatic compound CHEBI:33661 monocyclic compound CHEBI:33670 heteromonocyclic compound CHEBI:33671 A polycyclic compound in which at least one of the rings contains at least one non-carbon atom. heteropolycyclic compound CHEBI:33672 A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compound CHEBI:33674 An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity CHEBI:33675 A main group molecular entity that contains one or more atoms of a p-block element. p-block molecular entity CHEBI:33692 Hydrides are chemical compounds of hydrogen with other chemical elements. hydrides CHEBI:33693 oxygen hydride CHEBI:33694 A macromolecule formed by a living organism. biomacromolecule CHEBI:33695 information biomacromolecule CHEBI:33700 proteinogenic amino-acid residue CHEBI:33702 A cation consisting of more than one atom. polyatomic cation CHEBI:33704 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 CHEBI:33708 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 CHEBI:33709 A carboxylic acid containing one or more amino groups. amino acid CHEBI:33710 alpha-amino-acid residue CHEBI:33720 carbohydrate acid CHEBI:33721 carbohydrate acid anion CHEBI:33822 An organic compound having at least one hydroxy group attached to a carbon atom. organic hydroxy compound CHEBI:33832 Any organic molecule that consists of atoms connected in the form of a ring. organic cyclic compound CHEBI:33833 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 CHEBI:33836 benzenoid aromatic compound CHEBI:33837 Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion. conjugated protein CHEBI:33839 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 CHEBI:33859 Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring. aromatic carboxylic acid CHEBI:33893 A substance used in a chemical reaction to detect, measure, examine, or produce other substances. reagent CHEBI:33937 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 CHEBI:35106 nitrogen hydride CHEBI:35107 Saturated acyclic nitrogen hydrides having the general formula NnHn+2. azane CHEBI:35222 A substance that diminishes the rate of a chemical reaction. inhibitor CHEBI:35223 A substance that increases the rate of a reaction without modifying the overall standard Gibbs energy change in the reaction. catalyst CHEBI:35238 The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group. amino acid zwitterion CHEBI:35274 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 CHEBI:35337 Any drug that enhances the activity of the central nervous system. central nervous system stimulant CHEBI:35341 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 CHEBI:35352 Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compound CHEBI:35406 An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. oxoanion CHEBI:35441 A substance used in the prophylaxis or therapy of infectious diseases. antiinfective agent CHEBI:35470 A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system. central nervous system drug CHEBI:35471 A loosely defined grouping of drugs that have effects on psychological function. psychotropic drug CHEBI:35473 A traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behaviour. tranquilizing drug CHEBI:35474 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 CHEBI:35479 alkali metal salt CHEBI:35480 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 CHEBI:35482 A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. opioid analgesic CHEBI:35488 A loosely defined group of drugs that tend to reduce the activity of the central nervous system. central nervous system depressant CHEBI:35506 alkaloid fundamental parent CHEBI:35507 natural product fundamental parent CHEBI:35508 steroid fundamental parent CHEBI:35519 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 CHEBI:35524 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 CHEBI:35554 A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. cardiovascular drug CHEBI:35605 carbon oxoacid CHEBI:35617 A food additive that is used to added improve the taste or odour of a food. flavouring agent CHEBI:35620 A drug used to cause dilation of the blood vessels. vasodilator agent CHEBI:35640 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 CHEBI:35649 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 CHEBI:35692 Any carboxylic acid containing two carboxy groups. dicarboxylic acid CHEBI:35693 dicarboxylic acid anion CHEBI:35701 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 CHEBI:35703 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 CHEBI:35722 sulfated glycosaminoglycan CHEBI:35724 carbohydrate sulfate CHEBI:35881 pnictogen hydride CHEBI:35942 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 CHEBI:36054 Esters of benzoic acid or substituted benzoic acids. benzoate ester CHEBI:36078 cholanoid CHEBI:36080 A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. protein CHEBI:36277 A salt of a bile acid. bile acid salt CHEBI:36333 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 CHEBI:36338 Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). lepton CHEBI:36339 Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). baryon CHEBI:36340 Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion CHEBI:36342 A particle smaller than an atom. subatomic particle subatomic particle CHEBI:36343 A subatomic particle known to have substructure (i.e. consisting of smaller particles). composite particle CHEBI:36344 Hadron is a subatomic particle which experiences the strong force. hadron CHEBI:36347 A nucleus or any of its constituents in any of their energy states. nuclear particle CHEBI:36357 Any molecular entity consisting of more than one atom. polyatomic entity CHEBI:36358 An ion consisting of more than one atom. polyatomic ion CHEBI:36586 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 CHEBI:36587 Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. organic oxo compound CHEBI:36735 Compounds based on a biladiene skeleton. biladienes CHEBI:36902 chalcogen hydride CHEBI:36914 inorganic ion CHEBI:36915 inorganic cation CHEBI:36916 A monoatomic or polyatomic species having one or more elementary charges of the proton. cation CHEBI:36962 An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound CHEBI:36963 An organochalcogen compound containing at least one carbon-oxygen bond. organooxygen compound CHEBI:37022 amino-acid anion CHEBI:37175 organic hydride CHEBI:37176 mononuclear parent hydride CHEBI:37246 elemental sodium CHEBI:37332 tropane alkaloid CHEBI:37395 Any of the group of polysaccharides composed of alternating units from uronic acids and glycosamines, and commonly partially esterified with sulfuric acid. mucopolysaccharide CHEBI:37527 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 CHEBI:37577 A molecular entity consisting of two or more chemical elements. heteroatomic molecular entity CHEBI:37622 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 CHEBI:37716 Any imide in which the acyl substituents are any two from carboacyl, sulfonyl and phosphoryl mixed diacylamine CHEBI:37826 sulfuric acid derivative CHEBI:37838 A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid. carboacyl group CHEBI:37947 benzothiazoles CHEBI:37962 Any agent that acts on an adrenergic receptor or affects the life cycle of an adrenergic transmitter. adrenergic agent CHEBI:38077 A compound composed of two or more pyrrole units. polypyrrole CHEBI:38101 Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. organonitrogen heterocyclic compound CHEBI:38106 organosulfur heterocyclic compound CHEBI:38164 organic heteropentacyclic compound CHEBI:38166 organic heteropolycyclic compound CHEBI:38260 Any of a class of heterocyclic amines having a saturated five-membered ring. pyrrolidines CHEBI:38295 azabicycloalkane CHEBI:38323 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 CHEBI:38324 Any drug that binds to and activates cholinergic receptors. cholinergic agonist CHEBI:38515 isoquinoline alkaloid fundamental parent CHEBI:38632 Any agent that affects the transport of molecular entities across a biological membrane. membrane transport modulator CHEBI:38633 An agent that inhibits sodium influx through cell membranes. sodium channel blocker CHEBI:38700 organic sodium salt CHEBI:38716 Any dianion containing at least one carboxy group. carboxylic acid dianion CHEBI:38867 Substance which produces loss of feeling or sensation. anaesthetic CHEBI:39000 sodium channel modulator CHEBI:39141 A molecular entity capable of donating a hydron to an acceptor (Bronsted base). Bronsted acid CHEBI:39142 A molecular entity capable of accepting a hydron from a donor (Bronsted acid). Bronsted base CHEBI:39144 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 CHEBI:39162 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 CHEBI:43176 0 HO 17.00734 17.00274 *O[H] hydroxy group CHEBI:45696 -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 CHEBI:46629 0 O 15.99940 15.99491 O=* oxo group CHEBI:46775 N-alkylpyrrolidine CHEBI:46787 A liquid that can dissolve other substances (solutes) without any change in their chemical composition. solvent CHEBI:46883 0 CHO2 45.01744 44.99765 *C(=O)O carboxy group CHEBI:47867 Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc. indicator CHEBI:47958 An agonist that selectively binds to and activates a nicotinic acetylcholine receptor. nicotinic acetylcholine receptor agonist CHEBI:48154 sulfur oxide CHEBI:48218 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 CHEBI:48219 An antimicrobial agent that is applied to non-living objects to destroy harmful microorganisms or to inhibit their activity. disinfectant CHEBI:48278 serotonergic drug CHEBI:48354 A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds. polar solvent CHEBI:48356 A polar solvent that is capable of acting as a hydron (proton) donor. protic solvent CHEBI:48359 Solvent that is capable of acting as a hydron (proton) acceptor. protophilic solvent CHEBI:48360 Self-ionizing solvent possessing both characteristics of Bronsted acids and bases. amphiprotic solvent CHEBI:48560 A drug used for its effects on dopamine receptors, on the life cycle of dopamine, or on the survival of dopaminergic neurons. dopaminergic agent CHEBI:48705 Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own. agonist CHEBI:48706 Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances. antagonist CHEBI:49110 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 CHEBI:49637 0 H InChI=1S/H YZCKVEUIGOORGS-UHFFFAOYSA-N 1.00794 1.00783 [H] hydrogen atom CHEBI:50047 A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. organic amino compound CHEBI:50267 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 CHEBI:50312 onium compound CHEBI:50313 Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families. onium cation CHEBI:50505 Substance that sweeten food, beverages, medications, etc. sweetening agent CHEBI:50514 Drug used to cause constriction of the blood vessels. vasoconstrictor agent CHEBI:50584 An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position. alkyl alcohol CHEBI:50846 Biologically active substance whose activity affects or plays a role in the functioning of the immune system. immunomodulator CHEBI:50860 Any molecular entity that contains carbon. organic molecular entity CHEBI:50904 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 CHEBI:50905 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 CHEBI:50906 A role is particular behaviour which a material entity may exhibit. role CHEBI:50910 A poison that interferes with the functions of the nervous system. neurotoxin CHEBI:50949 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 CHEBI:50996 A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups. tertiary amino compound CHEBI:51039 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 CHEBI:51086 A role played by the molecular entity or part thereof within a chemical context. chemical role CHEBI:51143 nitrogen molecular entity CHEBI:51151 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 CHEBI:51422 Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s). organodiyl group CHEBI:51446 organic divalent group CHEBI:51447 organic univalent group CHEBI:51958 organic polycyclic compound CHEBI:52090 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 CHEBI:52092 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 CHEBI:52206 A biological role played by the molecular entity or part thereof within a biochemical context. biochemical role CHEBI:52208 biophysical role CHEBI:52209 A role played by the molecular entity or part thereof which causes the development of a pathological process. aetiopathogenetic role CHEBI:52210 A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties. pharmacological role CHEBI:52211 physiological role CHEBI:52217 Any substance introduced into a living organism with therapeutic or diagnostic purpose. pharmaceutical CHEBI:52290 A chemical substance that encourages a cell to commence cell division, triggering mitosis. mitogen CHEBI:52625 inorganic hydroxy compound CHEBI:53000 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 CHEBI:53309 A polymer carrying multiple negative charges. polyanionic macromolecule CHEBI:53368 A macromolecule containing ionic groups. ionic macromolecule CHEBI:55322 A compound that exhibits agonist activity at the mu-opioid receptor. mu-opioid receptor agonist CHEBI:55505 A benzothiazole consisting of a benzene ring fused to an isothiazole. 1,2-benzisothiazole CHEBI:5686 A cyclic compound having as ring members atoms of at least two different elements. heterocyclic compound CHEBI:57977 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-) CHEBI:58097 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+) CHEBI:58958 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 CHEBI:59163 A substance used as an indicator of a biological state. biomarker CHEBI:59252 An organic anion arising from deprotonation of a acyclic tetrapyrrole compound. linear tetrapyrrole anion CHEBI:59740 A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons. nucleophilic reagent CHEBI:59806 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+) CHEBI:59999 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 CHEBI:60004 A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. mixture CHEBI:60027 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 CHEBI:60056 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+) CHEBI:60164 An ionic polymer is a polymer, composed of ionic macromolecules. ionic polymer CHEBI:60242 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 CHEBI:60466 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 CHEBI:60598 Any agent that acts on an opioid receptor or affects the life cycle of an opioid transmitter. opioid agent CHEBI:60599 Any agent that acts on a mu-opioid receptor. mu-opioid agent CHEBI:60606 An agent that selectively binds to and activates an opioid receptor. opioid receptor agonist CHEBI:60643 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 CHEBI:60798 Any substance which inhibits the action of receptors for excitatory amino acids. excitatory amino acid antagonist CHEBI:60911 A racemate is an equimolar mixture of a pair of enantiomers. racemate CHEBI:61469 A polymer, composed of polyanion macromolecules. polyanionic polymer CHEBI:62732 An ester where the ester linkage is bonded directly to an aromatic system. aromatic ester CHEBI:63299 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 CHEBI:63436 A carbohydrate derivative that is formally obtained from a carbohydrate acid. carbohydrate acid derivative CHEBI:63551 A carboxylic acid anion resulting from the deprotonation of the carboxy group of a carbohydrate acid derivative. carbohydrate acid derivative anion CHEBI:64018 An agonist that selectively binds to and activates a protein kinase C receptor protein kinase C agonist CHEBI:64047 Any substance which is added to food to preserve or enhance its flavour and/or appearance. food additive CHEBI:64106 An agonist that selectively binds to and activates a protein kinase receptor. protein kinase agonist CHEBI:64708 An organic molecular entity containing a single carbon atom (C1). one-carbon compound CHEBI:64709 Any organic molecular entity that is acidic and contains carbon in covalent linkage. organic acid CHEBI:64909 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 CHEBI:65212 A carbohydrate derivative that is any derivative of a polysaccharide. polysaccharide derivative CHEBI:72695 Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. organic molecule CHEBI:72813 A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment. exopolysaccharide CHEBI:75763 Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms. eukaryotic metabolite CHEBI:75767 Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals. animal metabolite CHEBI:75768 Any animal metabolite produced during a metabolic reaction in mammals. mammalian metabolite CHEBI:75771 Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus). mouse metabolite CHEBI:75772 Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae). Saccharomyces cerevisiae metabolite CHEBI:75787 Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. prokaryotic metabolite CHEBI:76413 A gas in an atmosphere that absorbs and emits radiation within the thermal infrared range, so contributing to the 'greenhouse effect'. greenhouse gas CHEBI:76759 Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*). EC 3.* (hydrolase) inhibitor CHEBI:76764 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 CHEBI:76807 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 CHEBI:76924 Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms. plant metabolite CHEBI:76946 Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds. fungal metabolite CHEBI:76969 Any prokaryotic metabolite produced during a metabolic reaction in bacteria. bacterial metabolite CHEBI:76971 Any bacterial metabolite produced during a metabolic reaction in Escherichia coli. Escherichia coli metabolite CHEBI:77746 Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens). human metabolite CHEBI:77941 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 CHEBI:78295 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 CHEBI:78298 Any minor or unwanted substance introduced into the environment that can have undesired effects. environmental contaminant CHEBI:78433 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 CHEBI:78608 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 CHEBI:78616 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 CHEBI:79008 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+) CHEBI:79388 Any inorganic anion with a valency of two. divalent inorganic anion CHEBI:79389 Any inorganic anion with a valency of one. monovalent inorganic anion CHEBI:88188 Any drug which causes the onset of an allergic reaction. drug allergen CHEBI:90852 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 CHEBI:91007 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 COB:0000011 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 COB:0000013 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 COB:0000073 gene product COB:0000080 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) GO:0000003 reproduction GO:0000271 polysaccharide biosynthetic process GO:0000272 polysaccharide catabolic process GO:0001101 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 GO:0001501 skeletal system development GO:0001503 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 GO:0001659 temperature homeostasis GO:0001667 Note that this term refers to a mode of migration rather than to any particular cell type. ameboidal-type cell migration GO:0001696 gastric acid secretion GO:0001704 formation of primary germ layer GO:0001705 ectoderm formation GO:0001706 endoderm formation GO:0001707 mesoderm formation GO:0001763 morphogenesis of a branching structure GO:0001820 serotonin secretion GO:0001838 embryonic epithelial tube formation GO:0001841 neural tube formation GO:0001957 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 GO:0002009 morphogenesis of an epithelium GO:0002027 regulation of heart rate GO:0002053 positive regulation of mesenchymal cell proliferation GO:0002087 regulation of respiratory gaseous exchange by nervous system process GO:0002118 aggressive behavior GO:0002119 nematode larval development GO:0002120 https://github.com/geneontology/go-ontology/issues/18568 This term was obsoleted because it is outside the scope of GO. obsolete predatory behavior true GO:0002164 larval development GO:0002251 organ or tissue specific immune response GO:0002376 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 GO:0002384 hepatic immune response GO:0002682 regulation of immune system process GO:0002683 negative regulation of immune system process GO:0002684 positive regulation of immune system process GO:0002790 peptide secretion GO:0002791 regulation of peptide secretion GO:0002792 negative regulation of peptide secretion GO:0002793 positive regulation of peptide secretion GO:0003006 developmental process involved in reproduction GO:0003008 system process GO:0003012 muscle system process GO:0003013 circulatory system process GO:0003014 renal system process GO:0003015 heart process GO:0003016 respiratory system process GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. This is the same as GO molecular function gene product or complex activity molecular_function GO:0003824 catalytic activity GO:0005575 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 GO:0005576 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 GO:0005577 fibrinogen complex GO:0005581 collagen trimer GO:0005583 fibrillar collagen trimer GO:0005585 collagen type II trimer GO:0005587 collagen type IV trimer GO:0005604 Note that this term has no relationship to 'membrane ; GO:0016020' because the basement membrane is not a lipid bilayer. basement membrane GO:0005615 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 GO:0005622 https://github.com/geneontology/go-ontology/issues/17776 intracellular anatomical structure GO:0005737 https://github.com/geneontology/go-ontology/issues/23023 cytoplasm GO:0005856 cytoskeleton GO:0005884 actin filament GO:0005886 plasma membrane GO:0005902 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 GO:0005911 https://github.com/geneontology/go-ontology/issues/22122 cell-cell junction GO:0005938 cell cortex GO:0005975 https://github.com/geneontology/go-ontology/issues/22880 carbohydrate metabolic process GO:0005976 polysaccharide metabolic process GO:0005977 glycogen metabolic process GO:0005978 glycogen biosynthetic process GO:0005979 regulation of glycogen biosynthetic process GO:0005980 glycogen catabolic process GO:0005981 regulation of glycogen catabolic process GO:0005996 monosaccharide metabolic process GO:0006006 glucose metabolic process GO:0006082 organic acid metabolic process GO:0006091 generation of precursor metabolites and energy GO:0006109 regulation of carbohydrate metabolic process GO:0006112 energy reserve metabolic process GO:0006629 lipid metabolic process GO:0006694 steroid biosynthetic process GO:0006699 bile acid biosynthetic process GO:0006793 phosphorus metabolic process GO:0006796 phosphate-containing compound metabolic process GO:0006810 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 GO:0006811 monoatomic ion transport GO:0006837 serotonin transport GO:0006858 extracellular transport GO:0006869 lipid transport GO:0006886 intracellular protein transport GO:0006936 muscle contraction GO:0006937 regulation of muscle contraction GO:0006939 smooth muscle contraction GO:0006940 regulation of smooth muscle contraction GO:0006950 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 GO:0006955 immune response GO:0007154 cell communication GO:0007267 cell-cell signaling GO:0007275 https://github.com/geneontology/go-ontology/issues/21234 Note that this term was 'developmental process'. multicellular organism development GO:0007276 gamete generation GO:0007369 gastrulation GO:0007398 ectoderm development GO:0007399 nervous system development GO:0007492 endoderm development GO:0007498 mesoderm development GO:0007585 respiratory gaseous exchange by respiratory system GO:0007586 digestion GO:0007588 https://github.com/geneontology/go-ontology/issues/22368 excretion GO:0007589 body fluid secretion GO:0007600 sensory perception GO:0007601 visual perception GO:0007605 sensory perception of sound GO:0007606 sensory perception of chemical stimulus GO:0007608 sensory perception of smell GO:0007610 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 GO:0007617 mating behavior GO:0007619 courtship behavior GO:0007620 copulation GO:0007622 rhythmic behavior GO:0007623 circadian rhythm GO:0007625 groom grooming behavior GO:0007626 locomotory behavior GO:0007629 fly flight behavior GO:0007631 https://github.com/geneontology/go-ontology/issues/18547 See also the biological process term 'behavior ; GO:0007610'. feeding behavior GO:0007632 visual behavior GO:0007635 chemosensory behavior GO:0007638 mechanosensory behavior GO:0008015 blood circulation GO:0008016 regulation of heart contraction GO:0008049 male courtship behavior GO:0008050 female courtship behavior GO:0008104 https://github.com/geneontology/go-ontology/issues/23112 protein localization GO:0008150 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 GO:0008152 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 GO:0008202 steroid metabolic process GO:0008206 bile acid metabolic process GO:0008283 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 GO:0008284 positive regulation of cell population proliferation GO:0008285 negative regulation of cell population proliferation GO:0008344 See also the biological process term 'locomotory behavior ; GO:0007626'. adult locomotory behavior GO:0008610 lipid biosynthetic process GO:0009056 catabolic process GO:0009057 macromolecule catabolic process GO:0009058 biosynthetic process GO:0009059 http://amigo.geneontology.org/amigo/term/GO:0070589 macromolecule biosynthetic process GO:0009250 glucan biosynthetic process GO:0009251 glucan catabolic process GO:0009266 response to temperature stimulus GO:0009306 protein secretion GO:0009314 Note that 'radiation' refers to electromagnetic radiation of any wavelength. response to radiation GO:0009414 response to water deprivation GO:0009415 response to water GO:0009416 response to light stimulus GO:0009581 detection of external stimulus GO:0009582 detection of abiotic stimulus GO:0009583 detection of light stimulus GO:0009584 detection of visible light GO:0009593 detection of chemical stimulus GO:0009605 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 GO:0009612 response to mechanical stimulus GO:0009628 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 GO:0009653 anatomical structure morphogenesis GO:0009790 embryo development GO:0009791 post-embryonic development GO:0009792 embryo development ending in birth or egg hatching GO:0009888 tissue development GO:0009889 regulation of biosynthetic process GO:0009890 negative regulation of biosynthetic process GO:0009891 positive regulation of biosynthetic process GO:0009892 negative regulation of metabolic process GO:0009893 positive regulation of metabolic process GO:0009894 regulation of catabolic process GO:0009895 negative regulation of catabolic process GO:0009896 positive regulation of catabolic process GO:0009914 hormone transport GO:0009987 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 GO:0010033 response to organic substance GO:0010035 response to inorganic substance GO:0010463 mesenchymal cell proliferation GO:0010464 regulation of mesenchymal cell proliferation GO:0010470 regulation of gastrulation GO:0010556 regulation of macromolecule biosynthetic process GO:0010557 positive regulation of macromolecule biosynthetic process GO:0010558 negative regulation of macromolecule biosynthetic process GO:0010562 positive regulation of phosphorus metabolic process GO:0010563 negative regulation of phosphorus metabolic process GO:0010565 regulation of cellular ketone metabolic process GO:0010604 positive regulation of macromolecule metabolic process GO:0010605 negative regulation of macromolecule metabolic process GO:0010646 regulation of cell communication GO:0010647 positive regulation of cell communication GO:0010648 negative regulation of cell communication GO:0010700 negative regulation of norepinephrine secretion GO:0010701 positive regulation of norepinephrine secretion GO:0010817 regulation of hormone levels GO:0010876 lipid localization GO:0010893 positive regulation of steroid biosynthetic process GO:0010894 negative regulation of steroid biosynthetic process GO:0010906 regulation of glucose metabolic process GO:0010907 positive regulation of glucose metabolic process GO:0010962 regulation of glucan biosynthetic process GO:0010996 response to auditory stimulus GO:0012506 vesicle membrane GO:0014061 regulation of norepinephrine secretion GO:0014062 regulation of serotonin secretion GO:0014063 negative regulation of serotonin secretion GO:0014064 positive regulation of serotonin secretion GO:0014821 phasic smooth muscle contraction GO:0014832 urinary bladder smooth muscle contraction GO:0014848 urinary tract smooth muscle contraction GO:0015031 protein transport GO:0015629 actin cytoskeleton GO:0015695 organic cation transport GO:0015711 organic anion transport GO:0015718 monocarboxylic acid transport GO:0015721 bile acid and bile salt transport GO:0015833 peptide transport GO:0015837 amine transport GO:0015844 monoamine transport GO:0015849 organic acid transport GO:0015850 organic hydroxy compound transport GO:0015874 norepinephrine transport GO:0015980 energy derivation by oxidation of organic compounds GO:0016020 membrane GO:0016043 cellular component organization GO:0016048 detection of temperature stimulus GO:0016051 carbohydrate biosynthetic process GO:0016052 carbohydrate catabolic process GO:0016053 organic acid biosynthetic process true GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity GO:0016310 phosphorylation GO:0016331 morphogenesis of embryonic epithelium GO:0016477 https://github.com/geneontology/go-ontology/issues/24787 cell migration GO:0016740 transferase activity GO:0016772 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 GO:0019098 https://github.com/geneontology/go-ontology/issues/23491 reproductive behavior GO:0019216 regulation of lipid metabolic process GO:0019218 regulation of steroid metabolic process GO:0019220 regulation of phosphate metabolic process GO:0019222 regulation of metabolic process GO:0019233 sensory perception of pain GO:0019318 hexose metabolic process GO:0019752 carboxylic acid metabolic process GO:0019953 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 GO:0021915 neural tube development GO:0022410 circadian sleep/wake cycle process GO:0022412 cellular process involved in reproduction in multicellular organism GO:0022414 reproductive process GO:0022600 digestive system process GO:0022603 regulation of anatomical structure morphogenesis GO:0023051 regulation of signaling GO:0023052 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 GO:0023056 positive regulation of signaling GO:0023057 negative regulation of signaling GO:0023061 signal release GO:0030054 cell junction GO:0030072 peptide hormone secretion GO:0030073 https://github.com/geneontology/go-ontology/issues/11255#issuecomment-426191045 insulin secretion GO:0030278 regulation of ossification GO:0030279 negative regulation of ossification GO:0030312 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 GO:0030334 regulation of cell migration GO:0030335 positive regulation of cell migration GO:0030336 negative regulation of cell migration GO:0030421 defecation GO:0030431 sleep GO:0030432 peristalsis GO:0030534 See also the biological process term 'behavior ; GO:0007610'. adult behavior GO:0030659 cytoplasmic vesicle membrane GO:0030936 transmembrane collagen trimer GO:0031012 extracellular matrix GO:0031090 organelle membrane GO:0031223 auditory behavior GO:0031323 regulation of cellular metabolic process GO:0031324 negative regulation of cellular metabolic process GO:0031325 positive regulation of cellular metabolic process GO:0031326 regulation of cellular biosynthetic process GO:0031327 negative regulation of cellular biosynthetic process GO:0031328 positive regulation of cellular biosynthetic process GO:0031329 regulation of cellular catabolic process GO:0031330 negative regulation of cellular catabolic process GO:0031331 positive regulation of cellular catabolic process GO:0031410 cytoplasmic vesicle GO:0031644 regulation of nervous system process GO:0031645 negative regulation of nervous system process GO:0031646 positive regulation of nervous system process GO:0031982 vesicle GO:0031987 locomotion involved in locomotory behavior GO:0032024 positive regulation of insulin secretion GO:0032101 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 GO:0032102 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 GO:0032103 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 GO:0032368 regulation of lipid transport GO:0032369 negative regulation of lipid transport GO:0032370 positive regulation of lipid transport GO:0032386 regulation of intracellular transport GO:0032387 negative regulation of intracellular transport GO:0032388 positive regulation of intracellular transport GO:0032432 actin filament bundle GO:0032501 multicellular organismal process GO:0032502 developmental process GO:0032504 multicellular organism reproduction GO:0032594 protein transport within lipid bilayer GO:0032787 monocarboxylic acid metabolic process GO:0032838 plasma membrane bounded cell projection cytoplasm GO:0032879 regulation of localization GO:0032880 https://github.com/geneontology/go-ontology/issues/22021 regulation of protein localization GO:0032881 regulation of polysaccharide metabolic process GO:0032885 regulation of polysaccharide biosynthetic process GO:0032890 regulation of organic acid transport GO:0032891 negative regulation of organic acid transport GO:0032892 positive regulation of organic acid transport GO:0032940 secretion by cell GO:0032941 secretion by tissue GO:0032991 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 GO:0033036 macromolecule localization GO:0033157 regulation of intracellular protein transport GO:0033604 negative regulation of catecholamine secretion GO:0033605 positive regulation of catecholamine secretion GO:0033673 negative regulation of kinase activity GO:0033674 positive regulation of kinase activity GO:0035148 tube formation GO:0035176 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 GO:0035239 tube morphogenesis GO:0035295 tube development GO:0035592 establishment of protein localization to extracellular region GO:0035809 regulation of urine volume GO:0036072 direct ossification GO:0036477 somatodendritic compartment GO:0040011 locomotion GO:0040012 regulation of locomotion GO:0040013 negative regulation of locomotion GO:0040016 embryonic cleavage GO:0040017 positive regulation of locomotion GO:0040019 positive regulation of embryonic development GO:0042074 cell migration involved in gastrulation GO:0042127 regulation of cell population proliferation GO:0042180 cellular ketone metabolic process GO:0042221 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 GO:0042320 regulation of circadian sleep/wake cycle, REM sleep GO:0042321 negative regulation of circadian sleep/wake cycle, sleep GO:0042322 negative regulation of circadian sleep/wake cycle, REM sleep GO:0042323 negative regulation of circadian sleep/wake cycle, non-REM sleep GO:0042325 regulation of phosphorylation GO:0042326 negative regulation of phosphorylation GO:0042327 positive regulation of phosphorylation GO:0042592 homeostatic process GO:0042745 circadian sleep/wake cycle GO:0042747 circadian sleep/wake cycle, REM sleep GO:0042748 circadian sleep/wake cycle, non-REM sleep GO:0042749 regulation of circadian sleep/wake cycle GO:0042752 regulation of circadian rhythm GO:0042753 positive regulation of circadian rhythm GO:0042754 negative regulation of circadian rhythm GO:0042755 eating behavior GO:0042756 drinking behavior GO:0042886 amide transport GO:0042995 cell projection GO:0043005 neuron projection GO:0043009 chordate embryonic development GO:0043025 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 GO:0043085 positive regulation of catalytic activity GO:0043086 negative regulation of catalytic activity GO:0043170 macromolecule metabolic process GO:0043226 organelle GO:0043227 membrane-bounded organelle GO:0043228 https://github.com/geneontology/go-ontology/issues/21881 non-membrane-bounded organelle GO:0043229 intracellular organelle GO:0043230 extracellular organelle GO:0043231 intracellular membrane-bounded organelle GO:0043232 intracellular non-membrane-bounded organelle GO:0043255 regulation of carbohydrate biosynthetic process GO:0043264 extracellular non-membrane-bounded organelle GO:0043269 regulation of monoatomic ion transport GO:0043270 positive regulation of monoatomic ion transport GO:0043271 negative regulation of monoatomic ion transport GO:0043436 oxoacid metabolic process GO:0043467 regulation of generation of precursor metabolites and energy GO:0043470 regulation of carbohydrate catabolic process GO:0043549 regulation of kinase activity GO:0043576 regulation of respiratory gaseous exchange GO:0044042 glucan metabolic process GO:0044057 regulation of system process GO:0044058 regulation of digestive system process GO:0044060 regulation of endocrine process GO:0044062 regulation of excretion GO:0044065 regulation of respiratory system process GO:0044092 negative regulation of molecular function GO:0044093 positive regulation of molecular function GO:0044237 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 GO:0044238 primary metabolic process GO:0044248 cellular catabolic process GO:0044249 cellular biosynthetic process GO:0044281 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule metabolic process GO:0044283 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule biosynthetic process GO:0044297 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 GO:0045184 establishment of protein localization GO:0045187 regulation of circadian sleep/wake cycle, sleep GO:0045188 regulation of circadian sleep/wake cycle, non-REM sleep GO:0045297 This term was obsoleted because it was not precisely defined. obsolete post-mating behavior true GO:0045719 negative regulation of glycogen biosynthetic process GO:0045725 positive regulation of glycogen biosynthetic process GO:0045778 positive regulation of ossification GO:0045818 negative regulation of glycogen catabolic process GO:0045819 positive regulation of glycogen catabolic process GO:0045822 negative regulation of heart contraction GO:0045823 positive regulation of heart contraction GO:0045833 negative regulation of lipid metabolic process GO:0045834 positive regulation of lipid metabolic process GO:0045912 negative regulation of carbohydrate metabolic process GO:0045913 positive regulation of carbohydrate metabolic process GO:0045932 negative regulation of muscle contraction GO:0045933 positive regulation of muscle contraction GO:0045936 negative regulation of phosphate metabolic process GO:0045937 positive regulation of phosphate metabolic process GO:0045938 positive regulation of circadian sleep/wake cycle, sleep GO:0045939 negative regulation of steroid metabolic process GO:0045940 positive regulation of steroid metabolic process GO:0045986 negative regulation of smooth muscle contraction GO:0045987 positive regulation of smooth muscle contraction GO:0045992 negative regulation of embryonic development GO:0045995 regulation of embryonic development GO:0046005 positive regulation of circadian sleep/wake cycle, REM sleep GO:0046010 positive regulation of circadian sleep/wake cycle, non-REM sleep GO:0046394 carboxylic acid biosynthetic process GO:0046676 negative regulation of insulin secretion GO:0046717 acid secretion GO:0046879 hormone secretion GO:0046883 regulation of hormone secretion GO:0046887 positive regulation of hormone secretion GO:0046888 negative regulation of hormone secretion GO:0046889 positive regulation of lipid biosynthetic process GO:0046890 regulation of lipid biosynthetic process GO:0046903 secretion GO:0046907 intracellular transport GO:0046942 carboxylic acid transport GO:0048243 norepinephrine secretion GO:0048332 mesoderm morphogenesis GO:0048511 rhythmic process GO:0048512 circadian behavior GO:0048513 animal organ development GO:0048518 positive regulation of biological process GO:0048519 negative regulation of biological process GO:0048520 positive regulation of behavior GO:0048521 negative regulation of behavior GO:0048522 positive regulation of cellular process GO:0048523 negative regulation of cellular process GO:0048580 regulation of post-embryonic development GO:0048581 negative regulation of post-embryonic development GO:0048582 positive regulation of post-embryonic development GO:0048583 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 GO:0048584 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 GO:0048585 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 GO:0048598 embryonic morphogenesis GO:0048609 multicellular organismal reproductive process GO:0048646 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 GO:0048729 tissue morphogenesis GO:0048731 system development GO:0048754 branching morphogenesis of an epithelial tube GO:0048770 pigment granule GO:0048856 anatomical structure development GO:0048870 https://github.com/geneontology/go-ontology/issues/19809 cell motility GO:0048871 multicellular organismal-level homeostasis GO:0050432 catecholamine secretion GO:0050433 regulation of catecholamine secretion GO:0050708 regulation of protein secretion GO:0050709 negative regulation of protein secretion GO:0050714 positive regulation of protein secretion GO:0050776 regulation of immune response GO:0050777 negative regulation of immune response GO:0050778 positive regulation of immune response GO:0050789 regulation of biological process GO:0050790 regulation of catalytic activity GO:0050793 regulation of developmental process GO:0050794 regulation of cellular process GO:0050795 regulation of behavior GO:0050796 regulation of insulin secretion GO:0050802 circadian sleep/wake cycle, sleep GO:0050810 regulation of steroid biosynthetic process GO:0050877 https://github.com/geneontology/go-ontology/issues/13824 nervous system process GO:0050878 regulation of body fluid levels GO:0050879 multicellular organismal movement GO:0050881 musculoskeletal movement GO:0050882 voluntary musculoskeletal movement GO:0050885 neuromuscular process controlling balance GO:0050886 endocrine process GO:0050890 cognition GO:0050896 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 GO:0050905 neuromuscular process GO:0050906 detection of stimulus involved in sensory perception GO:0050907 detection of chemical stimulus involved in sensory perception GO:0050908 detection of light stimulus involved in visual perception GO:0050909 sensory perception of taste GO:0050910 detection of mechanical stimulus involved in sensory perception of sound GO:0050911 detection of chemical stimulus involved in sensory perception of smell GO:0050912 detection of chemical stimulus involved in sensory perception of taste GO:0050951 sensory perception of temperature stimulus GO:0050952 sensory perception of electrical stimulus GO:0050953 sensory perception of light stimulus GO:0050954 sensory perception of mechanical stimulus GO:0050955 thermoception GO:0050957 equilibrioception GO:0050960 detection of temperature stimulus involved in thermoception GO:0050961 detection of temperature stimulus involved in sensory perception GO:0050962 detection of light stimulus involved in sensory perception GO:0050963 detection of electrical stimulus involved in sensory perception GO:0050965 detection of temperature stimulus involved in sensory perception of pain GO:0050966 detection of mechanical stimulus involved in sensory perception of pain GO:0050967 detection of electrical stimulus involved in sensory perception of pain GO:0050968 detection of chemical stimulus involved in sensory perception of pain GO:0050973 detection of mechanical stimulus involved in equilibrioception GO:0050974 detection of mechanical stimulus involved in sensory perception GO:0050975 sensory perception of touch GO:0050976 detection of mechanical stimulus involved in sensory perception of touch GO:0050981 detection of electrical stimulus GO:0050982 detection of mechanical stimulus GO:0051046 regulation of secretion GO:0051047 positive regulation of secretion GO:0051048 negative regulation of secretion GO:0051049 regulation of transport GO:0051050 positive regulation of transport GO:0051051 negative regulation of transport GO:0051055 negative regulation of lipid biosynthetic process GO:0051093 negative regulation of developmental process GO:0051094 positive regulation of developmental process GO:0051128 regulation of cellular component organization GO:0051129 negative regulation of cellular component organization GO:0051130 positive regulation of cellular component organization GO:0051174 regulation of phosphorus metabolic process GO:0051179 localization GO:0051216 cartilage development GO:0051222 positive regulation of protein transport GO:0051223 regulation of protein transport GO:0051224 negative regulation of protein transport GO:0051234 establishment of localization GO:0051239 regulation of multicellular organismal process GO:0051240 positive regulation of multicellular organismal process GO:0051241 negative regulation of multicellular organismal process GO:0051301 Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division. cell division GO:0051302 regulation of cell division GO:0051338 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. regulation of transferase activity GO:0051347 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. positive regulation of transferase activity GO:0051348 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. negative regulation of transferase activity GO:0051356 visual perception involved in equilibrioception GO:0051602 response to electrical stimulus GO:0051606 detection of stimulus GO:0051641 cellular localization GO:0051649 establishment of localization in cell GO:0051703 https://github.com/geneontology/go-ontology/issues/20191 biological process involved in intraspecies interaction between organisms GO:0051781 positive regulation of cell division GO:0051782 negative regulation of cell division GO:0051930 regulation of sensory perception of pain GO:0051931 regulation of sensory perception GO:0051937 catecholamine transport GO:0051952 regulation of amine transport GO:0051953 negative regulation of amine transport GO:0051954 positive regulation of amine transport GO:0051960 regulation of nervous system development GO:0051961 negative regulation of nervous system development GO:0051962 positive regulation of nervous system development GO:0060004 reflex GO:0060005 vestibular reflex GO:0060047 heart contraction GO:0060073 micturition GO:0060083 smooth muscle contraction involved in micturition GO:0060179 male mating behavior GO:0060180 female mating behavior GO:0060255 regulation of macromolecule metabolic process GO:0060259 regulation of feeding behavior GO:0060273 crying behavior GO:0060341 regulation of cellular localization GO:0060429 epithelium development GO:0060453 regulation of gastric acid secretion GO:0060454 positive regulation of gastric acid secretion GO:0060455 negative regulation of gastric acid secretion GO:0060456 positive regulation of digestive system process GO:0060457 negative regulation of digestive system process GO:0060562 epithelial tube morphogenesis GO:0060688 regulation of morphogenesis of a branching structure GO:0061007 hepaticobiliary system process GO:0061024 membrane organization GO:0061035 regulation of cartilage development GO:0061036 positive regulation of cartilage development GO:0061037 negative regulation of cartilage development GO:0061062 regulation of nematode larval development GO:0061063 positive regulation of nematode larval development GO:0061064 negative regulation of nematode larval development GO:0061138 morphogenesis of a branching epithelium GO:0061448 connective tissue development GO:0062012 regulation of small molecule metabolic process GO:0062013 positive regulation of small molecule metabolic process GO:0062014 negative regulation of small molecule metabolic process GO:0062023 collagen-containing extracellular matrix GO:0062149 detection of stimulus involved in sensory perception of pain GO:0065007 biological regulation GO:0065008 regulation of biological quality GO:0065009 regulation of molecular function GO:0065010 extracellular membrane-bounded organelle GO:0070075 tear secretion GO:0070091 glucagon secretion GO:0070092 regulation of glucagon secretion GO:0070093 negative regulation of glucagon secretion GO:0070094 positive regulation of glucagon secretion GO:0070161 anchoring junction GO:0070201 regulation of establishment of protein localization GO:0070253 somatostatin secretion GO:0070254 mucus secretion GO:0070255 regulation of mucus secretion GO:0070256 negative regulation of mucus secretion GO:0070257 positive regulation of mucus secretion GO:0070727 cellular macromolecule localization GO:0070857 regulation of bile acid biosynthetic process GO:0070858 negative regulation of bile acid biosynthetic process GO:0070859 positive regulation of bile acid biosynthetic process GO:0070873 regulation of glycogen metabolic process GO:0070874 negative regulation of glycogen metabolic process GO:0070875 positive regulation of glycogen metabolic process GO:0071626 mastication GO:0071692 protein localization to extracellular region GO:0071702 organic substance transport GO:0071704 organic substance metabolic process GO:0071705 nitrogen compound transport GO:0071840 cellular component organization or biogenesis GO:0071944 cell periphery GO:0071953 elastic fiber GO:0072175 https://github.com/geneontology/go-ontology/issues/22302 epithelial tube formation GO:0072201 negative regulation of mesenchymal cell proliferation GO:0072330 monocarboxylic acid biosynthetic process GO:0080090 regulation of primary metabolic process GO:0080134 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 GO:0090087 regulation of peptide transport GO:0090257 regulation of muscle system process GO:0090273 regulation of somatostatin secretion GO:0090274 positive regulation of somatostatin secretion GO:0090275 negative regulation of somatostatin secretion GO:0090276 regulation of peptide hormone secretion GO:0090277 positive regulation of peptide hormone secretion GO:0090278 negative regulation of peptide hormone secretion GO:0090316 positive regulation of intracellular protein transport GO:0090317 negative regulation of intracellular protein transport GO:0090325 regulation of locomotion involved in locomotory behavior GO:0090326 positive regulation of locomotion involved in locomotory behavior GO:0090327 negative regulation of locomotion involved in locomotory behavior GO:0097254 https://github.com/geneontology/go-ontology/issues/22368 renal tubular secretion GO:0097708 intracellular vesicle GO:0098590 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 GO:0098642 network-forming collagen trimer GO:0098643 banded collagen fibril GO:0098644 complex of collagen trimers GO:0098645 collagen network GO:0098651 basement membrane collagen trimer GO:0098796 membrane protein complex GO:0098797 plasma membrane protein complex GO:0098801 regulation of renal system process GO:0098858 actin-based cell projection GO:0099080 supramolecular complex GO:0099081 supramolecular polymer GO:0099512 supramolecular fiber GO:0099513 polymeric cytoskeletal fiber GO:0099568 cytoplasmic region GO:0099738 cell cortex region GO:0110165 cellular anatomical entity GO:0120025 https://github.com/geneontology/go-ontology/issues/13193 plasma membrane bounded cell projection GO:0120111 https://github.com/geneontology/go-ontology/issues/14472 neuron projection cytoplasm GO:0140352 export from cell GO:1901360 organic cyclic compound metabolic process GO:1901362 organic cyclic compound biosynthetic process GO:1901575 organic substance catabolic process GO:1901576 organic substance biosynthetic process GO:1901615 organic hydroxy compound metabolic process GO:1901617 organic hydroxy compound biosynthetic process GO:1901700 response to oxygen-containing compound GO:1902074 response to salt GO:1902435 regulation of male mating behavior GO:1902436 negative regulation of male mating behavior GO:1902437 positive regulation of male mating behavior GO:1902584 positive regulation of response to water deprivation GO:1903522 regulation of blood circulation GO:1903523 negative regulation of blood circulation GO:1903524 positive regulation of blood circulation GO:1903530 regulation of secretion by cell GO:1903531 negative regulation of secretion by cell GO:1903532 positive regulation of secretion by cell GO:1903561 extracellular vesicle GO:1903828 https://github.com/geneontology/go-ontology/issues/22021 negative regulation of protein localization GO:1903829 https://github.com/geneontology/go-ontology/issues/22021 positive regulation of protein localization GO:1903941 negative regulation of respiratory gaseous exchange GO:1903942 positive regulation of respiratory gaseous exchange GO:1903998 regulation of eating behavior GO:1903999 negative regulation of eating behavior GO:1904000 positive regulation of eating behavior GO:1904057 negative regulation of sensory perception of pain GO:1904058 positive regulation of sensory perception of pain GO:1904251 regulation of bile acid metabolic process GO:1904252 negative regulation of bile acid metabolic process GO:1904253 positive regulation of bile acid metabolic process GO:1904318 regulation of smooth muscle contraction involved in micturition GO:1904319 negative regulation of smooth muscle contraction involved in micturition GO:1904320 positive regulation of smooth muscle contraction involved in micturition GO:1904950 negative regulation of establishment of protein localization GO:1904951 positive regulation of establishment of protein localization GO:1905276 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). regulation of epithelial tube formation GO:1905277 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). negative regulation of epithelial tube formation GO:1905278 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). positive regulation of epithelial tube formation GO:1905330 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). regulation of morphogenesis of an epithelium GO:1905331 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). negative regulation of morphogenesis of an epithelium GO:1905332 An example of this is MMRN2 in human (Q9H8L6) in PMID:25745997 (inferred from direct assay). positive regulation of morphogenesis of an epithelium GO:1905787 regulation of detection of mechanical stimulus involved in sensory perception of touch GO:1905788 negative regulation of detection of mechanical stimulus involved in sensory perception of touch GO:1905789 positive regulation of detection of mechanical stimulus involved in sensory perception of touch GO:1905790 regulation of mechanosensory behavior GO:1905791 negative regulation of mechanosensory behavior GO:1905792 positive regulation of mechanosensory behavior GO:1905902 regulation of mesoderm formation GO:1905903 negative regulation of mesoderm formation GO:1905904 positive regulation of mesoderm formation GO:1905952 regulation of lipid localization GO:1905953 negative regulation of lipid localization GO:1905954 positive regulation of lipid localization GO:2000026 regulation of multicellular organismal development GO:2000070 regulation of response to water deprivation GO:2000145 regulation of cell motility GO:2000146 negative regulation of cell motility GO:2000147 positive regulation of cell motility GO:2000241 regulation of reproductive process GO:2000242 negative regulation of reproductive process GO:2000243 positive regulation of reproductive process GO:2000252 negative regulation of feeding behavior GO:2000253 positive regulation of feeding behavior GO:2000292 regulation of defecation GO:2000293 negative regulation of defecation GO:2000294 positive regulation of defecation GO:2000380 regulation of mesoderm development GO:2000381 negative regulation of mesoderm development GO:2000382 positive regulation of mesoderm development GO:2000383 regulation of ectoderm development GO:2000384 negative regulation of ectoderm development GO:2000385 positive regulation of ectoderm development GO:2000542 negative regulation of gastrulation GO:2000543 positive regulation of gastrulation GO:2000821 regulation of grooming behavior NBO:0000001 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 NBO:0000002 2011-04-14T01:03:39Z George Gkoutos behavior_ontology whole body movement NBO:0000003 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 NBO:0000005 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 NBO:0000006 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 NBO:0000007 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 NBO:0000008 2011-04-14T01:03:39Z George Gkoutos behavior_ontology GO:0007622 rhythmic behavior NBO:0000009 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 NBO:0000010 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 NBO:0000011 "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 NBO:0000012 2011-04-14T01:03:39Z George Gkoutos behavior_ontology HP:0001250 MP:0002064 seizures/epilepsy NBO:0000013 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 NBO:0000014 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 NBO:0000015 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 NBO:0000016 "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 NBO:0000017 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 NBO:0000018 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 NBO:0000019 The act of stroking or touching with the tongue [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos lick behavior_ontology licking NBO:0000020 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 NBO:0000022 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 NBO:0000023 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 NBO:0000024 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 NBO:0000025 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 NBO:0000026 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 NBO:0000027 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 NBO:0000028 Absence of voluntary movement. 2011-04-14T12:59:27Z George Gkoutos behavior_ontology akinesia Absence of voluntary movement. NBO:GVG NBO:0000029 Reduction of voluntary movement. 2011-04-14T01:03:39Z George Gkoutos hypokinesia behavior_ontology bradykinesia Reduction of voluntary movement. NBO:GVG NBO:0000030 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 NBO:0000031 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 NBO:0000032 "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 NBO:0000033 "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 NBO:0000034 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 NBO:0000035 2011-04-14T01:03:39Z George Gkoutos behavior_ontology emission behavior NBO:0000036 2011-04-14T01:03:39Z George Gkoutos produce sound behavior_ontology behavioral control of production of sound NBO:0000037 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 NBO:0000038 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 NBO:0000039 The behavioral control of defecation. [wikipedia:defecation] 2011-04-14T01:03:39Z George Gkoutos behavior_ontology behavioral control of defecation NBO:0000040 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 NBO:0000041 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 NBO:0000042 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 NBO:0000043 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 NBO:0000044 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 NBO:0000045 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 NBO:0000047 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 NBO:0000048 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 NBO:0000049 "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 NBO:0000051 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 NBO:0000052 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 NBO:0000053 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 NBO:0000054 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 NBO:0000055 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 NBO:0000056 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 NBO:0000057 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 NBO:0000059 2011-04-14T01:03:39Z George Gkoutos behavior_ontology nuzzling NBO:0000060 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 NBO:0000061 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: NBO:0000062 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 NBO:0000063 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 NBO:0000064 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 NBO:0000065 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 NBO:0000066 "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 NBO:0000067 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 NBO:0000068 Repetitive movement of a body part. 2011-04-14T01:20:02Z George Gkoutos behavior_ontology shaking Repetitive movement of a body part. NBO:GVG NBO:0000069 2011-04-14T01:20:02Z George Gkoutos behavior_ontology swaying NBO:0000070 2011-04-14T01:20:02Z George Gkoutos behavior_ontology tilting NBO:0000071 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 NBO:0000073 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 NBO:0000074 2011-04-14T01:20:02Z George Gkoutos behavior_ontology yawning NBO:0000075 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 NBO:0000076 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 NBO:0000077 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 NBO:0000078 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 NBO:0000079 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 NBO:0000080 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 NBO:0000081 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 NBO:0000082 2011-04-14T01:20:02Z George Gkoutos writhe behavior_ontology writhing NBO:0000084 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 NBO:0000085 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 NBO:0000086 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 NBO:0000087 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 NBO:0000088 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 NBO:0000089 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 NBO:0000090 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 NBO:0000091 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 NBO:0000092 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 NBO:0000093 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 NBO:0000094 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 NBO:0000095 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 NBO:0000096 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 NBO:0000097 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 NBO:0000098 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 NBO:0000099 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 NBO:0000100 2011-03-31T10:28:39Z George Gkoutos behavior_ontology GO:0035640 exploration behavior NBO:0000101 Moving backwards. 2011-03-31T10:32:40Z George Gkoutos behavior_ontology retropulsion Moving backwards. NBO:GVG NBO:0000102 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 NBO:0000103 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 NBO:0000104 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 NBO:0000105 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 NBO:0000106 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 NBO:0000107 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 NBO:0000108 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 NBO:0000109 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 NBO:0000110 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 NBO:0000111 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 NBO:0000112 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 NBO:0000113 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 NBO:0000114 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 NBO:0000115 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 NBO:0000116 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 NBO:0000117 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 NBO:0000118 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 NBO:0000119 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 NBO:0000120 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 NBO:0000121 2011-03-31T11:42:15Z George Gkoutos agonism behavior_ontology agonistic behavior NBO:0000122 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 NBO:0000123 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 NBO:0000124 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 NBO:0000125 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 NBO:0000126 2011-03-31T11:47:31Z George Gkoutos behavior_ontology subordination behavior NBO:0000127 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 NBO:0000128 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 NBO:0000129 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 NBO:0000130 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 NBO:0000131 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 NBO:0000132 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 NBO:0000133 2011-03-31T12:41:50Z George Gkoutos behavior_ontology liquid preference/aversion NBO:0000134 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 NBO:0000135 2011-03-31T12:43:07Z George Gkoutos behavior_ontology food preference/aversion NBO:0000136 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 NBO:0000137 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 NBO:0000138 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 NBO:0000139 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 NBO:0000140 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 NBO:0000141 2011-03-31T12:58:43Z George Gkoutos behavior_ontology food preference NBO:0000142 2011-03-31T12:59:08Z George Gkoutos behavior_ontology food aversion NBO:0000143 2011-03-31T12:59:56Z George Gkoutos behavior_ontology saccharin preference NBO:0000144 2011-03-31T02:16:59Z George Gkoutos behavior_ontology mating frequency NBO:0000145 2011-03-31T02:17:22Z George Gkoutos mate choice behavior_ontology mating preference NBO:0000146 2011-03-31T02:17:36Z George Gkoutos behavior_ontology mating receptivity NBO:0000147 2011-03-31T02:21:53Z George Gkoutos mate attraction behavior behavior_ontology sexual display behavior NBO:0000148 2011-03-31T02:24:12Z George Gkoutos behavior_ontology social investigation NBO:0000149 2011-03-31T02:25:12Z George Gkoutos behavior_ontology reclusive behavior NBO:0000150 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 NBO:0000151 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 NBO:0000152 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 NBO:0000153 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 NBO:0000154 2011-03-31T02:35:33Z George Gkoutos behavior_ontology maternal crouching NBO:0000155 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 NBO:0000156 2011-03-31T02:53:42Z George Gkoutos behavior_ontology nesting behavior NBO:0000157 2011-03-31T02:54:15Z George Gkoutos behavior_ontology nest building behavior NBO:0000158 2011-03-31T02:59:33Z George Gkoutos behavior_ontology sleep pattern NBO:0000159 2011-03-31T03:00:57Z George Gkoutos REM sleep paradoxical sleep behavior_ontology rapid eye movement sleep NBO:0000160 2011-03-31T03:09:27Z George Gkoutos behavior_ontology sleep duration NBO:0000161 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 NBO:0000162 Duration of REM sleep. 2011-03-31T03:15:38Z George Gkoutos behavior_ontology REM duration Duration of REM sleep. NBO:GVG NBO:0000163 2011-03-31T03:15:49Z George Gkoutos behavior_ontology REM frequency NBO:0000164 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 NBO:0000165 2011-03-31T03:16:10Z George Gkoutos behavior_ontology NREM frequency NBO:0000166 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 NBO:0000167 2011-03-31T03:23:15Z George Gkoutos behavior_ontology circadian period NBO:0000168 2011-03-31T03:23:58Z George Gkoutos behavior_ontology circadian persistence NBO:0000169 2011-03-31T03:24:52Z George Gkoutos behavior_ontology circadian phase NBO:0000170 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 NBO:0000171 "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 NBO:0000172 2011-04-01T01:54:09Z George Gkoutos behavior_ontology GO:0008355 olfactory learning behavior NBO:0000173 2011-04-01T01:54:15Z George Gkoutos behavior_ontology GO:0008542 visual learning behavior NBO:0000174 2011-04-01T01:56:08Z George Gkoutos behavior_ontology motor learning NBO:0000175 2011-04-01T01:57:20Z George Gkoutos behavior_ontology spatial learning NBO:0000176 "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 NBO:0000177 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 NBO:0000178 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 NBO:0000179 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 NBO:0000180 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 NBO:0000181 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 NBO:0000182 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 NBO:0000183 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 NBO:0000184 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 NBO:0000185 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 NBO:0000186 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 NBO:0000187 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 NBO:0000188 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 NBO:0000190 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 NBO:0000191 "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 NBO:0000192 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 NBO:0000193 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 NBO:0000194 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 NBO:0000195 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 NBO:0000196 "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 NBO:0000197 2011-04-02T08:37:43Z George Gkoutos behavior_ontology iconic memory NBO:0000198 "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 NBO:0000199 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 NBO:0000200 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 NBO:0000201 2011-04-02T08:55:04Z George Gkoutos repetition behavior_ontology direct priming NBO:0000202 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 NBO:0000203 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 NBO:0000204 2011-04-02T08:58:44Z George Gkoutos behavior_ontology response priming NBO:0000205 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 NBO:0000206 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 NBO:0000207 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 NBO:0000208 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 NBO:0000209 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 NBO:0000210 2011-04-03T09:01:08Z George Gkoutos behavior_ontology avoidance learning behavior NBO:0000211 2011-04-03T09:04:57Z George Gkoutos Garcia conditioning behavior_ontology GO:0001661 conditioned taste aversion NBO:0000212 "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 NBO:0000213 2011-04-03T09:08:06Z George Gkoutos behavior_ontology imprinting behavior NBO:0000214 2011-04-03T09:11:00Z George Gkoutos behavior_ontology latent learning behavior NBO:0000215 2011-04-03T09:11:31Z George Gkoutos modeling vicarious learning behavior_ontology observational learning NBO:0000216 2011-04-03T09:11:44Z George Gkoutos behavior_ontology language learning behavior NBO:0000217 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 NBO:0000218 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 NBO:0000219 Avoid a situation completely. 2011-04-04T03:25:10Z George Gkoutos behavior_ontology escape learning behavior Avoid a situation completely. NBO:GVG NBO:0000220 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 NBO:0000221 2011-04-04T03:36:48Z George Gkoutos behavior_ontology conditioned emotional response NBO:0000222 2011-04-04T03:40:11Z George Gkoutos behavior_ontology conditioned place preference behavior NBO:0000223 2011-04-04T03:42:37Z George Gkoutos behavior_ontology contextual conditioning behavior NBO:0000224 2011-04-04T03:43:11Z George Gkoutos behavior_ontology cued conditioning behavior NBO:0000225 "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 NBO:0000226 2011-04-04T03:48:50Z George Gkoutos behavior_ontology spinal conditioning NBO:0000227 2011-04-04T03:55:46Z George Gkoutos behavior_ontology eye blink conditioning behavior NBO:0000228 2011-04-04T03:57:01Z George Gkoutos behavior_ontology jaw movement conditioning behavior NBO:0000229 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 NBO:0000230 2011-04-04T07:49:51Z George Gkoutos behavior_ontology pleasure behavior NBO:0000231 2011-04-04T07:50:00Z George Gkoutos behavior_ontology excitement behavior NBO:0000232 2011-04-04T07:50:20Z George Gkoutos behavior_ontology distress behavior NBO:0000233 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 NBO:0000234 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 NBO:0000235 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 NBO:0000236 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 NBO:0000237 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 NBO:0000238 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 NBO:0000239 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 NBO:0000240 2011-04-04T08:35:53Z George Gkoutos behavior_ontology anorexia nervosa NBO:0000241 2011-04-04T08:36:00Z George Gkoutos behavior_ontology bulimia nervosa NBO:0000242 2011-04-04T08:36:17Z George Gkoutos behavior_ontology obesity NBO:0000243 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 NBO:0000244 2011-04-04T08:51:52Z George Gkoutos hysteria pathological anxiety disorder behavior_ontology pathological anxiety NBO:0000245 "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 NBO:0000246 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 NBO:0000247 "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 NBO:0000248 "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 NBO:0000249 "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 NBO:0000250 "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 NBO:0000251 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 NBO:0000252 2011-04-04T08:54:15Z George Gkoutos behavior_ontology dissociative disorders NBO:0000253 2011-04-04T08:54:26Z George Gkoutos behavior_ontology dissociative amnesia NBO:0000254 2011-04-04T08:54:36Z George Gkoutos behavior_ontology dissociative fugue NBO:0000255 2011-04-04T08:54:45Z George Gkoutos behavior_ontology dissociative identity disorder NBO:0000256 2011-04-04T08:55:19Z George Gkoutos behavior_ontology mood disorder NBO:0000257 2011-04-04T08:55:36Z George Gkoutos MDD clinical depression major depression unipolar depression behavior_ontology major depressive disorder NBO:0000258 "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 NBO:0000259 2011-04-04T08:56:39Z George Gkoutos behavior_ontology HP:0000709 psychotic disorder NBO:0000260 2011-04-04T08:56:56Z George Gkoutos behavior_ontology paranoid schizophrenia NBO:0000261 2011-04-04T08:57:08Z George Gkoutos behavior_ontology catatonic schizophrenia NBO:0000262 2011-04-04T08:57:19Z George Gkoutos behavior_ontology disorganized (hebephrenic) schizophrenia NBO:0000263 2011-04-04T08:57:32Z George Gkoutos behavior_ontology undifferentiated schizophrenia NBO:0000264 2011-04-04T08:57:44Z George Gkoutos behavior_ontology residual schizophrenia NBO:0000265 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 NBO:0000266 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 NBO:0000267 2011-04-04T09:01:41Z George Gkoutos behavior_ontology delirium NBO:0000268 2011-04-04T09:01:50Z George Gkoutos behavior_ontology HP:0000726 dementia NBO:0000269 2011-04-04T09:02:00Z George Gkoutos behavior_ontology amnestic disorder NBO:0000270 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 NBO:0000271 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 NBO:0000272 2011-04-04T09:05:38Z George Gkoutos behavior_ontology social facilitation NBO:0000273 2011-04-04T09:05:52Z George Gkoutos social loafing behavior_ontology social interference NBO:0000274 2011-04-04T09:06:11Z George Gkoutos behavior_ontology group polarization NBO:0000275 2011-04-04T09:06:30Z George Gkoutos behavior_ontology groupthink NBO:0000276 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 NBO:0000277 2011-04-04T09:11:04Z George Gkoutos <new synonym> discrimination prejudice behavior_ontology discriminatory behavior NBO:0000278 2011-04-04T09:12:21Z George Gkoutos sexism behavior_ontology gender specific discriminatory behavior NBO:0000279 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 NBO:0000280 2011-04-04T09:16:35Z George Gkoutos behavior_ontology attraction-related behavior NBO:0000281 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 NBO:0000282 Wanting to be with another person. 2011-04-04T09:17:02Z George Gkoutos behavior_ontology liking Wanting to be with another person. NBO:GVG NBO:0000283 2011-04-04T09:17:59Z George Gkoutos behavior_ontology friendship NBO:0000284 2011-04-04T09:18:24Z George Gkoutos behavior_ontology love NBO:0000285 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 NBO:0000286 "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 NBO:0000287 "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 NBO:0000288 "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 NBO:0000289 2011-04-04T09:26:44Z George Gkoutos behavior_ontology social influence related behavior NBO:0000290 2011-04-04T09:27:04Z George Gkoutos behavior_ontology conformity NBO:0000291 2011-04-04T09:27:43Z George Gkoutos behavior_ontology obedience to authority NBO:0000292 2011-04-04T09:27:57Z George Gkoutos behavior_ontology bystander intervention NBO:0000293 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 NBO:0000294 "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 NBO:0000295 2011-04-18T10:37:53Z George Gkoutos behavior_ontology satiation NBO:0000296 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 NBO:0000297 "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 NBO:0000298 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 NBO:0000299 2011-04-04T09:36:53Z George Gkoutos behavior_ontology alloparental behavior NBO:0000300 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 NBO:0000301 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 NBO:0000302 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 NBO:0000303 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 NBO:0000304 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 NBO:0000305 2011-04-04T09:49:41Z George Gkoutos behavior_ontology memory encoding behavior NBO:0000306 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 NBO:0000307 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 NBO:0000308 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 NBO:0000309 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 NBO:0000310 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 NBO:0000311 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 NBO:0000312 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 NBO:0000313 "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 NBO:0000314 "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 NBO:0000315 "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 NBO:0000316 "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 NBO:0000317 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 NBO:0000318 2011-04-05T10:44:05Z George Gkoutos behavior_ontology balance NBO:0000319 2011-04-05T10:44:19Z George Gkoutos behavior_ontology body rotation sensation behavior NBO:0000320 2011-04-05T10:44:34Z George Gkoutos behavior_ontology gravitation sensation behavior NBO:0000321 2011-04-05T10:44:55Z George Gkoutos behavior_ontology movement sensation behavior NBO:0000322 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 NBO:0000323 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 NBO:0000324 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 NBO:0000326 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 NBO:0000327 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 NBO:0000328 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 NBO:0000329 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 NBO:0000330 2011-04-05T11:11:48Z George Gkoutos behavior_ontology cutaneous sensation behavior NBO:0000331 2011-04-05T11:13:27Z George Gkoutos nociception pain behavior_ontology nociceptive behavior NBO:0000332 2011-04-05T11:36:23Z George Gkoutos behavior_ontology touch related behavior NBO:0000333 2011-04-05T12:38:39Z George Gkoutos chemical nociception behaviour behavior_ontology chemical nociceptive behavior NBO:0000334 2011-04-05T12:39:46Z George Gkoutos mechanical nociception behaviour behavior_ontology mechanical nociceptive behavior NBO:0000335 2011-04-05T12:41:15Z George Gkoutos thermal nociception behaviour behavior_ontology thermal nociceptive behavior NBO:0000336 2011-04-05T12:45:31Z George Gkoutos chemically-elicited antinociception behaviour behavior_ontology chemically-elicited antinociceptive behavior NBO:0000337 2011-04-05T02:06:22Z George Gkoutos behavior_ontology pressure related behavior NBO:0000338 "Movement behavior of the body or its parts." 2011-04-05T02:08:47Z George Gkoutos behavior_ontology kinesthetic behavior NBO:0000339 "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 NBO:0000341 "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 NBO:0000342 The coordination of limb movement. 2011-04-05T03:49:12Z George Gkoutos behavior_ontology limb coordination The coordination of limb movement. NBO:GVG NBO:0000343 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 NBO:0000344 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 NBO:0000345 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 NBO:0000346 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 NBO:0000347 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 NBO:0000348 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 NBO:0000349 2011-04-05T04:17:46Z George Gkoutos behavior_ontology manual dexterity NBO:0000350 Coordination involved in writing. 2011-04-05T04:19:34Z George Gkoutos behavior_ontology graphomotor coordination Coordination involved in writing. NBO:GVG NBO:0000351 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 NBO:0000352 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 NBO:0000353 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 NBO:0000354 2011-04-05T05:33:26Z George Gkoutos behavior_ontology bilateral coordination NBO:0000355 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 NBO:0000356 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 NBO:0000357 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 NBO:0000358 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 NBO:0000359 Behavior associated with surface locomotion. 2011-04-06T09:44:37Z George Gkoutos behavior_ontology terrestrial locomotory behavior Behavior associated with surface locomotion. NBO:GVG NBO:0000360 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 NBO:0000361 "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 NBO:0000362 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 NBO:0000363 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 NBO:0000364 "Behavior related to the locomotion of animals in trees." [wikipedia:Arboreal_locomotion] 2011-04-06T11:40:46Z George Gkoutos behavior_ontology arboreal locomotion behavior NBO:0000365 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 NBO:0000366 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 NBO:0000367 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 NBO:0000368 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 NBO:0000369 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 NBO:0000370 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 NBO:0000371 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 NBO:0000372 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 NBO:0000373 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 NBO:0000374 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 NBO:0000375 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 NBO:0000376 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 NBO:0000377 "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 NBO:0000378 "Locomotory orientation in response to gravity." [GO:0048062] 2011-04-06T01:27:22Z George Gkoutos geotactic behaviour gravitaxis behavior_ontology GO:0042332 gravitactic behavior NBO:0000379 "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 NBO:0000380 "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 NBO:0000381 "Locomotory orientation in response to touch." [GO:0001966] 2011-04-06T01:45:18Z George Gkoutos stereotaxis behavior_ontology thigmotaxis NBO:0000382 "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 NBO:0000383 "Locomotory orientation in response to light." [GO:0042331] 2011-04-06T01:48:33Z George Gkoutos phototaxis behavior_ontology GO:0042331 phototactic behavior NBO:0000384 "Locomotory orientation in response to a temperature gradient." [GO:0043052] 2011-04-06T01:50:19Z George Gkoutos behavior_ontology GO:0043052 thermotaxis NBO:0000385 Locomotory orientation in response to sound. 2011-04-06T01:58:40Z George Gkoutos behavior_ontology phonotaxis Locomotory orientation in response to sound. NBO:GVG NBO:0000386 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 NBO:0000387 Locomotory orientation in response to pressure. 2011-04-06T02:01:21Z George Gkoutos behavior_ontology barotaxis Locomotory orientation in response to pressure. NBO:GVG NBO:0000388 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 NBO:0000389 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 NBO:0000390 "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 NBO:0000391 "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 NBO:0000392 "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 NBO:0000393 "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 NBO:0000394 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 NBO:0000395 "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 NBO:0000396 "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 NBO:0000397 "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 NBO:0000398 "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 NBO:0000399 "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 NBO:0000400 "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 NBO:0000401 "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 NBO:0000402 "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 NBO:0000403 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 NBO:0000404 "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 NBO:0000405 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 NBO:0000406 "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 NBO:0000407 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 NBO:0000408 "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 NBO:0000409 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 NBO:0000410 "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 NBO:0000411 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 NBO:0000412 "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 NBO:0000413 "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 NBO:0000414 2011-04-06T04:30:58Z George Gkoutos masseter reflex behavior_ontology jaw jerk reflex NBO:0000415 "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 NBO:0000416 "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 NBO:0000417 "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 NBO:0000418 "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 NBO:0000419 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 NBO:0000420 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 NBO:0000421 "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 NBO:0000422 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 NBO:0000423 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 NBO:0000424 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 NBO:0000425 "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 NBO:0000426 "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 NBO:0000427 "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 NBO:0000428 "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 NBO:0000429 "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 NBO:0000430 "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 NBO:0000431 "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 NBO:0000432 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 NBO:0000433 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 NBO:0000434 "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 NBO:0000435 "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 NBO:0000436 "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 NBO:0000437 "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 NBO:0000438 "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 NBO:0000439 "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 NBO:0000440 "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 NBO:0000441 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 NBO:0000442 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 NBO:0000443 "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 NBO:0000444 2011-04-08T12:22:02Z George Gkoutos behavior_ontology eye movement NBO:0000445 2011-04-08T12:22:13Z George Gkoutos behavior_ontology tail movement NBO:0000446 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 NBO:0000447 Activation of locomotory behavior. 2011-04-08T12:27:51Z George Gkoutos behavior_ontology locomotor activation behavior NBO:0000448 2011-04-08T12:28:10Z George Gkoutos behavior_ontology vertical activity NBO:0000449 Kinesthetic behavior initiated in the absence of specific sensory input. 2011-04-08T12:28:25Z George Gkoutos behavior_ontology spontaneous movement behavior NBO:0000450 "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 NBO:0000451 "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 NBO:0000452 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 NBO:0000453 2011-04-08T12:52:15Z George Gkoutos behavior_ontology obsolete behavior related to feelings experiencing true NBO:0000455 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 NBO:0000456 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 NBO:0000457 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 NBO:0000458 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 NBO:0000459 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 NBO:0000460 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 NBO:0000461 "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 NBO:0000462 "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 NBO:0000463 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 NBO:0000464 "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 NBO:0000465 "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 NBO:0000466 "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 NBO:0000467 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 NBO:0000468 "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 NBO:0000469 "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 NBO:0000470 "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 NBO:0000471 2011-04-08T02:00:36Z George Gkoutos behavior_ontology predator avoidance behavior NBO:0000472 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 NBO:0000473 2011-04-08T02:18:40Z George Gkoutos behavior_ontology rhythmic behavior phenotype NBO:0000474 2011-04-08T02:19:42Z George Gkoutos pathological circadian behaviour behavior_ontology circadian behavior phenotype NBO:0000475 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 NBO:0000476 2011-04-08T02:21:57Z George Gkoutos behavior_ontology intrinsic sleep disorder NBO:0000477 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 NBO:0000478 "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 NBO:0000479 "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 NBO:0000480 "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 NBO:0000481 "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 NBO:0000482 2011-04-08T02:35:59Z George Gkoutos behavior_ontology extrinsic sleep disorder NBO:0000483 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 NBO:0000484 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 NBO:0000485 "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 NBO:0000486 "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 NBO:0000487 2011-04-08T02:54:52Z George Gkoutos behavior_ontology intrinsic circadian rhythm sleep disorder NBO:0000488 "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 NBO:0000489 2011-04-08T02:57:20Z George Gkoutos SWSD behavior_ontology shift work sleep disorder NBO:0000490 "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 NBO:0000491 "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 NBO:0000492 "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 NBO:0000493 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 NBO:0000494 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 NBO:0000495 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 NBO:0000496 "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 NBO:0000497 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 NBO:0000498 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 NBO:0000499 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 NBO:0000500 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 NBO:0000501 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 NBO:0000502 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 NBO:0000503 "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 NBO:0000504 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 NBO:0000505 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 NBO:0000506 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 NBO:0000507 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 NBO:0000508 "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 NBO:0000509 "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 NBO:0000510 "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 NBO:0000511 "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 NBO:0000512 "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 NBO:0000513 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 NBO:0000514 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 NBO:0000515 2011-04-09T12:28:31Z George Gkoutos NBO:0000523 DD-NOS depressive disorder not otherwise specified behavior_ontology HP:0000716 depressive disorder NBO:0000516 "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 NBO:0000517 "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 NBO:0000518 "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 NBO:0000519 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 NBO:0000520 "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 NBO:0000521 "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 NBO:0000522 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 NBO:0000524 "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 NBO:0000525 "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 NBO:0000526 "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 NBO:0000527 "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 NBO:0000528 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 NBO:0000529 "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 NBO:0000530 2011-04-10T01:33:58Z George Gkoutos behavior_ontology substance induced mood disorder NBO:0000531 2011-04-10T01:34:12Z George Gkoutos behavior_ontology alcohol induced mood disorder NBO:0000532 2011-04-10T01:34:25Z George Gkoutos behavior_ontology benzodiazepine induced mood disorder NBO:0000533 2011-04-10T01:34:41Z George Gkoutos behavior_ontology Interferon-alpha induced mood disorder NBO:0000534 "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 NBO:0000535 "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 NBO:0000536 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 NBO:0000537 "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 NBO:0000538 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 NBO:0000539 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 NBO:0000540 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 NBO:0000541 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 NBO:0000542 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 NBO:0000543 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 NBO:0000544 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 NBO:0000545 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 NBO:0000546 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 NBO:0000547 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 NBO:0000548 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 NBO:0000549 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 NBO:0000550 "Ability to correctly remember something that has been encountered before." [wikipedia:Recognition_memory] 2011-04-14T01:53:29Z George Gkoutos behavior_ontology recognition memory NBO:0000551 "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 NBO:0000552 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 NBO:0000553 2011-04-14T02:03:00Z George Gkoutos behavior_ontology short term object recognition memory NBO:0000554 2011-04-14T02:09:28Z George Gkoutos behavior_ontology visual short term memory NBO:0000555 2011-04-14T02:10:17Z George Gkoutos behavior_ontology spatial working memory NBO:0000556 "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 NBO:0000557 "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 NBO:0000558 2011-04-14T02:19:43Z George Gkoutos behavior_ontology long term spatial memory NBO:0000559 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 NBO:0000560 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 NBO:0000561 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 NBO:0000562 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 NBO:0000563 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 NBO:0000564 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 NBO:0000565 2011-04-14T08:24:50Z George Gkoutos behavior_ontology MP:0001361 social withdrawal NBO:0000566 2011-04-14T08:25:50Z George Gkoutos behavior_ontology social withdrawal in childhood NBO:0000567 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 NBO:0000568 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 NBO:0000569 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 NBO:0000570 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 NBO:0000571 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 NBO:0000572 "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 NBO:0000573 2011-04-14T09:04:45Z George Gkoutos behavior_ontology MP:0002573 behavioral despair NBO:0000574 "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 NBO:0000575 "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 NBO:0000576 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 NBO:0000577 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 NBO:0000578 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 NBO:0000579 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 NBO:0000580 "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 NBO:0000581 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: NBO:0000582 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 NBO:0000583 "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 NBO:0000584 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: NBO:0000585 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: NBO:0000586 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: NBO:0000587 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 NBO:0000588 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 NBO:0000589 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 NBO:0000590 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 NBO:0000591 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 NBO:0000592 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 NBO:0000593 Overshooting the intended position. 2011-04-14T11:34:23Z George Gkoutos behavior_ontology hypermetria Overshooting the intended position. wikipedia:Dysmetria NBO:0000594 Undershooting the intended position. 2011-04-14T11:34:31Z George Gkoutos behavior_ontology hypometria Undershooting the intended position. wikipedia:Dysmetria NBO:0000595 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 NBO:0000596 "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 NBO:0000597 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: NBO:0000598 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 NBO:0000599 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 NBO:0000600 "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 NBO:0000601 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 NBO:0000602 "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 NBO:0000603 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 NBO:0000604 "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 NBO:0000605 "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 NBO:0000606 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 NBO:0000607 Behaviour related to cognitive processes. 2011-04-14T03:51:13Z George Gkoutos behavior_ontology cognitive behavior Behaviour related to cognitive processes. NBO:JH NBO:0000608 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 NBO:0000609 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 NBO:0000610 "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 NBO:0000611 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 NBO:0000612 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 NBO:0000613 "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 NBO:0000614 "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 NBO:0000615 "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 NBO:0000616 "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 NBO:0000617 2011-04-14T04:51:05Z George Gkoutos behavior_ontology laughing behavior NBO:0000618 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 NBO:0000619 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 NBO:0000620 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 NBO:0000621 "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 NBO:0000622 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 NBO:0000623 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 NBO:0000624 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 NBO:0000626 "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 NBO:0000627 "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 NBO:0000628 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 NBO:0000629 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 NBO:0000630 "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 NBO:0000631 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 NBO:0000632 "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 NBO:0000633 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 NBO:0000634 2011-04-19T02:05:35Z George Gkoutos behavior_ontology irritable aggressive behavior NBO:0000635 "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 NBO:0000636 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 NBO:0000637 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 NBO:0000638 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 NBO:0000639 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 NBO:0000640 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 NBO:0000641 2011-05-06T03:56:31Z George Gkoutos behavior_ontology discrimination learning NBO:0000642 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 NBO:0000643 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 NBO:0000644 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 NBO:0000645 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 NBO:0000646 "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 NBO:0000647 "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 NBO:0000648 "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 NBO:0000649 2011-05-27T01:51:38Z George Gkoutos behavior_ontology being conscious NBO:0000650 "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 NBO:0000651 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 NBO:0000652 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 NBO:0000653 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 NBO:0000654 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 NBO:0000655 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 NBO:0000656 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 NBO:0000657 2011-05-27T03:21:20Z George Gkoutos behavior_ontology cutaneous sensation behavior phenotype NBO:0000658 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 NBO:0000659 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 NBO:0000660 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 NBO:0000661 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 NBO:0000662 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 NBO:0000663 2011-05-27T03:49:54Z George Gkoutos behavior_ontology HP:0007334 partial seizure evolving to secondarily generalized seizure NBO:0000664 2011-05-27T03:50:07Z George Gkoutos behavior_ontology simple partial seizure evolving to generalized seizure NBO:0000665 2011-05-27T03:50:26Z George Gkoutos behavior_ontology complex partial seizure evolving to generalized seizure NBO:0000666 2011-05-27T03:50:49Z George Gkoutos behavior_ontology simple partial seizure evolving to complex partial seizure evolving to generalized seizure NBO:0000667 2011-05-27T03:51:50Z George Gkoutos behavior_ontology simple partial onset, followed by impairment of consciousness NBO:0000668 2011-05-27T03:52:02Z George Gkoutos behavior_ontology with impairment of consciousness at onset NBO:0000669 "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 NBO:0000670 "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 NBO:0000671 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 NBO:0000672 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 NBO:0000673 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 NBO:0000674 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 NBO:0000675 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 NBO:0000676 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 NBO:0000677 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 NBO:0000678 "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 NBO:0000679 "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 NBO:0000680 "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 NBO:0000681 "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 NBO:0000682 "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 NBO:0000683 "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 NBO:0000684 2011-05-27T05:32:59Z George Gkoutos pyknolepsy behavior_ontology childhood absence epilepsy NBO:0000685 2011-05-27T05:39:40Z George Gkoutos behavior_ontology continuous seizure NBO:0000686 "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 NBO:0000687 "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 NBO:0000688 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 NBO:0000689 "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 NBO:0000690 "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 NBO:0000691 2011-05-27T06:42:06Z George Gkoutos behavior_ontology non-convulsive status epilepticus NBO:0000692 2011-05-27T06:42:29Z George Gkoutos behavior_ontology generalised convulsive status epilepticus NBO:0000693 "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 NBO:0000694 2011-05-27T07:21:27Z George Gkoutos behavior_ontology absence status epilepticus NBO:0000695 "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 NBO:0000696 "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 NBO:0000697 "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 NBO:0000698 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 NBO:0000699 "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 NBO:0000700 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 NBO:0000701 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 NBO:0000702 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 NBO:0000703 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 NBO:0000704 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 NBO:0000705 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 NBO:0000706 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 NBO:0000707 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 NBO:0000708 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 NBO:0000709 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 NBO:0000710 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 NBO:0000711 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 NBO:0000712 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 NBO:0000713 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 NBO:0000714 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 NBO:0000715 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 NBO:0000716 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 NBO:0000717 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 NBO:0000718 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 NBO:0000719 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 NBO:0000720 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 NBO:0000721 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 NBO:0000722 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 NBO:0000723 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 NBO:0000724 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 NBO:0000726 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 NBO:0000727 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 NBO:0000728 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 NBO:0000729 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 NBO:0000730 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 NBO:0000731 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 NBO:0000732 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 NBO:0000733 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 NBO:0000734 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 NBO:0000735 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 NBO:0000736 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 NBO:0000737 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 NBO:0000738 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 NBO:0000739 "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 NBO:0000740 2012-02-16T01:16:13Z gkoutos behavior_ontology aggressive behavior by intent NBO:0000741 2012-02-16T01:16:31Z gkoutos behavior_ontology aggressive behavior by means NBO:0000742 Agressive behavior towards oneself. 2012-02-16T01:16:55Z gkoutos behavior_ontology autoaggressive behavior Agressive behavior towards oneself. NBO:GVG NBO:0000743 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 NBO:0000744 2012-03-16T04:51:23Z gkoutos behavior_ontology perception behavior phenotype NBO:0000745 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 NBO:0000746 2012-03-16T05:57:42Z gkoutos behavior_ontology spatial perception NBO:0000747 2012-03-17T09:51:17Z gkoutos behavior_ontology jaw movement NBO:0000748 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 NBO:0000749 2012-03-17T09:53:29Z gkoutos behavior_ontology blinking NBO:0000750 2012-03-17T09:54:30Z gkoutos behavior_ontology eyelid movement NBO:0000751 2012-03-16T05:23:06Z gkoutos behavior_ontology perception behavior by means NBO:0000752 2012-03-17T03:59:12Z gkoutos behavior_ontology electrical nociceptive behavior NBO:0000753 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 NBO:0000754 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 NBO:0000755 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 NBO:0000756 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 NBO:0000757 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 NBO:0000758 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 NBO:0000759 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 NBO:0000760 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 NBO:0000761 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 NBO:0000762 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 NBO:0000763 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 NBO:0000764 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 NBO:0000765 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 NBO:0000766 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 NBO:0000767 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 NBO:0000768 2012-03-19T03:46:31Z gkoutos behavior_ontology emission behavior phenotype NBO:0000769 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 NBO:0000770 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 NBO:0000771 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 NBO:0000772 2012-03-20T05:24:59Z gkoutos behavior_ontology behavioral control of production of sound phenotype NBO:0000773 2012-03-20T05:25:03Z gkoutos behavior_ontology behavioral control of external secretion phenotype NBO:0000774 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 NBO:0000775 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 NBO:0000776 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 NBO:0000777 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 NBO:0000778 2012-03-23T10:05:56Z gkoutos behavior_ontology emotional conditioning NBO:0000851 increased amount of liquid in a single drinking act NBO:0000886 increased amount of liquid in drinking regulation NBO:0000929 'participates in' some ('regulation of drinking behavior' and (has_quality some (frequency and (towards some 'liquid consumption')))) frequency of drinking NBO:0000961 increased frequency of drinking NBO:0000993 decreased frequency of drinking NBO:0001536 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 NBO:0001571 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 NBO:0001632 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 NBO:0001679 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 NBO:0001728 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 NBO:0001763 Behavior as a result of sensitivity to cocaine alcohol. behavioral response to alcohol Behavior as a result of sensitivity to cocaine alcohol. NBOC:GVG NBO:0001786 "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 NBO:0001824 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 NBO:0001845 Behavior related to the intake of substances. George Gkoutos ingest consumption behavior Behavior related to the intake of substances. NBOC:GVG NBO:0001884 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 NBO:0001915 Behavior related to the intake of cocaine. George Gkoutos cocaine consumption Behavior related to the intake of cocaine. NBOC:GVG NBO:0001952 Behavior related to the intake of morphine. George Gkoutos morphine consumption Behavior related to the intake of morphine. NBOC:GVG NBO:0001987 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 NBO:0002021 Behavior as a result of sensitivity to morphine George Gkoutos behavioral response to morphine Behavior as a result of sensitivity to morphine NBOC:GVG NBO:0002065 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 NBO:0002086 Behavior related to the intake of nicotine. George Gkoutos nicotine consumption Behavior related to the intake of nicotine. NBOC:GVG NBO:0002132 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 NBO:0002169 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 NBO:0002234 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 NBO:0002273 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 NBO:0002308 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 NBO:0002362 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 NBO:0002379 Maternal behavior related to the nursing offspring. nursing behavior Maternal behavior related to the nursing offspring. NBOC:GVG NBO:0002436 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 NBO:0002468 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 NBO:0002511 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 NBO:0002519 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 NBO:0002569 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 NBO:0002603 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 NBO:0002660 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 NBO:0002702 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 NBO:0002743 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 NBO:0002794 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 NBO:0002869 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 NBO:0002916 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 NBO:0002948 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 NBO:0002950 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 NBO:0002952 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 NBO:0002986 Behavior response to addictive substance resulting from the discontinuation of an addictive substance. [NBOC:GVG] withdrawal response NBO:0003047 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 NBO:0003104 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 NBO:0003142 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 NBO:0003161 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 NBO:0003194 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 NBO:0009001 rotation behavior NBO:0009002 Deactiviation of locomotory behavior. locomotor inactivation behavior NBO:0009003 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 NBO:0015000 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 NBO:0015001 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 NBO:0015002 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 NBO:0015003 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 NBO:0015004 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 NBO:0015005 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 NBO:0015006 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 NBO:0015007 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 NBO:0015008 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 NBO:0015009 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 NBO:0020007 Consumption of specific compounds that facilitate processing of food items. Luke Slater aiding digestion NBO:0020010 Assessment of cues and signals from encountered individual to determine reproductive condition. Luke Slater reproductive status assessment NBO:0020015 Postures or signals that alert other animals to presence or approach of a predator. Luke Slater warn other prey NBO:0020018 Behavior in which one animal causes the death of another. Luke Slater killing kill NBO:0020023 Signal or behavior that reveals presence of the signaller directed to multiple receivers and not limited to particular receivers. Luke Slater broadcast advertisement NBO:0020031 Threat that will not be acted upon. Luke Slater bluff NBO:0020033 Agonistic behavior involving direct physical contact including (but not limited to) biting, kicking, grabbing. Luke Slater contact aggression NBO:0020034 Perform behaviors that may induce one or more other animals to share food with the performer. Luke Slater beg food NBO:0020037 Surveillance for presence or approach of predators. Luke Slater vigilance NBO:0020040 Active pursuit of fleeing prey. Luke Slater chase prey NBO:0020045 Behaviors in which predator forces potential prey to emerge from cover. Luke Slater flush prey NBO:0020047 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 NBO:0020048 Deposition of eggs either into the medium, or onto a substrate. Luke Slater facilitating oviposition NBO:0020054 One member of a recently mating pair prevents the other from subsequent matings with other individuals. Luke Slater mate guarding NBO:0020059 Currently reside in constructed or existing structure that provides reduced predator and/or environmental risk. Luke Slater occupy refuge NBO:0020063 Forcible alteration of behavior of one animal by another. Luke Slater coercion NBO:0020066 Facilitating release or transfer of gametes. Luke Slater gamete release function NBO:0020068 Caching or hoarding of food for later use and for protection from competitors, or use of specific substrates for cultivation. Luke Slater food storage NBO:0020071 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 NBO:0020077 Performance of behaviors that demonstrate physical condition of performer to a detected predator. Luke Slater display condition (to predator) NBO:0020079 Emission of signals in such a way as to prevent effective use of signals emitted by other parties. Luke Slater jamming NBO:0020084 Active search for possible mates. Luke Slater mate finding behavior NBO:0020088 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 NBO:0020091 Sensory assessment of a resource (usually using olfaction or taste), for suitability of subsequent usage. Luke Slater suitability assessment NBO:0020093 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 NBO:0020096 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 NBO:0020098 Behavior by one animals soliciting food provision by a potential mate. Luke Slater courtship begging NBO:0020101 Consumption of one member of a mating pair, usually the male, usually after the mating. Luke Slater sexual cannibalism NBO:0020102 Process of retaining developing eggs in the mouth cavity. Luke Slater mouth brooding NBO:0020105 Construction of a structure in which builder can benefit from reduced predation risk and/or environmental stress. Luke Slater create refuge NBO:0020108 Behavior that signifies hostility and predicts an increased probability of attack. Luke Slater threat NBO:0020109 Use of specialized male organs to remove sperm already deposited in female's reproductive tract. Luke Slater sperm scraping NBO:0020111 Behavior in which one animal causes bodily damage to another. Luke Slater injuring injure NBO:0020112 Carrying or manipulation of infants or equivalent items to reduce chances of aggression on carrier by other animals. Luke Slater agonistic buffering NBO:0020117 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 NBO:0020121 Insertion of sperm not in a spermatophore into female body. Luke Slater insemination NBO:0020137 Building of a trap, web, net, or other structure to help ensnare potential food items. Luke Slater construct capturing device NBO:0020139 Behaviors that reduce detectability of performer against background. Luke Slater enhance crypsis NBO:0020141 Chasing of one animal by another during an agonistic conflict. Luke Slater agonistic chase NBO:0020142 The identification, avoidance, or neutralization of toxic substances in food. Luke Slater dealing with toxins NBO:0020144 Removal of food resource from previously-stored supply of food. Luke Slater recovery from cache NBO:0020145 Alarm behavior triggered by agonistic actions or postures. 0000-0002-4277-2151 Luke Slater agonistic alarm NBO:0020149 Signals emitted by an animal trapped or captured by a presumed predator. Luke Slater distress signaling NBO:0020159 Behaviors that serve to reduce body temperature as by moving to shade or panting. Luke Slater cooling behaviour NBO:0020160 Approach to prey in manner designed to avoid early detection by prey. Luke Slater stalk prey NBO:0020170 Behaviors that reveal a hidden food resource, such as digging, cracking, or breaking. Luke Slater food exposure NBO:0020173 Behaviors in which animals solicit or allow other animals to utilize a resource they currently control. Luke Slater share food NBO:0020174 Release of gametes one or both sexes into the ambient medium. Luke Slater spawning NBO:0020175 Halting or diminution of activity to minimize detection by predator. Luke Slater reduce activity NBO:0020177 Obtaining food that has been procured by other conspecifics or heterospecifics. Luke Slater social acquisition of food NBO:0020182 Increasing intensity of directed agonistic behavior. Luke Slater escalation NBO:0020188 Movement directed to the detection of new resources. Luke Slater nutrient locating NBO:0020199 Become immobile and reduce other evidence of living state. Luke Slater feign death NBO:0020204 Spawning in which male and female are clasped or attached to ensure close proximity of released gametes Luke Slater mating amplexus NBO:0020219 Behaviors directed towards presumed predators to redirect their attention away from a location of importance to the performer. Luke Slater misdirect predator NBO:0020220 Behavior that serves to exlude an animal from a group. Luke Slater exclusion NBO:0020223 Conspicuous orientation towards and/or approach to detected predator. Luke Slater inspect predator NBO:0020230 Perform physically violent acts on a presumed predator. Luke Slater attack predator NBO:0020239 Display behavior by the winner of a prior agonistic contest. Luke Slater triumph NBO:0020241 Performance of a behavior that indicates the performer's willingness to mate or bond Luke Slater mating solicitation NBO:0020242 Creation of or modification of a structure or area that is used in attraction of mates. Luke Slater build display structure NBO:0020245 Behaviors, anatomical structures, or signals that imitate aposematic animals, plants, or inanimate objects that are undesirable to predators of performer. Luke Slater mimicry enhancement NBO:0020251 Erratic movements or similar behaviors that would confuse a predator. Luke Slater promote confusion NBO:0020253 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 NBO:0020254 Any of several behaviors directed towards one animal unwilling to mate by another eager to do so. Luke Slater sexual harassment NBO:0020255 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 NBO:0020264 Provision of food to a potential mate Luke Slater courtship feeding NBO:0020266 Deposition of spermatophore either on substrate or in body of female. Luke Slater spermatophore deposition NBO:0020268 Depart [from] current location of predator. Luke Slater flee NBO:0020272 Active searching of potential mate Luke Slater hunt for mate NBO:0020273 Actions resulting in establishment or use of one locale for reproductive activity. Luke Slater breeding site selection NBO:0020279 Behaviors that appear to signifiy lack of hostility and to reduce chances of attack. Luke Slater appeasement NBO:0020281 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 NBO:0020282 Behaviors related to acquisition and utilization of external resources. Luke Slater nutrient acquisition NBO:0020286 Removal of food items from location by use of appendage or tool. Luke Slater food extraction NBO:0020287 Conspicuous postures or signals (often coloration) that potential predators learn to associate with strong defense mechanisms of performer Luke Slater aposematism NBO:0020289 Postures or signals that can communicate to predator that it has been detected by performer. Luke Slater (predator) detection notification NBO:0020291 Behavior that precedes and facilitates attaining food. Luke Slater nutrient preparation NBO:0020292 Suite of behaviors involved in securing a prey item once it has been located. Luke Slater capturing behaviour NBO:0020293 Behaviors that result in ending flight of prey with successful predation. Luke Slater capturing prey NBO:0020294 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 NBO:0020295 Behaviors that prepare food for consumption, such as nut-cracking or peeling. Luke Slater food processing NBO:0020296 Uninvited taking of food from another animal. Luke Slater scrounge NBO:0020297 Behavior associated with locating and acquiring food that has been killed or procured by another animal. Luke Slater scavenge NBO:0020298 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 NBO:0020299 Behavior associated with refusing courtship or solicitation behaviors by avoidance, retreat, or other active repulsion of suitor. Luke Slater mate rejection NBO:0040000 A behavior associated with the gathering of organisms together in some locality. [Wikipedia:Aggregation_(ethology)] https://orcid.org/0000-0002-9611-1279 aggregation behavior NBO:0040001 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 NBO:0040002 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 NBO:0040003 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 NBO:0040004 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 NBO:0040005 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 NBO:0045000 Any habitual use of the tobacco plant leaf and its products. 2020-01-27T20:46:57Z tobacco consumption NBO:0045001 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 NBO:0045002 The inhalation and exhalation of tobacco smoke. 2020-01-27T20:51:34Z tobacco smoking behavior NBO:0045003 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 NBO:0045004 2020-01-27T21:03:19Z cannabis consumption NBO:0045005 The inhalation and exhalation of marijuana smoke. 2020-01-27T21:04:14Z marijuana smoking behavior pot smoking behavior weed smoking behavior cannabis smoking behavior NBO:0045006 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 NBO:0045007 The consuming of cannabis through eating or applying the oil sublingually. 2020-01-27T21:04:49Z marijuana oil consumption cannabis oil consumption NBO:0050000 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 NBO:0050001 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 NBO:0050002 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 NBO:0070000 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 NBO:0070001 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 NBO:0070002 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 NBO:0070003 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 NBO:0070004 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 NCBITaxon:1 root NCBITaxon:10066 Muridae NCBITaxon:10114 Rattus NCBITaxon:105389 Sedentaria NCBITaxon:105391 Canalipalpata NCBITaxon:110814 Xenoturbellida NCBITaxon:110815 Xenoturbella NCBITaxon:117570 Teleostomi NCBITaxon:117571 Euteleostomi NCBITaxon:119089 Chromadorea NCBITaxon:1206794 Ecdysozoa NCBITaxon:1206795 Lophotrochozoa NCBITaxon:123365 Neoteleostei NCBITaxon:123366 Eurypterygia NCBITaxon:123367 Ctenosquamata NCBITaxon:123368 Acanthomorphata NCBITaxon:123369 Euacanthomorphacea NCBITaxon:1312402 Xenacoelomorpha NCBITaxon:131567 cellular organisms NCBITaxon:1329799 Archelosauria NCBITaxon:1329911 Toxicofera NCBITaxon:1329912 Episquamata NCBITaxon:1329950 Unidentata NCBITaxon:1329961 Bifurcata NCBITaxon:1338369 Dipnotetrapodomorpha NCBITaxon:1437010 Boreoeutheria NCBITaxon:147099 Acoelomorpha NCBITaxon:1489341 Osteoglossocephalai NCBITaxon:1489388 Euteleosteomorpha NCBITaxon:1489872 Percomorphaceae NCBITaxon:1489922 Eupercaria NCBITaxon:1547233 Xenoturbellidae NCBITaxon:186623 Actinopteri NCBITaxon:186625 Clupeocephala NCBITaxon:186626 Otophysi NCBITaxon:186627 Cypriniphysae NCBITaxon:186634 Otomorpha NCBITaxon:1963758 Myomorpha NCBITaxon:197562 Pancrustacea NCBITaxon:197563 Mandibulata NCBITaxon:207598 Homininae NCBITaxon:2301116 Rhabditina NCBITaxon:2301119 Rhabditomorpha NCBITaxon:262014 Xenopus <subgenus> NCBITaxon:2697495 Spiralia NCBITaxon:2743709 Danionidae NCBITaxon:2743711 Danioninae NCBITaxon:2759 Eukaryota NCBITaxon:30319 Pipoidea NCBITaxon:30727 Cyprinoidei NCBITaxon:31022 Tetraodontiformes NCBITaxon:31028 Tetraodontoidei NCBITaxon:31031 Tetraodontidae NCBITaxon:31032 Takifugu NCBITaxon:31033 Takifugu rubripes NCBITaxon:314146 Euarchontoglires NCBITaxon:314147 Glires NCBITaxon:314293 Simiiformes NCBITaxon:314295 Hominoidea NCBITaxon:32341 Sophophora NCBITaxon:32346 melanogaster group NCBITaxon:32351 melanogaster subgroup NCBITaxon:32443 Teleostei NCBITaxon:32517 Tetradontoidea NCBITaxon:32519 Ostariophysi NCBITaxon:32523 Tetrapoda NCBITaxon:32524 Amniota NCBITaxon:32525 Theria <mammals> NCBITaxon:32561 Sauria NCBITaxon:33154 Opisthokonta NCBITaxon:33208 Metazoa NCBITaxon:33213 Bilateria NCBITaxon:33317 Protostomia NCBITaxon:33340 Neoptera NCBITaxon:33392 Endopterygota NCBITaxon:33511 Deuterostomia NCBITaxon:337687 Muroidea NCBITaxon:376913 Haplorrhini NCBITaxon:39107 Murinae NCBITaxon:40674 Mammalia NCBITaxon:41324 Siboglinidae NCBITaxon:41665 Neopterygii NCBITaxon:41666 Batrachia NCBITaxon:436486 Dinosauria NCBITaxon:436489 Saurischia NCBITaxon:436491 Theropoda NCBITaxon:436492 Coelurosauria NCBITaxon:43733 Muscomorpha NCBITaxon:43738 Schizophora NCBITaxon:43741 Acalyptratae NCBITaxon:43746 Ephydroidea NCBITaxon:43845 Drosophilinae NCBITaxon:46877 Drosophilini NCBITaxon:480117 Cyclorrhapha NCBITaxon:480118 Eremoneura NCBITaxon:50557 Insecta NCBITaxon:55879 Rhabditoidea NCBITaxon:55885 Peloderinae NCBITaxon:6040 Porifera NCBITaxon:6072 Eumetazoa NCBITaxon:6073 Cnidaria NCBITaxon:6157 Platyhelminthes NCBITaxon:6231 Nematoda NCBITaxon:6236 Rhabditida NCBITaxon:6237 Caenorhabditis NCBITaxon:6239 Caenorhabditis elegans NCBITaxon:6243 Rhabditidae NCBITaxon:6340 Annelida NCBITaxon:6341 Polychaeta NCBITaxon:6362 Sabellida NCBITaxon:6656 Arthropoda NCBITaxon:6960 Hexapoda NCBITaxon:7147 Diptera NCBITaxon:7203 Brachycera NCBITaxon:7214 Drosophilidae NCBITaxon:7215 Drosophila <flies,genus> NCBITaxon:7227 Drosophila melanogaster NCBITaxon:7496 Pterygota <insects> NCBITaxon:7711 Chordata NCBITaxon:7712 Tunicata NCBITaxon:7742 Vertebrata <vertebrates> NCBITaxon:7776 Gnathostomata <vertebrates> NCBITaxon:7777 Chondrichthyes NCBITaxon:7863 Holocephali NCBITaxon:7864 Chimaeriformes NCBITaxon:7878 Dipnomorpha NCBITaxon:7898 Actinopterygii NCBITaxon:7952 Cypriniformes NCBITaxon:7954 Danio NCBITaxon:7955 Danio rerio NCBITaxon:8287 Sarcopterygii NCBITaxon:8292 Amphibia NCBITaxon:8342 Anura NCBITaxon:8352 Pipidae NCBITaxon:8353 Xenopus <genus> NCBITaxon:8355 Xenopus laevis NCBITaxon:8360 Xenopodinae NCBITaxon:8457 Sauropsida NCBITaxon:8492 Archosauria NCBITaxon:8504 Lepidosauria NCBITaxon:8505 Sphenodontia NCBITaxon:8506 Sphenodontidae NCBITaxon:8507 Sphenodon NCBITaxon:8509 Squamata NCBITaxon:85512 Dicondylia NCBITaxon:8570 Serpentes NCBITaxon:8782 Aves NCBITaxon:8783 Palaeognathae NCBITaxon:8798 Struthioniformes NCBITaxon:8799 Struthionidae NCBITaxon:8800 Struthio NCBITaxon:8801 Struthio camelus NCBITaxon:8825 Neognathae NCBITaxon:88770 Panarthropoda NCBITaxon:8929 Columbiformes NCBITaxon:8930 Columbidae NCBITaxon:89593 Craniata <chordates> NCBITaxon:9254 Prototheria NCBITaxon:9255 Monotremata NCBITaxon:9259 Tachyglossidae NCBITaxon:9347 Eutheria NCBITaxon:9443 Primates NCBITaxon:9526 Catarrhini NCBITaxon:9604 Hominidae NCBITaxon:9605 Homo NCBITaxon:9606 Homo sapiens NCBITaxon:9989 Rodentia PATO:0000001 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 PATO:0000014 color PATO:0000025 For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). composition PATO:0000040 distance PATO:0000044 frequency PATO:0000051 morphology PATO:0000052 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 PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative PATO:0000069 deviation (from_normal) PATO:0000070 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 PATO:0000117 size PATO:0000125 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 PATO:0000136 closure PATO:0000141 structure PATO:0000146 temperature PATO:0000150 texture PATO:0000161 rate PATO:0000186 behavioral quality PATO:0000188 coordination PATO:0000261 maturity PATO:0000374 increased distance PATO:0000375 decreased distance PATO:0000380 increased frequency PATO:0000381 decreased frequency PATO:0000402 branched PATO:0000407 flat PATO:0000411 circular PATO:0000461 normal PATO:0000462 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 PATO:0000467 present PATO:0000470 increased amount PATO:0000498 increased duration PATO:0000499 decreased duration PATO:0000586 increased size PATO:0000587 decreased size PATO:0000608 closed PATO:0000770 uncoordinated PATO:0000911 decreased rate PATO:0000912 increased rate PATO:0000947 elliptic PATO:0000957 opacity PATO:0000963 opaque PATO:0000964 transparent PATO:0000992 viscosity PATO:0000998 viscous PATO:0001018 physical quality PATO:0001031 elasticity PATO:0001171 elastic PATO:0001185 larval PATO:0001236 See comments of relational quality of a physical entity. process quality PATO:0001241 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 PATO:0001300 optical quality PATO:0001305 increased temperature PATO:0001306 decreased temperature PATO:0001309 duration PATO:0001333 temporally extended PATO:0001472 decreased depth PATO:0001547 quality of a gas PATO:0001548 quality of a liquid PATO:0001555 has number of PATO:0001558 lacking processual parts PATO:0001562 decreased mass PATO:0001563 increased mass PATO:0001564 extra or missing processual parts PATO:0001579 contractility PATO:0001580 increased contractility PATO:0001581 decreased contractility PATO:0001591 curvature PATO:0001595 depth PATO:0001596 increased depth PATO:0001690 This refers to the disposition of the bearer. contractile PATO:0001693 increased viscosity PATO:0001694 decreased viscosity PATO:0001708 1-D extent PATO:0001727 disposition PATO:0001735 liquid configuration PATO:0001863 chronic PATO:0001873 cylindrical PATO:0001987 saccular PATO:0001992 cellularity PATO:0001993 multicellular PATO:0001995 organismal quality PATO:0001997 decreased amount PATO:0001999 lacks parts or has fewer parts of type PATO:0002000 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 PATO:0002001 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 PATO:0002002 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 PATO:0002006 2-D shape PATO:0002007 Use this term or an is_a child of this term when the entire shape of the object is known. convex 3-D shape PATO:0002009 branchiness PATO:0002014 structure, cavities PATO:0002045 dendritic PATO:0002062 physical quality of a process PATO:0002078 hollow PATO:0002083 altered number of PATO:0002124 laminar PATO:0002198 quality of a substance PATO:0002254 Becoming flat but not necessarily completely flat. flattened PATO:0002255 grooved PATO:0002266 3-D shape PATO:0002287 increased elasticity PATO:0002288 decreased elasticity PATO:0002299 tubular PATO:0002300 increased quality PATO:0002301 decreased quality PATO:0002302 decreased process quality PATO:0002303 decreased object quality PATO:0002304 increased process quality PATO:0002305 increased object quality PATO:0002318 superelliptic PATO:0002323 temporal distribution quality PATO:0002324 offset quality PATO:0002360 tendency PATO:0002361 increased tendency PATO:0002362 decreased tendency PATO:0002422 Acinus is Latin for berry. acinar PATO:0002462 collagenous PATO:0002468 distensible PATO:0010001 disconnected PATO:0015008 distensibility PATO:0050000 rate of occurence PATO:0055003 increased rate of occurrence PATO:0055004 decreased rate of occurrence PATO:0070060 quality of interaction of a substance with electromagnetic radiation RO:0002577 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 UBERON:0000000 processual entity UBERON:0000005 chemosensory organ UBERON:0000006 islet of Langerhans http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png UBERON:0000009 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 UBERON:0000010 peripheral nervous system http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png UBERON:0000012 somatic nervous system UBERON:0000013 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 UBERON:0000014 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 UBERON:0000015 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 UBERON:0000016 create a separate class for distributed pancreas, eg cyclostomes? endocrine pancreas UBERON:0000017 exocrine pancreas UBERON:0000018 compound eye https://github.com/obophenotype/uberon/issues/457 UBERON:0000019 camera-type eye UBERON:0000020 sense organ http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png UBERON:0000025 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 UBERON:0000026 appendicular this is currently a subtype of organism subdivision - which would exclude feathers appendage UBERON:0000030 lamina propria https://upload.wikimedia.org/wikipedia/commons/f/fb/GI_Organization.svg UBERON:0000031 lamina propria of trachea UBERON:0000033 head UBERON:0000042 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 UBERON:0000043 tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg UBERON:0000045 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 UBERON:0000047 simple eye UBERON:0000055 vessel UBERON:0000056 ureteral ureteric in humans, consists of adventitial, muscular and mucoa layers ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg UBERON:0000057 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 UBERON:0000058 Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. duct UBERON:0000059 large intestine UBERON:0000060 anatomical wall UBERON:0000061 anatomical structure UBERON:0000062 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 UBERON:0000063 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 UBERON:0000064 currently defined in a very broad sense, may be replaced by more specific classes in the future organ part UBERON:0000065 respiratory tract UBERON:0000066 fully formed stage https://github.com/obophenotype/uberon/issues/566 UBERON:0000068 embryo stage UBERON:0000069 Uberon includes clade-specific subclasses, e.g. nematod larva larval stage UBERON:0000071 death stage UBERON:0000072 proximo-distal subdivision of respiratory tract UBERON:0000073 regional part of nervous system UBERON:0000075 subdivision of skeletal system UBERON:0000076 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 UBERON:0000077 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 UBERON:0000078 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 UBERON:0000080 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 UBERON:0000081 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 UBERON:0000083 TODO check mesonephric tubule UBERON:0000084 ureteric bud UBERON:0000085 morula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png UBERON:0000086 zona pellucida http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png UBERON:0000087 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 UBERON:0000088 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 UBERON:0000091 bilaminar disc http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png UBERON:0000092 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 UBERON:0000094 membrane organ UBERON:0000095 cardiac neural crest UBERON:0000102 lung vasculature UBERON:0000104 life cycle https://github.com/obophenotype/uberon/issues/532 UBERON:0000105 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 UBERON:0000106 zygote stage UBERON:0000107 cleavage stage UBERON:0000108 consider adding a preceding stage 'morula stage' as part of cleavage blastula stage http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png UBERON:0000109 gastrula stage UBERON:0000110 neurula stage https://github.com/obophenotype/uberon/issues/343 UBERON:0000111 organogenesis stage https://github.com/obophenotype/uberon/issues/533 UBERON:0000114 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 UBERON:0000115 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 UBERON:0000117 respiratory tube UBERON:0000118 clarify successors - include bronchi? lung bud http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png UBERON:0000122 neuron projection bundle UBERON:0000125 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 UBERON:0000126 cranial nerve nucleus http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png UBERON:0000153 anterior region of body UBERON:0000154 posterior region of body UBERON:0000158 membranous layer UBERON:0000159 requires alignment with EHDAA2 and complete developmental relationships anal canal https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png UBERON:0000160 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 UBERON:0000161 orifice UBERON:0000162 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 UBERON:0000163 this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. embryonic cloaca UBERON:0000164 primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png UBERON:0000165 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 UBERON:0000166 oral opening UBERON:0000167 oral cavity UBERON:0000168 proximal-distal subdivision of colon 1 1 UBERON:0000170 pair of lungs UBERON:0000171 respiration organ UBERON:0000174 excreta UBERON:0000178 This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. blood UBERON:0000179 haemolymphatic fluid UBERON:0000304 TODO - add layer relations. 'tendon sheath' GAT in FMA. tendon sheath UBERON:0000307 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 UBERON:0000309 defined generically to encompass both vertebrates and invertebrates body wall UBERON:0000317 colonic mucosa UBERON:0000320 duodenal mucosa UBERON:0000325 gastric gland UBERON:0000326 pancreatic juice UBERON:0000328 We model the digestive tract as consisting of two parts: the wall and the lumen. gut wall UBERON:0000333 Note that some sources treat 'intestinal gland' as synonymous with crypts intestinal gland UBERON:0000344 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 UBERON:0000348 Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html] ophthalmic nerve UBERON:0000353 parenchymal parenchyma UBERON:0000355 pharyngeal mucosa UBERON:0000358 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 UBERON:0000375 mandibular nerve http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png UBERON:0000377 maxillary nerve http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png UBERON:0000378 tongue muscle http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png UBERON:0000379 tracheal mucosa UBERON:0000383 consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 musculature of body UBERON:0000389 lens cortex UBERON:0000390 lens nucleus UBERON:0000397 colonic epithelium UBERON:0000409 serous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png UBERON:0000410 bronchial mucosa UBERON:0000414 mucous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png UBERON:0000415 artery wall UBERON:0000456 secretion of exocrine gland UBERON:0000457 cavernous artery UBERON:0000463 organism substance UBERON:0000464 anatomical space UBERON:0000465 material anatomical entity UBERON:0000466 immaterial anatomical entity UBERON:0000467 anatomical system UBERON:0000468 TODO - split body and mc organism? body continues after death stage organismal multicellular organism UBERON:0000471 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 UBERON:0000474 female reproductive system http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg UBERON:0000475 Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency organism subdivision UBERON:0000476 acellular anatomical structure UBERON:0000477 anatomical cluster UBERON:0000478 see also conceptus extraembryonic component in EHDAA2. extraembryonic structure UBERON:0000479 changed label and definition to reflect CARO2 tissue UBERON:0000481 multi-tissue structure UBERON:0000483 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 UBERON:0000484 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 UBERON:0000485 simple columnar epithelium http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png UBERON:0000486 multilaminar epithelium UBERON:0000487 simple squamous epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg UBERON:0000488 atypical epithelium UBERON:0000489 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 UBERON:0000490 consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable unilaminar epithelium UBERON:0000912 mucoid mucous mucus UBERON:0000915 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 UBERON:0000916 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 UBERON:0000922 embryonic embryo https://github.com/obophenotype/uberon/issues/503 https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg UBERON:0000923 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 UBERON:0000924 ectodermal ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png UBERON:0000925 endodermal endoderm http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png UBERON:0000926 mesodermal mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png UBERON:0000930 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 UBERON:0000931 removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. proctodeal proctodeum https://github.com/obophenotype/uberon/issues/685 UBERON:0000945 stomach https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg UBERON:0000947 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 UBERON:0000948 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 UBERON:0000949 endocrine endocrine system UBERON:0000955 requires review for applicability to invertebrate structures, e.g. synganglion brain UBERON:0000957 TODO - merge with cell layer? laminar lamina http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png UBERON:0000963 this term should be ceded to the arthropod anatomy ontology head sensillum UBERON:0000964 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 UBERON:0000965 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 UBERON:0000966 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 UBERON:0000970 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 UBERON:0000971 ommatidial ommatidium UBERON:0000974 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 UBERON:0000982 skeletal joint UBERON:0000988 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 UBERON:0000990 consider splitting genitalia from reproductive system reproductive system http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg UBERON:0000991 gonadal gonad UBERON:0000992 ovarian ovary http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png UBERON:0001003 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 UBERON:0001004 respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg UBERON:0001005 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 UBERON:0001007 digestive digestive system UBERON:0001008 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 UBERON:0001009 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 UBERON:0001013 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 UBERON:0001015 musculature http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png UBERON:0001016 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 UBERON:0001017 central nervous system UBERON:0001021 nervous nerve UBERON:0001027 sensory nerve UBERON:0001032 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 UBERON:0001033 gustatory gustatory system UBERON:0001040 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 UBERON:0001041 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 UBERON:0001042 Consider generalizing to deuterostome pharynx chordate pharynx UBERON:0001043 esophageal esophagus http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg UBERON:0001045 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 UBERON:0001046 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 UBERON:0001048 primordium UBERON:0001049 neural tube http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png UBERON:0001052 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 UBERON:0001062 anatomical entity UBERON:0001064 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 UBERON:0001068 TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of back UBERON:0001070 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 UBERON:0001071 The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] superficial cervical artery UBERON:0001072 posterior vena cava http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png UBERON:0001073 ileocecal junction UBERON:0001074 pericardial cavity UBERON:0001081 endocardium of ventricle UBERON:0001082 epicardium of ventricle UBERON:0001083 myocardium of ventricle UBERON:0001084 TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of head UBERON:0001085 TODO - distinguish between entire skin of region and arbitrary zone of skin on region skin of trunk UBERON:0001088 kidney excreta from some taxa (e.g. in aves) may not be liquid urine UBERON:0001090 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 UBERON:0001096 wall of esophagus UBERON:0001113 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 UBERON:0001114 right lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png UBERON:0001115 left lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png UBERON:0001133 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 UBERON:0001134 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 UBERON:0001135 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 UBERON:0001136 mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg UBERON:0001137 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 UBERON:0001138 superior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png UBERON:0001139 common iliac vein https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif UBERON:0001140 renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png UBERON:0001141 right renal vein UBERON:0001142 left renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png UBERON:0001143 todo - add developmental relationships for other taxa hepatic vein http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png UBERON:0001145 ovarian vein http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg UBERON:0001152 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 UBERON:0001155 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 UBERON:0001159 sigmoid colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg UBERON:0001161 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 UBERON:0001165 pyloric antrum http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg UBERON:0001166 We follow Kardong in defining stomach regions by glands pyloric pylorus http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg UBERON:0001167 wall of stomach UBERON:0001168 wall of small intestine UBERON:0001169 wall of large intestine UBERON:0001170 mesentery of small intestine UBERON:0001171 portal lobule UBERON:0001172 hepatic acinus UBERON:0001173 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 UBERON:0001174 common bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png UBERON:0001175 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 UBERON:0001176 right hepatic duct UBERON:0001177 left hepatic duct UBERON:0001178 visceral peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png UBERON:0001179 peritoneal cavity UBERON:0001184 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 UBERON:0001185 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 UBERON:0001186 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 UBERON:0001190 ovarian artery http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png UBERON:0001193 currently defined in a generic fashion. hepatic artery http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png UBERON:0001194 splenic artery https://github.com/obophenotype/uberon/issues/268 http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png UBERON:0001199 mucosa of stomach https://upload.wikimedia.org/wikipedia/commons/1/1c/Normal_gastric_mucosa_intermed_mag.jpg UBERON:0001200 submucosa of stomach UBERON:0001201 TODO - check serosa/peritoneum serosa of stomach UBERON:0001202 pyloric sphincter UBERON:0001204 mucosa of small intestine UBERON:0001205 submucosa of small intestine UBERON:0001206 duodenum, 1st part serosa, 2nd - 4th adventitia serosa of small intestine UBERON:0001207 mucosa of large intestine UBERON:0001208 submucosa of large intestine UBERON:0001209 TODO - check serosa/peritoneum serosa of large intestine UBERON:0001212 currently defined as equivalent to any submucosal gland in the duodenum. duodenal gland UBERON:0001213 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 UBERON:0001215 inferior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png UBERON:0001222 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right ureter UBERON:0001223 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left ureter UBERON:0001224 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 UBERON:0001225 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 UBERON:0001231 nephron tubule UBERON:0001232 collecting duct of renal tubule UBERON:0001238 lamina propria of small intestine UBERON:0001242 intestinal mucosa UBERON:0001243 TODO - check serosa/peritoneum serosa of intestine UBERON:0001245 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 UBERON:0001246 interlobular bile duct UBERON:0001252 adventitia of ureter UBERON:0001253 lamina propria of ureter UBERON:0001255 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 UBERON:0001256 wall of urinary bladder UBERON:0001259 mucosa of urinary bladder UBERON:0001260 TODO - check serosa/peritoneum serosa of urinary bladder UBERON:0001261 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 UBERON:0001262 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 UBERON:0001263 pancreatic acinus UBERON:0001264 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 UBERON:0001268 peritoneal fluid UBERON:0001271 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 UBERON:0001276 epithelium of stomach UBERON:0001277 intestinal epithelium UBERON:0001278 epithelium of large intestine UBERON:0001279 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 UBERON:0001280 liver parenchyma UBERON:0001282 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 UBERON:0001285 kidney terms require review for cross-vertebrate compatibility and developmental relationships. nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png UBERON:0001312 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 UBERON:0001317 internal iliac vein http://upload.wikimedia.org/wikipedia/commons/c/cb/Internaliliacv.png UBERON:0001325 muscle of pelvis UBERON:0001334 female urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png UBERON:0001338 urethral gland UBERON:0001353 anal region https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png UBERON:0001366 parietal peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png UBERON:0001415 skin of pelvis UBERON:0001416 skin of abdomen UBERON:0001417 skin of neck UBERON:0001418 skin of thorax UBERON:0001419 skin of limb UBERON:0001421 this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). pectoral girdle region UBERON:0001434 skeletal skeletal system https://github.com/obophenotype/uberon/wiki/The-skeletal-system UBERON:0001440 TODO - find a home for: FMA:24139 ! skeleton of upper limb forelimb skeleton UBERON:0001441 TOOD - find a home for: FMA:24140 hindlimb skeleton UBERON:0001444 subdivision of head UBERON:0001456 facial face http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg UBERON:0001458 skin of lip UBERON:0001474 bone element UBERON:0001484 articular capsule http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png UBERON:0001496 ascending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg UBERON:0001497 muscle of pelvic girdle UBERON:0001508 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 UBERON:0001514 results from fusion of left and right dorsal aortae descending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg UBERON:0001515 thoracic aorta http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png UBERON:0001516 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 UBERON:0001529 brachiocephalic artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg UBERON:0001530 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 UBERON:0001532 internal carotid artery http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png UBERON:0001533 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 UBERON:0001534 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 UBERON:0001555 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 UBERON:0001556 lower urinary tract UBERON:0001558 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 UBERON:0001568 muscle of larynx UBERON:0001571 genioglossus muscle http://upload.wikimedia.org/wikipedia/commons/7/7e/Genioglossus.png UBERON:0001572 hyoglossus muscle http://upload.wikimedia.org/wikipedia/commons/7/7e/Hyoglossus.png UBERON:0001575 extrinsic muscle of tongue UBERON:0001576 intrinsic muscle of tongue UBERON:0001584 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 UBERON:0001585 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 UBERON:0001586 internal jugular vein http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png UBERON:0001592 bronchial vein UBERON:0001605 ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png UBERON:0001606 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 UBERON:0001607 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 UBERON:0001608 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 UBERON:0001610 lingual artery https://upload.wikimedia.org/wikipedia/commons/3/3c/Lingual_artery.PNG UBERON:0001612 facial artery http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png UBERON:0001616 maxillary artery http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png UBERON:0001619 ophthalmic artery http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png UBERON:0001622 lacrimal artery http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png UBERON:0001630 muscular muscle organ UBERON:0001637 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 UBERON:0001638 TODO - check with MA - vein vs venous blood vessel venous vein http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg UBERON:0001639 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 UBERON:0001640 dorsal aorta in Kardong celiac artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png UBERON:0001645 trigeminal nerve https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png UBERON:0001649 glossopharyngeal nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png UBERON:0001650 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 UBERON:0001651 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 UBERON:0001652 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 UBERON:0001653 facial vein http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png UBERON:0001675 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 UBERON:0001676 occipital bone http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png UBERON:0001678 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 UBERON:0001685 hyoid bone http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png UBERON:0001701 glossopharyngeal ganglion UBERON:0001703 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 UBERON:0001708 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 UBERON:0001710 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 UBERON:0001714 cranial ganglion UBERON:0001723 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 UBERON:0001725 cranial synchondrosis UBERON:0001726 papilla of tongue UBERON:0001727 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 UBERON:0001731 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 UBERON:0001737 laryngeal larynx http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg UBERON:0001739 laryngeal cartilage UBERON:0001750 TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal lacrimal apparatus http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png UBERON:0001759 vagus nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png UBERON:0001766 anterior chamber of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg UBERON:0001768 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 UBERON:0001769 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 UBERON:0001772 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 UBERON:0001773 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 UBERON:0001774 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 UBERON:0001775 ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg UBERON:0001776 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 UBERON:0001777 substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png UBERON:0001778 ciliary epithelium UBERON:0001779 iris stroma http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png UBERON:0001780 spinal nerve https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg UBERON:0001781 layer of retina UBERON:0001785 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 UBERON:0001796 aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg UBERON:0001800 sensory ganglion UBERON:0001801 anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png UBERON:0001802 posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg UBERON:0001803 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 UBERON:0001804 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 UBERON:0001805 autonomic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png UBERON:0001806 sympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png UBERON:0001817 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 UBERON:0001824 mucosa of larynx UBERON:0001827 secretion of lacrimal gland UBERON:0001833 labial lip http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg UBERON:0001835 lower lip http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg UBERON:0001851 cortical cortex UBERON:0001891 developmental relationships need revised mesencephalic midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG UBERON:0001892 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 UBERON:0001895 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 UBERON:0001896 medulla oblongata http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg UBERON:0001901 epithelium of trachea UBERON:0001902 epithelium of small intestine UBERON:0001915 endothelium of capillary UBERON:0001916 endothelium of arteriole UBERON:0001917 endothelium of artery UBERON:0001918 endothelium of venule UBERON:0001919 endothelium of vein UBERON:0001943 '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 UBERON:0001948 regional part of spinal cord UBERON:0001956 cartilage of bronchus UBERON:0001957 submucosa of bronchus UBERON:0001958 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 UBERON:0001969 blood plasma UBERON:0001970 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 UBERON:0001971 gastric juice UBERON:0001972 submucosa of esophagus UBERON:0001974 lamina propria of esophagus UBERON:0001975 serosa of esophagus UBERON:0001976 TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar epithelium of esophagus UBERON:0001978 parenchyma of pancreas UBERON:0001979 venule https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg UBERON:0001980 arteriole https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg UBERON:0001981 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 UBERON:0001982 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 UBERON:0001985 corneal endothelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png UBERON:0001986 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 UBERON:0001988 fecal feces UBERON:0001994 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 UBERON:0002012 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 UBERON:0002015 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 UBERON:0002016 pulmonary vein https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png UBERON:0002017 portal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png UBERON:0002019 accessory XI nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png UBERON:0002020 gray matter https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg UBERON:0002028 rhombencephalic hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg UBERON:0002029 epithelium of gall bladder UBERON:0002031 epithelium of bronchus UBERON:0002036 striated muscle tissue UBERON:0002040 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 UBERON:0002047 pontine raphe nucleus UBERON:0002048 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 UBERON:0002049 see also: vascular system. Consider merging? vascular vasculature http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg UBERON:0002050 embryonic structure UBERON:0002051 epithelium of bronchiole UBERON:0002061 truncus arteriosus UBERON:0002062 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 UBERON:0002063 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 UBERON:0002067 Consider adding a layer-of-skin grouping class for all skin layers dermal dermis http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg UBERON:0002072 hypodermal subcutaneous subcutaneus hypodermis http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg UBERON:0002075 viscus UBERON:0002078 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 UBERON:0002079 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 UBERON:0002080 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 UBERON:0002081 cardiac atrium UBERON:0002082 cardiac ventricle UBERON:0002084 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 UBERON:0002085 interatrial septum http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png UBERON:0002090 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 UBERON:0002091 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 UBERON:0002092 brain dura mater UBERON:0002093 spinal dura mater UBERON:0002094 interventricular septum http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png UBERON:0002095 mesenteric mesentery http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png UBERON:0002097 consider 'integumentary system' for invertebrates skin of body http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg UBERON:0002099 'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations' cardiac septum UBERON:0002100 trunk UBERON:0002101 limb UBERON:0002102 Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm forelimb UBERON:0002103 crural hindlimb http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png UBERON:0002104 visual system UBERON:0002105 vestibulo-auditory system http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg UBERON:0002106 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 UBERON:0002107 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 UBERON:0002108 small intestine http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg UBERON:0002110 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 UBERON:0002111 artery smooth muscle tissue UBERON:0002112 smooth muscle of esophagus UBERON:0002113 renal kidney UBERON:0002114 duodenal duodenum http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg UBERON:0002118 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right ovary UBERON:0002119 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left ovary UBERON:0002120 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 UBERON:0002128 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 UBERON:0002148 TODO - check ZFA/pons. also GO says part of dorsorostral pons locus ceruleus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png UBERON:0002149 superior salivatory nucleus http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png UBERON:0002165 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 UBERON:0002166 endocardium of atrium UBERON:0002167 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right lung http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png UBERON:0002168 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left lung http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png UBERON:0002185 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 UBERON:0002186 bronchiolar bronchiole https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png UBERON:0002187 terminal bronchiole https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png UBERON:0002190 subcutaneous adipose tissue UBERON:0002193 hemolymphoid system UBERON:0002199 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 UBERON:0002200 vasculature of head UBERON:0002201 vasculature of trunk UBERON:0002202 submucosa of trachea UBERON:0002203 vasculature of eye UBERON:0002204 musculoskeletal musculoskeletal system UBERON:0002209 fibrous joint UBERON:0002213 cartilaginous joint UBERON:0002215 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 UBERON:0002216 consider adding fibrocartilage class symphysis http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray298.png UBERON:0002217 synovial joint UBERON:0002224 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 UBERON:0002240 TODO - add superclass to unify with VNC? spinal cord http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg UBERON:0002241 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 UBERON:0002268 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 UBERON:0002275 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 UBERON:0002294 biliary system http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png UBERON:0002296 dorsal mesentery http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png UBERON:0002298 '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 UBERON:0002302 myocardium of atrium UBERON:0002308 nucleus of brain UBERON:0002315 gray matter of spinal cord UBERON:0002323 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 UBERON:0002324 muscle of back UBERON:0002325 epithelium of urethra UBERON:0002326 lamina propria of urethra UBERON:0002328 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 UBERON:0002329 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 UBERON:0002330 exocrine system UBERON:0002333 pulmonary trunk https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png UBERON:0002338 lamina propria of bronchus UBERON:0002342 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 UBERON:0002343 distinction between abdomen muscle and abdomen musculature abdomen musculature UBERON:0002345 descending thoracic aorta UBERON:0002346 neurectodermal we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here neurectoderm UBERON:0002348 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 UBERON:0002349 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 UBERON:0002350 EHDAA2 divides the system from the tissue conducting system of heart UBERON:0002355 pelvic pelvic region of trunk UBERON:0002357 serous pericardium UBERON:0002358 TODO - in ZFA is_a epithelium peritoneal peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png UBERON:0002359 most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium] fibrous pericardium UBERON:0002360 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 UBERON:0002363 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 UBERON:0002365 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 UBERON:0002368 endocrine gland http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png UBERON:0002376 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 UBERON:0002377 muscle of neck UBERON:0002378 muscle of abdomen UBERON:0002384 connective tissue UBERON:0002385 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 UBERON:0002390 hematopoietic hematopoietic system UBERON:0002394 bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png UBERON:0002405 immune system UBERON:0002406 pericardial sac http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png UBERON:0002407 pericardial pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png UBERON:0002408 parietal serous pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png UBERON:0002409 pericardial fluid UBERON:0002410 autonomic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png UBERON:0002416 integumental system UBERON:0002417 abdominal segment of trunk UBERON:0002418 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 UBERON:0002419 check FMA, use plural for now as general class not there skin gland UBERON:0002423 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 UBERON:0002424 consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) oral epithelium UBERON:0002425 visceral serous pericardium UBERON:0002428 the formal definition is very inclusive, and includes sesamoids limb bone UBERON:0002443 cannot find singular in FMA, using Set class choroidal blood vessel UBERON:0002457 intersomitic artery UBERON:0002458 spinal artery UBERON:0002460 vesical vein http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png UBERON:0002466 intestine secretion UBERON:0002469 esophagus mucosa UBERON:0002481 see https://github.com/obophenotype/uberon/issues/27 bone tissue UBERON:0002506 iris epithelium UBERON:0002513 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 UBERON:0002514 intramembranous bone UBERON:0002521 elastic tissue http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png UBERON:0002522 May be composed of smooth muscle and elastic tissue tunica media https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg UBERON:0002523 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 UBERON:0002530 glandular gland http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png UBERON:0002532 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 UBERON:0002536 this term should be ceded to the arthropod anatomy ontology arthropod sensillum UBERON:0002539 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 UBERON:0002546 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 UBERON:0002548 TODO discriminate between stages and organisms larval larva UBERON:0002553 anatomical cavity UBERON:0002558 organ cavity UBERON:0002561 lumen of central nervous system UBERON:0002616 regional part of brain UBERON:0002871 hypoglossal nucleus http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png UBERON:0002925 trigeminal nucleus UBERON:0002926 gustatory epithelium UBERON:0003023 involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum] pontine tegmentum https://upload.wikimedia.org/wikipedia/commons/9/9c/Brainstem_Abducens.png UBERON:0003037 septal general anatomical term in FMA septum UBERON:0003052 consider adding class for organizer. Consider adding separate class for isthmus as a structure midbrain-hindbrain boundary UBERON:0003055 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 UBERON:0003056 pre-chordal neural plate UBERON:0003057 chordal neural plate UBERON:0003059 presomitic mesoderm UBERON:0003060 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 UBERON:0003061 blood island UBERON:0003063 TODO - check; developmental relationship to anterior hypoblast in ZFA? prechordal plate UBERON:0003064 intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png UBERON:0003066 2 pharyngeal arch 2 http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png UBERON:0003067 The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode dorsolateral placode UBERON:0003068 axial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png UBERON:0003070 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 UBERON:0003071 eye primordium UBERON:0003072 optic cup UBERON:0003073 lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png UBERON:0003074 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 UBERON:0003075 neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png UBERON:0003076 posterior neural tube UBERON:0003077 paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png UBERON:0003078 epibranchial placode UBERON:0003080 TODO - add grouping class for the anterior end of the neural tube at all stages anterior neural tube UBERON:0003081 lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png UBERON:0003082 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 UBERON:0003083 trunk neural crest UBERON:0003084 should probably be merged with heart rudiment. heart primordium UBERON:0003089 sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png UBERON:0003099 cranial neural crest UBERON:0003100 female organism UBERON:0003102 consider obsoleting. See issue/1305 surface structure UBERON:0003103 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 UBERON:0003104 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 UBERON:0003113 wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007 dermatocranium UBERON:0003114 3 pharyngeal arch 3 UBERON:0003115 4 pharyngeal arch 4 UBERON:0003117 6 pharyngeal arch 6 UBERON:0003118 Disappears early in development in tetrapods pharyngeal arch artery 1 UBERON:0003119 pharyngeal arch artery 2 UBERON:0003120 pharyngeal arch artery 3 UBERON:0003121 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 UBERON:0003123 pharyngeal arch artery 6 UBERON:0003126 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 UBERON:0003128 cranial cranium UBERON:0003129 in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton skull UBERON:0003133 reproductive organ UBERON:0003134 female reproductive organ UBERON:0003212 gustatory organ UBERON:0003218 ovary septum UBERON:0003220 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 UBERON:0003236 epithelium of lower jaw UBERON:0003257 yolk sac endoderm UBERON:0003258 TODO - check endoderm of foregut UBERON:0003259 TODO - check endoderm of midgut UBERON:0003260 TODO - check endoderm of hindgut UBERON:0003269 skeletal muscle tissue of eye UBERON:0003278 skeleton of lower jaw UBERON:0003279 endothelium of trachea UBERON:0003281 TODO - check primitive vs developed mesentery of stomach UBERON:0003282 mesentery of heart UBERON:0003283 mesentery of oesophagus UBERON:0003284 mesentery of midgut UBERON:0003288 consider changing genus to subdivision of meninx meninx of midbrain UBERON:0003291 consider changing genus to subdivision of meninx meninx of hindbrain UBERON:0003292 meninx of spinal cord UBERON:0003294 gland of foregut UBERON:0003295 pharyngeal gland UBERON:0003297 gland of integumental system UBERON:0003304 mesoderm blood island UBERON:0003314 TODO - change mesenchyme relationships to precursor_of eye mesenchyme UBERON:0003315 mesenchyme of ovary UBERON:0003316 mesenchyme of yolk sac UBERON:0003324 mesenchyme of lower jaw UBERON:0003329 submucosa of anal canal UBERON:0003330 submucosa of rectum UBERON:0003331 submucosa of colon UBERON:0003332 submucosa of duodenum UBERON:0003334 serosa of rectum UBERON:0003335 serosa of colon UBERON:0003336 1st part serosa, 2nd - 4th adventitia serosa of duodenum UBERON:0003338 ganglion of peripheral nervous system UBERON:0003339 ganglion of central nervous system UBERON:0003342 mucosa of anal canal UBERON:0003343 mucosa of oral region UBERON:0003346 mucosa of rectum UBERON:0003350 lies on top of lamina propria epithelium of mucosa UBERON:0003351 pharyngeal epithelium UBERON:0003352 epithelium of midgut UBERON:0003353 epithelium of hindgut UBERON:0003354 epithelium of rectum UBERON:0003357 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 UBERON:0003364 epithelium of right lung UBERON:0003365 epithelium of left lung UBERON:0003371 pelvic appendage bud ectoderm UBERON:0003372 pectoral appendage bud ectoderm UBERON:0003379 cardiac muscle of right atrium UBERON:0003380 cardiac muscle of left atrium UBERON:0003381 cardiac muscle of right ventricle UBERON:0003382 cardiac muscle of left ventricle UBERON:0003383 cardiac muscle tissue of interventricular septum UBERON:0003384 skeletal muscle tissue of pharynx UBERON:0003386 Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle smooth muscle of eye UBERON:0003387 smooth muscle of trachea UBERON:0003388 mesothelium of pericardial cavity UBERON:0003393 mesentery of urinary system UBERON:0003394 mesentery of hindgut UBERON:0003395 mesentery of rectum UBERON:0003396 mesentery of colon UBERON:0003397 mesentery of duodenum UBERON:0003406 cartilage of respiratory system UBERON:0003408 gland of digestive tract UBERON:0003409 gland of tongue UBERON:0003412 pelvic appendage bud mesenchyme UBERON:0003413 pectoral appendage bud mesenchyme UBERON:0003416 TODO - develops_from mesenchyme of tongue UBERON:0003426 dermis adipose tissue UBERON:0003429 abdomen nerve UBERON:0003430 neck nerve UBERON:0003438 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 UBERON:0003439 nerve of trunk region UBERON:0003440 limb nerve UBERON:0003441 forelimb nerve UBERON:0003442 hindlimb nerve UBERON:0003443 consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve thoracic cavity nerve UBERON:0003444 pelvis nerve UBERON:0003457 Different sources vary regarding which bones are craniofacial; e.g. hyoid bone head bone UBERON:0003458 neck bone UBERON:0003462 test whether 'facial bone' is an exact synonym facial bone UBERON:0003463 trunk bone UBERON:0003464 hindlimb bone UBERON:0003468 ureteric segment of renal artery UBERON:0003469 respiratory system artery UBERON:0003471 artery of lower lip UBERON:0003473 thoracic cavity artery UBERON:0003474 meningeal artery UBERON:0003475 ureteric vein UBERON:0003476 respiratory system venous blood vessel UBERON:0003478 vein of lower lip http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png UBERON:0003479 thoracic cavity vein UBERON:0003489 respiratory system capillary endothelium UBERON:0003494 respiratory system venule UBERON:0003495 respiratory system arteriole UBERON:0003496 head blood vessel UBERON:0003497 abdomen blood vessel UBERON:0003498 heart blood vessel UBERON:0003499 brain blood vessel UBERON:0003500 follow up on tracker item corneal blood vessel UBERON:0003501 retina blood vessel UBERON:0003502 neck blood vessel UBERON:0003504 respiratory system blood vessel UBERON:0003505 trachea blood vessel UBERON:0003509 only in MA - supertype of artery, arteriole, aorta. arterial blood vessel UBERON:0003511 iris blood vessel UBERON:0003512 lung blood vessel UBERON:0003513 trunk blood vessel UBERON:0003514 limb blood vessel UBERON:0003515 forelimb blood vessel UBERON:0003516 hindlimb blood vessel UBERON:0003517 kidney blood vessel UBERON:0003519 thoracic cavity blood vessel UBERON:0003520 pelvis blood vessel UBERON:0003526 respiratory system capillary UBERON:0003527 kidney capillary UBERON:0003528 brain gray matter UBERON:0003531 TODO - check free limb vs pectoral complex forelimb skin UBERON:0003532 TODO - check free limb vs pelvic complex hindlimb skin UBERON:0003538 right lung bronchiole UBERON:0003539 left lung bronchiole UBERON:0003540 right lung terminal bronchiole UBERON:0003541 left lung terminal bronchiole UBERON:0003547 brain meninx UBERON:0003562 midbrain dura mater UBERON:0003565 hindbrain dura mater UBERON:0003566 head connective tissue UBERON:0003567 abdomen connective tissue UBERON:0003568 neck connective tissue UBERON:0003570 respiratory system connective tissue UBERON:0003571 trachea connective tissue UBERON:0003580 lower respiratory tract connective tissue UBERON:0003583 larynx connective tissue UBERON:0003585 dermis connective tissue UBERON:0003586 trunk connective tissue UBERON:0003587 limb connective tissue UBERON:0003588 forelimb connective tissue UBERON:0003589 hindlimb connective tissue UBERON:0003592 bronchus connective tissue UBERON:0003593 thoracic cavity connective tissue UBERON:0003594 pelvis connective tissue UBERON:0003601 neck cartilage UBERON:0003603 lower respiratory tract cartilage UBERON:0003604 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 UBERON:0003605 eye skin gland UBERON:0003609 aorta elastic tissue UBERON:0003610 heart elastic tissue UBERON:0003611 respiratory system elastic tissue UBERON:0003613 cardiovascular system elastic tissue UBERON:0003614 blood vessel elastic tissue UBERON:0003615 lung elastic tissue UBERON:0003616 bronchus elastic tissue UBERON:0003617 trachea elastic tissue UBERON:0003618 aorta tunica media UBERON:0003619 aorta tunica intima UBERON:0003643 respiratory system arterial blood vessel UBERON:0003644 kidney arterial blood vessel UBERON:0003657 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses limb joint UBERON:0003661 limb muscle UBERON:0003662 forelimb muscle UBERON:0003663 hindlimb muscle UBERON:0003684 abdominal cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg UBERON:0003685 cranial suture UBERON:0003687 Design pattern notes: check whether this fits the foramen design pattern foramen magnum http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png UBERON:0003697 abdominal wall http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg UBERON:0003703 includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct extrahepatic bile duct UBERON:0003704 includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts intrahepatic bile duct UBERON:0003711 brachiocephalic vein http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png UBERON:0003712 cavernous sinus UBERON:0003713 splenic vein http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png UBERON:0003714 neural tissue UBERON:0003715 All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers splanchnic nerve UBERON:0003716 recurrent laryngeal nerve UBERON:0003721 lingual nerve UBERON:0003729 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 UBERON:0003824 nerve of thoracic segment UBERON:0003825 nerve of abdominal segment UBERON:0003827 thoracic segment bone UBERON:0003828 abdominal segment bone UBERON:0003829 urethra muscle tissue UBERON:0003830 thoracic segment muscle UBERON:0003831 respiratory system muscle UBERON:0003832 merge muscle and muscle layer? esophagus muscle UBERON:0003833 abdominal segment muscle UBERON:0003834 thoracic segment blood vessel UBERON:0003835 abdominal segment blood vessel UBERON:0003836 abdominal segment skin UBERON:0003837 thoracic segment connective tissue UBERON:0003838 abdominal segment connective tissue UBERON:0003839 forelimb joint UBERON:0003840 hindlimb joint UBERON:0003842 neural tube lumen UBERON:0003848 gonadal vein http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png UBERON:0003849 mesencephalic neural crest UBERON:0003852 rhombencephalon neural crest UBERON:0003853 spinal cord neural crest UBERON:0003854 spinal cord neural plate UBERON:0003855 gonad mesenchyme UBERON:0003859 forelimb mesenchyme UBERON:0003860 hindlimb mesenchyme UBERON:0003869 presumptive ganglion UBERON:0003886 future coelemic cavity lumen UBERON:0003887 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 UBERON:0003891 stromal stroma UBERON:0003894 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 UBERON:0003897 axial muscle UBERON:0003898 skeletal muscle tissue of trunk UBERON:0003902 retinal neural layer UBERON:0003914 contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers epithelial tube UBERON:0003915 endothelial tube UBERON:0003918 check this kidney mesenchyme UBERON:0003920 Compare to: vein venous blood vessel UBERON:0003921 revisit after standardizing terms 'primordium', 'anlagen', 'bud' pancreas primordium http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png UBERON:0003922 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 UBERON:0003923 dorsal pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png UBERON:0003924 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 UBERON:0003928 digestive system duct UBERON:0003929 digestive tract epithelium UBERON:0003932 cartilage element of chondrocranium UBERON:0003933 cranial cartilage UBERON:0003937 reproductive gland UBERON:0003942 somatosensory system UBERON:0003952 anterior stroma of cornea UBERON:0003953 posterior stroma of cornea UBERON:0003967 cutaneous elastic tissue UBERON:0003978 valvular valve UBERON:0004015 embryonic-extraembryonic boundary UBERON:0004016 Not to be confused with 'dermatome segment of skin'. dermatome http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png UBERON:0004022 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 UBERON:0004058 biliary ductule UBERON:0004060 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 UBERON:0004061 neural tube mantle layer UBERON:0004062 neural tube marginal layer UBERON:0004064 neural tube basal plate UBERON:0004087 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 UBERON:0004088 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 UBERON:0004100 renal collecting system http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png 2 UBERON:0004111 anatomical conduit UBERON:0004117 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 UBERON:0004118 vasculature of iris UBERON:0004119 Grouping term for query purposes endoderm-derived structure UBERON:0004120 Grouping term for query purposes mesoderm-derived structure UBERON:0004121 Grouping term for query purposes ectoderm-derived structure UBERON:0004122 genitourinary urogenital genitourinary system UBERON:0004128 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 UBERON:0004133 salivatory nucleus UBERON:0004139 TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO cardiogenic plate UBERON:0004140 primary heart field UBERON:0004141 heart tube UBERON:0004142 outflow tract septum UBERON:0004145 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 UBERON:0004148 cardiac vein UBERON:0004151 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 UBERON:0004160 propepicardial Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA] proepicardium UBERON:0004161 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 UBERON:0004176 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 external genitalia UBERON:0004177 consider splitting out lymph organ, compare with lymph node hemopoietic organ UBERON:0004178 aorta smooth muscle tissue UBERON:0004185 endodermal part of digestive tract UBERON:0004203 cortical collecting duct UBERON:0004208 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 UBERON:0004209 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 UBERON:0004211 nephron epithelium UBERON:0004215 back nerve UBERON:0004219 urethra smooth muscle layer UBERON:0004220 large intestine smooth muscle UBERON:0004221 intestine smooth muscle UBERON:0004222 stomach smooth muscle UBERON:0004225 respiratory system smooth muscle UBERON:0004226 gastrointestinal system smooth muscle UBERON:0004227 kidney pelvis smooth muscle UBERON:0004228 urinary bladder smooth muscle UBERON:0004231 anal region smooth muscle UBERON:0004233 lower respiratory tract smooth muscle UBERON:0004234 see notes for muscle of iris. iris smooth muscle UBERON:0004236 arteriole smooth muscle UBERON:0004237 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 UBERON:0004238 spleen smooth muscle UBERON:0004239 small intestine smooth muscle UBERON:0004240 gallbladder smooth muscle UBERON:0004242 bronchus smooth muscle UBERON:0004246 outflow tract smooth muscle UBERON:0004247 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 UBERON:0004253 review as part of general integumentary system review - part of skin, or more generally, integumental system skin muscle UBERON:0004258 back blood vessel UBERON:0004265 outflow tract myocardium UBERON:0004267 back connective tissue UBERON:0004271 outflow tract pericardium UBERON:0004273 cartilaginous joint suture UBERON:0004277 eye muscle UBERON:0004288 skeletal skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system UBERON:0004290 dermomyotome UBERON:0004291 heart rudiment UBERON:0004292 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 UBERON:0004297 respiratory system blood vessel smooth muscle UBERON:0004341 primitive streak http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png UBERON:0004345 distinction between trophectoderm and trophoblast unclear/inconsistent in many sources trophectodermal trophectoderm UBERON:0004347 developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm limb bud UBERON:0004348 optic eminence UBERON:0004356 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 UBERON:0004357 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 UBERON:0004362 1 pharyngeal arch 1 http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png UBERON:0004363 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 UBERON:0004365 vitelline blood vessel UBERON:0004367 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 UBERON:0004370 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 UBERON:0004374 vitelline vasculature UBERON:0004375 bone of free limb or fin UBERON:0004381 skeleton of limb UBERON:0004455 neurula embryo UBERON:0004456 note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs entire sense organ system UBERON:0004461 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 UBERON:0004462 define generically to encompass both vertebrates and invertebrates musculature of body wall UBERON:0004464 musculature of thorax UBERON:0004465 musculature of neck UBERON:0004469 musculature of back UBERON:0004470 musculature of pelvic girdle UBERON:0004471 musculature of pectoral girdle UBERON:0004473 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 UBERON:0004478 currently defined by location rather than attachment musculature of larynx UBERON:0004479 currently defined by location rather than attachment musculature of trunk UBERON:0004480 currently defined by location rather than attachment musculature of limb UBERON:0004481 currently defined by location rather than attachment musculature of upper limb UBERON:0004482 currently defined by location rather than attachment musculature of lower limb UBERON:0004490 cardiac muscle tissue of atrium UBERON:0004491 cardiac muscle tissue of interatrial septum UBERON:0004492 cardiac muscle tissue of cardiac septum UBERON:0004493 Note placement of MA class based on parthood relationship cardiac muscle tissue of myocardium UBERON:0004515 smooth muscle tissue of bronchiole UBERON:0004516 smooth muscle tissue of terminal bronchiole UBERON:0004521 vasculature of muscle organ UBERON:0004522 vasculature of musculoskeletal system UBERON:0004535 we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. cardiovascular system UBERON:0004537 blood vasculature UBERON:0004538 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left kidney UBERON:0004539 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right kidney UBERON:0004548 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left eye UBERON:0004549 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right eye UBERON:0004571 systemic arterial system UBERON:0004572 arterial system UBERON:0004573 systemic artery UBERON:0004581 systemic venous system UBERON:0004582 venous system UBERON:0004590 sphincter muscle UBERON:0004638 blood vessel endothelium UBERON:0004647 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 UBERON:0004663 aorta wall UBERON:0004664 aorta tunica adventitia UBERON:0004666 interventricular septum membranous part UBERON:0004667 interventricular septum muscular part UBERON:0004681 vestibular system UBERON:0004684 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 UBERON:0004688 costo-cervical trunk http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png UBERON:0004695 arterial system smooth muscle UBERON:0004696 venous system smooth muscle UBERON:0004698 vena cava endothelium UBERON:0004699 outflow tract endothelium UBERON:0004700 arterial system endothelium UBERON:0004701 venous system endothelium UBERON:0004702 respiratory system blood vessel endothelium UBERON:0004706 TODO - check relationship to bulbus arteriosus bulbus cordis http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png UBERON:0004708 this class is the union of the classes limb, pectoral fin and pelvic fin. paired limb/fin UBERON:0004709 pelvic appendage UBERON:0004710 pectoral appendage UBERON:0004711 jugular vein http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png UBERON:0004716 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 UBERON:0004729 nematode larval stage https://github.com/obophenotype/uberon/issues/567 UBERON:0004731 We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted neuromere UBERON:0004732 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 UBERON:0004733 segmental subdivision of hindbrain UBERON:0004734 gastrula UBERON:0004737 metanephric collecting duct UBERON:0004742 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 UBERON:0004755 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 UBERON:0004756 dermal skeletal element UBERON:0004760 gland of anal canal UBERON:0004761 cartilaginous neurocranium UBERON:0004764 intramembranous bone tissue UBERON:0004765 skeletal element UBERON:0004766 here cranium = skull - mandible cranial bone UBERON:0004768 Do not manually classify under here - bones are automatically classified bone of lower jaw UBERON:0004770 articular system UBERON:0004777 respiratory system submucosa UBERON:0004778 larynx submucosa UBERON:0004779 respiratory system lamina propria UBERON:0004780 gastrointestinal system lamina propria UBERON:0004781 gallbladder lamina propria UBERON:0004782 gastrointestinal system serosa UBERON:0004783 gallbladder serosa UBERON:0004784 heart ventricle wall UBERON:0004785 TODO - split respiratory tract mucosa from respiratory system mucosa respiratory system mucosa UBERON:0004786 The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 gastrointestinal system mucosa UBERON:0004789 larynx mucous gland UBERON:0004790 See comments for 'skin mucus' skin mucous gland UBERON:0004792 secretion of endocrine pancreas UBERON:0004793 secretion of exocrine pancreas UBERON:0004794 esophagus secretion UBERON:0004795 pancreas secretion UBERON:0004797 blood vessel layer https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg UBERON:0004802 respiratory tract epithelium UBERON:0004807 respiratory system epithelium UBERON:0004808 gastrointestinal system epithelium UBERON:0004810 See https://github.com/obophenotype/uberon/issues/1305 nephron tubule epithelium UBERON:0004815 lower respiratory tract epithelium UBERON:0004816 composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0] larynx epithelium UBERON:0004817 lacrimal gland epithelium UBERON:0004819 kidney epithelium UBERON:0004820 bile duct epithelium UBERON:0004822 extrahepatic bile duct epithelium UBERON:0004823 intrahepatic bile duct epithelium UBERON:0004829 urethra skeletal muscle tissue UBERON:0004830 respiratory system skeletal muscle UBERON:0004831 Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal esophagus skeletal muscle UBERON:0004832 anal region skeletal muscle UBERON:0004833 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 UBERON:0004834 hepatic duct smooth muscle UBERON:0004848 respiratory system arterial endothelium UBERON:0004849 respiratory system venous endothelium UBERON:0004851 aorta endothelium UBERON:0004852 consider merging with 'endothelium' cardiovascular system endothelium UBERON:0004854 gastrointestinal system mesentery UBERON:0004857 skeletal muscle connective tissue UBERON:0004859 Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands eye gland UBERON:0004864 vasculature of retina UBERON:0004872 splanchnic layer of lateral plate mesoderm UBERON:0004873 TODO - check relationship to LPM splanchnopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png UBERON:0004874 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 UBERON:0004875 part_of or develops_from urogenital ridge? nephrogenic cord UBERON:0004876 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 UBERON:0004880 WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. chordamesoderm UBERON:0004883 lung mesenchyme UBERON:0004902 urogenital sinus epithelium UBERON:0004904 for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II) neuron projection bundle connecting eye with brain UBERON:0004905 articulation UBERON:0004906 ectodermal part of digestive tract UBERON:0004907 lower digestive tract UBERON:0004908 upper digestive tract UBERON:0004909 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 UBERON:0004911 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 UBERON:0004912 biliary bud http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png UBERON:0004913 hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg UBERON:0004914 duodenal papilla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png UBERON:0004915 sphincter of hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png UBERON:0004916 anal sphincter UBERON:0004917 urethral sphincter UBERON:0004921 intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. subdivision of digestive tract UBERON:0004923 organ component layer UBERON:0004924 submucosa of pharynx UBERON:0004926 submucosa of cystic duct UBERON:0004932 submucosa of sigmoid colon UBERON:0004934 submucosa of body of stomach UBERON:0004936 submucosa of pyloric antrum UBERON:0004937 submucosa of pylorus UBERON:0004938 submucosa of biliary tree UBERON:0004939 submucosa of common bile duct UBERON:0004940 submucosa of common hepatic duct UBERON:0004941 submucosa of right hepatic duct UBERON:0004942 submucosa of left hepatic duct UBERON:0004943 submucosa of urinary bladder UBERON:0004952 submucosa of bronchiole UBERON:0004980 mucosa of ureter UBERON:0004988 mucosa of cystic duct UBERON:0004993 mucosa of sigmoid colon UBERON:0004995 mucosa of body of stomach UBERON:0004997 mucosa of pyloric antrum UBERON:0004998 mucosa of pylorus UBERON:0004999 mucosa of biliary tree UBERON:0005000 mucosa of common bile duct UBERON:0005001 mucosa of common hepatic duct UBERON:0005002 mucosa of right hepatic duct UBERON:0005003 mucosa of left hepatic duct UBERON:0005004 mucosa of right ureter UBERON:0005005 mucosa of left ureter UBERON:0005006 mucosa of renal pelvis UBERON:0005014 mucosa of female urethra UBERON:0005020 mucosa of tongue UBERON:0005032 mucosa of lower lip UBERON:0005033 mucosa of gallbladder UBERON:0005039 mucosa of bronchiole UBERON:0005040 mucosa of terminal bronchiole UBERON:0005056 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 UBERON:0005057 immune organ UBERON:0005058 hemolymphoid system gland UBERON:0005061 neural groove UBERON:0005062 neural fold UBERON:0005068 neural rod UBERON:0005076 hindbrain-spinal cord boundary UBERON:0005080 metanephric ureteric bud UBERON:0005081 ureter ureteric bud UBERON:0005082 tube lumen UBERON:0005085 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 UBERON:0005090 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 UBERON:0005092 right horn of sinus venosus UBERON:0005095 class added for consistency with GO - consider merging with kidney mesenchyme. kidney rudiment UBERON:0005103 mesonephric epithelium UBERON:0005106 metanephric tubule UBERON:0005108 metanephric epithelium UBERON:0005109 metanephric smooth muscle tissue UBERON:0005110 metanephric nephron UBERON:0005113 metanephric cortex mesenchyme UBERON:0005115 metanephric cortical collecting duct UBERON:0005134 metanephric nephron epithelium UBERON:0005137 metanephric capsule UBERON:0005146 metanephric nephron tubule UBERON:0005147 metanephric renal vesicle UBERON:0005153 epithelial bud UBERON:0005156 reproductive structure UBERON:0005157 epithelial fold UBERON:0005158 parenchyma of central nervous system UBERON:0005162 multi cell part structure UBERON:0005171 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 UBERON:0005172 abdomen element UBERON:0005173 abdominal segment element UBERON:0005174 dorsal region element UBERON:0005177 trunk region element UBERON:0005178 thoracic cavity element UBERON:0005179 pelvic region element UBERON:0005181 thoracic segment organ UBERON:0005194 thoracic vein UBERON:0005204 larynx submucosa gland UBERON:0005208 right atrium valve UBERON:0005216 optic eminence surface ectoderm UBERON:0005221 liver right lobe parenchyma UBERON:0005222 liver left lobe parenchyma UBERON:0005234 optic eminence ectoderm UBERON:0005239 basal plate metencephalon UBERON:0005243 TODO - split? interventricular septum endocardium UBERON:0005248 bulbus cordis myocardium UBERON:0005249 metanephric renal pelvis UBERON:0005250 check this stomatodeum gland UBERON:0005251 yolk sac cavity UBERON:0005253 head mesenchyme UBERON:0005256 trunk mesenchyme UBERON:0005268 renal cortex artery UBERON:0005269 renal cortex vein UBERON:0005290 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 UBERON:0005291 embryonic tissue UBERON:0005292 extraembryonic tissue UBERON:0005309 pronephric nephron UBERON:0005310 pronephric nephron tubule UBERON:0005316 endocardial endothelium UBERON:0005317 pulmonary artery endothelium UBERON:0005319 mesonephric collecting duct UBERON:0005321 mesonephric smooth muscle tissue UBERON:0005322 mesonephric nephron UBERON:0005323 mesonephric mesenchyme UBERON:0005330 mesonephric nephron epithelium UBERON:0005331 mesonephric renal vesicle UBERON:0005334 oral lamina propria UBERON:0005337 outflow tract of ventricle UBERON:0005338 merge with LVOT? outflow tract aortic component UBERON:0005339 merge with RVOT? outflow tract pulmonary component UBERON:0005362 vagus X ganglion UBERON:0005388 photoreceptor array UBERON:0005389 directing or focusing light onto light receptors transparent eye structure UBERON:0005396 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 UBERON:0005398 female reproductive gland UBERON:0005409 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 UBERON:0005417 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 UBERON:0005418 Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick. hindlimb bud UBERON:0005419 at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future pectoral appendage bud UBERON:0005420 at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future pelvic appendage bud UBERON:0005421 pectoral appendage apical ectodermal ridge UBERON:0005422 pelvic appendage apical ectodermal ridge UBERON:0005423 developing anatomical structure UBERON:0005425 presumptive neural retina UBERON:0005426 lens vesicle UBERON:0005427 corneal primordium UBERON:0005428 vagal neural crest UBERON:0005432 aortic sac UBERON:0005436 common hepatic artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png UBERON:0005456 jugular foramen http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG UBERON:0005460 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left vitelline vein UBERON:0005472 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right vitelline vein UBERON:0005478 sulcus limitans of neural tube UBERON:0005486 the MA placement should be checked venous dural sinus https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.gif UBERON:0005487 vitelline vein http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png UBERON:0005491 glossopharyngeal neural crest UBERON:0005496 neural tube lateral wall UBERON:0005497 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 UBERON:0005498 primitive heart tube UBERON:0005501 rhombomere lateral wall UBERON:0005563 todo - compare ZFA and EHDAA2 representation trigeminal neural crest UBERON:0005564 this is a very broad grouping class gonad primordium UBERON:0005594 in humans this includes somites 1-4 head somite UBERON:0005597 lung primordium UBERON:0005598 trunk somite UBERON:0005602 dorsal mesogastrium UBERON:0005604 extrahepatic part of hepatic duct UBERON:0005610 iliac vein UBERON:0005613 left dorsal aorta UBERON:0005614 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 UBERON:0005616 includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries mesenteric artery UBERON:0005617 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 UBERON:0005622 right dorsal aorta UBERON:0005631 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 UBERON:0005637 pyloric region epithelium UBERON:0005638 anterior chamber epithelium UBERON:0005656 lens vesicle epithelium UBERON:0005660 2nd arch ectoderm UBERON:0005661 3rd arch ectoderm UBERON:0005662 4th arch ectoderm UBERON:0005664 2nd arch endoderm UBERON:0005665 3rd arch endoderm UBERON:0005666 4th arch endoderm UBERON:0005669 peritoneal cavity mesothelium UBERON:0005672 right lung endothelium UBERON:0005673 left lung endothelium UBERON:0005685 midgut dorsal mesentery UBERON:0005688 lens vesicle cavity UBERON:0005689 2nd arch mesenchyme UBERON:0005690 3rd arch mesenchyme UBERON:0005691 4th arch mesenchyme UBERON:0005702 optic eminence mesenchyme UBERON:0005711 foregut duodenum mesentery UBERON:0005712 midgut duodenum mesentery UBERON:0005720 hindbrain venous system UBERON:0005721 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 UBERON:0005725 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 UBERON:0005726 chemosensory system UBERON:0005728 extraembryonic mesoderm UBERON:0005729 pectoral appendage field UBERON:0005730 pelvic appendage field UBERON:0005732 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 UBERON:0005733 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 UBERON:0005734 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 UBERON:0005740 tunica intima of artery UBERON:0005742 adventitia http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg UBERON:0005744 bone foramen http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png UBERON:0005753 caudal part of nephrogenic cord UBERON:0005754 rostral part of nephrogenic cord UBERON:0005764 acellular membrane UBERON:0005769 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 UBERON:0005792 TODO - check ridge vs cord vs nephrogenic cord vs blastema nephric ridge UBERON:0005800 section of aorta UBERON:0005805 dorsal aorta http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png UBERON:0005806 portal system UBERON:0005856 developing mesenchymal condensation UBERON:0005863 cartilaginous condensation UBERON:0005865 pre-muscle condensation UBERON:0005866 pre-cartilage condensation UBERON:0005867 check develops_from mandibular prominence UBERON:0005884 hyoid arch skeleton UBERON:0005902 TODO - check occipital region UBERON:0005906 See notes for serous membrane serous sac UBERON:0005911 endo-epithelium UBERON:0005913 zone of bone organ UBERON:0005944 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 UBERON:0005946 outflow tract of atrium UBERON:0005953 outflow part of right ventricle UBERON:0005956 outflow part of left ventricle UBERON:0005965 outflow part of right atrium UBERON:0005966 outflow part of left atrium UBERON:0005983 heart layer UBERON:0005985 TODO - change relation from part_of coronary vessel UBERON:0005989 atrioventricular septum UBERON:0006002 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 UBERON:0006003 add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. integumentary adnexa UBERON:0006056 posterior surface of head UBERON:0006170 mesonephric capsule UBERON:0006207 aortico-pulmonary spiral septum http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png UBERON:0006211 buccopharyngeal membrane http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png UBERON:0006217 cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png UBERON:0006218 common atrial chamber UBERON:0006235 foregut-midgut junction UBERON:0006238 future brain UBERON:0006241 future spinal cord UBERON:0006242 gallbladder primordium UBERON:0006260 the collection consisting of the two lateral swellings and the medial swelling lingual swellings UBERON:0006264 mouth-foregut junction UBERON:0006267 TODO - check ordering; awaiting confirmation from JB notochordal plate UBERON:0006268 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 UBERON:0006283 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 UBERON:0006293 spleen primordium UBERON:0006304 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 UBERON:0006311 chamber of eyeball UBERON:0006312 ocular refraction ocular refractive media UBERON:0006314 bodily fluid UBERON:0006331 brainstem nucleus 2 UBERON:0006347 Grouping for anterior and posterior communicating artery UBERON:0006355 inferred from artery superior vesical vein UBERON:0006535 skin secretion UBERON:0006537 female reproductive gland secretion UBERON:0006538 respiratory system fluid/secretion UBERON:0006544 kidney vasculature UBERON:0006553 renal duct UBERON:0006555 excretory tube UBERON:0006562 currently this is an extremely generic class, encompassing both protostomes and deuterostomes. 2023-04-20 branchial pharyngeal pharynx UBERON:0006563 tunica media of pulmonary trunk UBERON:0006565 female urethral meatus UBERON:0006566 left ventricle myocardium UBERON:0006567 right ventricle myocardium UBERON:0006574 pectinate line http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png UBERON:0006585 vestibular organ UBERON:0006595 presumptive endoderm UBERON:0006596 presumptive blood UBERON:0006598 Consider merging with anlage presumptive structure UBERON:0006601 presumptive ectoderm UBERON:0006603 presumptive mesoderm 2 UBERON:0006606 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 UBERON:0006615 check if it is valid to group ZFA class here. venous sinus UBERON:0006660 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 UBERON:0006668 carotid canal http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png UBERON:0006675 venous valve UBERON:0006677 surface of epithelium UBERON:0006682 hypoglossal canal UBERON:0006756 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 UBERON:0006757 paired lateral lingual swelling http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png UBERON:0006761 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 UBERON:0006799 consider splitting epithelium from epithelial tissue glandular epithelium UBERON:0006815 areolar connective tissue UBERON:0006833 lumen of trachea UBERON:0006834 uterus or analog UBERON:0006846 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 UBERON:0006855 muscular coat of ureter UBERON:0006866 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 UBERON:0006876 vasculature of organ UBERON:0006877 vasculature of liver UBERON:0006904 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 UBERON:0006905 mandibular process mesenchyme UBERON:0006909 lumen of digestive tract UBERON:0006913 lip epithelium UBERON:0006914 squamous epithelium UBERON:0006915 stratified squamous epithelium UBERON:0006916 non-keratinized epithelium of tongue UBERON:0006919 tongue squamous epithelium UBERON:0006920 esophagus squamous epithelium UBERON:0006921 stomach squamous epithelium UBERON:0006924 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 UBERON:0006925 digestive system gland UBERON:0006929 glandular columnar epithelium UBERON:0006931 stomach glandular region mucosa UBERON:0006934 sensory epithelium UBERON:0006960 ovary stroma UBERON:0006965 vascular cord UBERON:0006966 coronary capillary UBERON:0006984 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 UBERON:0007005 consider FBbt:00005541 ! cardiogenic mesoderm review EHDAA2 placement cardiogenic splanchnic mesoderm UBERON:0007010 cleaving embryo UBERON:0007026 presumptive gut UBERON:0007037 mechanosensory system UBERON:0007098 mandibular neural crest UBERON:0007099 hyoid neural crest UBERON:0007100 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 UBERON:0007122 pharyngeal pouch 1 UBERON:0007123 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 UBERON:0007124 pharyngeal pouch 3 UBERON:0007134 trunk ganglion UBERON:0007135 neural keel UBERON:0007147 lumen of midgut UBERON:0007148 lumen of hindgut UBERON:0007158 lumen of anal canal UBERON:0007159 lumen of colon UBERON:0007160 inferior petrosal sinus UBERON:0007177 lamina propria of mucosa of colon UBERON:0007188 mesothelium of serous pericardium UBERON:0007196 tracheobronchial tree UBERON:0007204 brachiocephalic vasculature UBERON:0007213 mesenchyme derived from head neural crest UBERON:0007214 mesenchyme derived from trunk neural crest UBERON:0007237 relationship to Meckel's cartilage to be added 1st arch mandibular component UBERON:0007239 tunica media of artery UBERON:0007240 tunica adventitia of artery UBERON:0007241 tunica adventitia of vein UBERON:0007242 tunica intima of vein UBERON:0007243 tunica media of vein UBERON:0007245 nuclear complex of neuraxis UBERON:0007247 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 UBERON:0007267 trachea pre-cartilage rings UBERON:0007269 currently defined by location rather than attachment pectoral appendage musculature UBERON:0007270 currently defined by location rather than attachment pelvic appendage musculature UBERON:0007271 currently defined by location rather than attachment appendage musculature UBERON:0007272 pectoral appendage skeleton UBERON:0007273 pelvic appendage skeleton UBERON:0007277 TODO - unify naming conventions presumptive hindbrain UBERON:0007278 presumptive sinus venosus UBERON:0007280 presumptive endocardium UBERON:0007281 presumptive midbrain hindbrain boundary UBERON:0007282 presumptive segmental plate UBERON:0007284 consider merging presumptive neural plate UBERON:0007285 presumptive paraxial mesoderm UBERON:0007297 presumptive pronephric mesoderm UBERON:0007300 pectoral appendage blood vessel UBERON:0007301 appendage blood vessel UBERON:0007302 pectoral appendage vasculature UBERON:0007303 pharyngeal vasculature UBERON:0007304 appendage vasculature UBERON:0007324 TODO - check In mice many lobules lack islets, in contrast to other mammals including humans pancreatic lobule UBERON:0007329 this class groups together accessory (dorsal) and main (ventral) pancreatic ducts pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png UBERON:0007367 surface of tongue UBERON:0007376 this grouping class exists primarily to align with GO - see GO:0008544. outer epithelium UBERON:0007383 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 UBERON:0007389 paired limb/fin cartilage UBERON:0007390 pectoral appendage cartilage tissue UBERON:0007391 pelvic appendage cartilage tissue UBERON:0007414 this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species nucleus of midbrain tegmentum UBERON:0007473 lumen of epithelial sac UBERON:0007475 matrix-based tissue UBERON:0007499 epithelial sac UBERON:0007500 epithelial tube open at both ends UBERON:0007501 arborizing epithelial duct system UBERON:0007503 epithelial vesicle UBERON:0007521 smooth muscle sphincter UBERON:0007524 dense mesenchyme tissue UBERON:0007530 this class will be an important part of the NC reorganization migrating mesenchyme population UBERON:0007592 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 UBERON:0007601 ciliated epithelium UBERON:0007616 layer of synovial tissue UBERON:0007617 synovial cavity of joint UBERON:0007625 pigment epithelium of eye UBERON:0007635 nucleus of medulla oblongata UBERON:0007641 trigeminal nuclear complex http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png UBERON:0007645 decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx future meninx UBERON:0007647 ectomeninx 2 UBERON:0007651 anatomical junction UBERON:0007652 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 UBERON:0007684 uriniferous tubule UBERON:0007687 kidney field UBERON:0007688 anlage UBERON:0007690 relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' early pharyngeal endoderm UBERON:0007691 gustatory pore https://upload.wikimedia.org/wikipedia/commons/0/0e/Taste_bud.svg UBERON:0007719 bone of reproductive organ UBERON:0007771 epidermis gland UBERON:0007779 transudative characteristically low in protein and cellular content (unless there has been secondary concentration) transudate UBERON:0007794 secretion of serous gland UBERON:0007798 consider merging with vasculature vascular system UBERON:0007808 adipose tissue of abdominal region UBERON:0007811 craniocervical region UBERON:0007823 this encompasses non-skeletal tissue appendage girdle region UBERON:0007826 peritoneal mesentery UBERON:0007828 girdle bone/zone UBERON:0007829 pectoral girdle bone UBERON:0007830 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 UBERON:0007831 pectoral girdle skeleton http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg UBERON:0007832 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 UBERON:0007842 membrane bone UBERON:0007844 cartilage element UBERON:0007845 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 UBERON:0007846 dense regular connective tissue UBERON:0007914 bone of craniocervical region UBERON:0008001 irregular bone UBERON:0008114 joint of girdle UBERON:0008115 surface of cartilage UBERON:0008193 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 UBERON:0008196 muscle of pectoral girdle UBERON:0008203 pelvic cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg UBERON:0008229 craniocervical region musculature UBERON:0008307 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 UBERON:0008339 microvascular endothelium https://github.com/obophenotype/uberon/issues/2186 UBERON:0008342 intestinal villus of duodenum UBERON:0008346 duodenal epithelium UBERON:0008397 tracheobronchial epithelium UBERON:0008780 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 UBERON:0008814 Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing pharyngeal arch system UBERON:0008816 embryonic head UBERON:0008823 a reasoner should automatically classify all the vertebrate ontology brain classes here neural tube derived brain https://github.com/obophenotype/uberon/issues/338 UBERON:0008835 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 UBERON:0008836 liver bud UBERON:0008856 stomach muscularis externa UBERON:0008858 pyloric canal https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg UBERON:0008861 check relationship to pylorus vs antrum pyloric gastric gland http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png UBERON:0008876 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 UBERON:0008886 pulmonary vascular system UBERON:0008895 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 UBERON:0008896 post-hyoid pharyngeal arch UBERON:0008907 other AOs are not yet in sync with this classification dermal bone UBERON:0008909 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 UBERON:0008946 lung parenchyma UBERON:0008947 respiratory primordium UBERON:0008962 forelimb bone UBERON:0008987 renal parenchyma UBERON:0008989 submucosal esophageal gland http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg UBERON:0008998 vasculature of brain UBERON:0009010 periurethral tissue UBERON:0009027 vesical artery UBERON:0009029 pudendal vein UBERON:0009030 left pulmonary vein UBERON:0009032 right pulmonary vein UBERON:0009117 typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] indifferent gonad UBERON:0009125 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion petrosal placode UBERON:0009127 Epibranchial ganglia orchestrate the development of the cranial neurogenic crest epibranchial ganglion UBERON:0009129 right atrium endocardium UBERON:0009141 craniocervical region vein UBERON:0009142 consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) entire embryonic mesenchyme UBERON:0009145 pharyngeal region of foregut UBERON:0009196 indifferent external genitalia 2 UBERON:0009198 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 UBERON:0009199 facial suture UBERON:0009200 limb epidermis UBERON:0009201 pronephric duct or mesonephric duct nephric duct UBERON:0009471 dorsum of tongue UBERON:0009479 ectoderm of buccopharyngeal membrane UBERON:0009480 endoderm of buccopharyngeal membrane UBERON:0009482 associated mesenchyme of foregut-midgut junction UBERON:0009483 mesentery of foregut-midgut junction UBERON:0009494 pharyngeal arch mesenchymal region UBERON:0009497 epithelium of foregut-midgut junction UBERON:0009503 mesenchyme of hindgut UBERON:0009505 mesenchyme of trachea UBERON:0009521 anal membrane endodermal component UBERON:0009522 lateral lingual swelling epithelium UBERON:0009550 endoderm of foregut-midgut junction UBERON:0009566 intestinal submucosa UBERON:0009569 subdivision of trunk UBERON:0009570 spinal cord sulcus limitans UBERON:0009576 medulla oblongata sulcus limitans UBERON:0009577 metencephalon sulcus limitans UBERON:0009578 myelencephalon sulcus limitans UBERON:0009581 midbrain mantle layer UBERON:0009583 spinal cord mantle layer UBERON:0009584 1st arch mandibular mesenchyme UBERON:0009602 left lung associated mesenchyme UBERON:0009603 right lung associated mesenchyme UBERON:0009615 TODO - developmental relationships for lines midbrain hindbrain boundary neural plate UBERON:0009616 TODO - unify naming conventions presumptive midbrain UBERON:0009617 A major contributor to neurocranium [PMID:16313393] head paraxial mesoderm UBERON:0009618 trunk paraxial mesoderm UBERON:0009644 trachea non-cartilage connective tissue UBERON:0009651 nephron tubule basement membrane UBERON:0009652 bronchus basement membrane UBERON:0009653 trachea basement membrane UBERON:0009657 artery of lip UBERON:0009661 midbrain nucleus UBERON:0009662 hindbrain nucleus UBERON:0009664 gut mesentery https://github.com/obophenotype/uberon/issues/509 UBERON:0009669 embryonic cloacal lumen UBERON:0009670 rectal lumen UBERON:0009708 dorsal pancreas UBERON:0009709 ventral pancreas UBERON:0009712 endocardium of right ventricle UBERON:0009713 endocardium of left ventricle UBERON:0009715 stomodeal lumen UBERON:0009722 entire pharyngeal arch endoderm UBERON:0009749 limb mesenchyme UBERON:0009751 decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts cardiac mesenchyme UBERON:0009752 pancreas mesenchyme UBERON:0009758 abdominal ganglion UBERON:0009773 this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules renal tubule UBERON:0009842 acinar glandular acinus http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png UBERON:0009844 urogenital sinus lumen UBERON:0009846 embryonic cloacal epithelium UBERON:0009850 nematode larva UBERON:0009854 digestive tract diverticulum UBERON:0009856 sac UBERON:0009870 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 UBERON:0009871 see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish. nephrogenic zone UBERON:0009881 anterior lateral plate mesoderm UBERON:0009883 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 UBERON:0009885 interlobar artery https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png UBERON:0009887 interlobar vein https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png UBERON:0009889 in mouse has left ventricular identity[PMID:22855565] secondary heart field UBERON:0009891 facial mesenchyme UBERON:0009911 todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland) lobule UBERON:0009912 anatomical lobe UBERON:0009913 todo - add has_part relationships. renal lobe https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png UBERON:0009914 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 UBERON:0009916 wall of ureter UBERON:0009919 ureter smooth muscle UBERON:0009920 optic neural crest UBERON:0009953 post-embryonic organism https://github.com/obophenotype/uberon/issues/667 UBERON:0009955 Includes: trigeminal, otic, lateral line and epibranchial placodes. neurogenic placode UBERON:0009970 in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this epithelium of pancreatic duct UBERON:0009972 ureteropelvic junction UBERON:0009973 ureterovesical junction UBERON:0010000 multicellular anatomical structure UBERON:0010009 May be obsoleted. aggregate regional part of brain UBERON:0010031 6th arch mesenchyme UBERON:0010039 This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates food storage organ UBERON:0010042 1st arch mesenchyme UBERON:0010046 entire pharyngeal arch associated mesenchyme UBERON:0010047 oral gland UBERON:0010052 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 UBERON:0010056 future tongue UBERON:0010059 hypoglossal cord UBERON:0010077 TODO - coordinate with CL, add cuboidal cell cuboidal epithelium UBERON:0010081 future common hepatic duct UBERON:0010083 check development future dermis UBERON:0010091 future hindbrain meninx UBERON:0010092 future metencephalon UBERON:0010096 future myelencephalon UBERON:0010125 future superior salivatory nucleus UBERON:0010131 conducting tissue of heart UBERON:0010133 neuroendocrine gland UBERON:0010152 skin mucus UBERON:0010161 lumen of blood vessel UBERON:0010187 female urethral gland UBERON:0010188 requires review protuberance UBERON:0010189 right atrium venous valve UBERON:0010191 aortic system UBERON:0010192 genital artery UBERON:0010194 hepatic portal system UBERON:0010199 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 UBERON:0010212 check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton laryngeal apparatus UBERON:0010213 laryngeal pre-cartilage condensation UBERON:0010221 Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6? laryngeal associated mesenchyme UBERON:0010227 future cardiac atrium UBERON:0010230 See notes for camera-type eye eyeball of camera-type eye UBERON:0010252 1st arch mandibular mesenchyme from neural crest UBERON:0010254 2nd arch mesenchyme from neural crest UBERON:0010255 3rd arch mesenchyme from neural crest UBERON:0010256 4th arch mesenchyme from neural crest UBERON:0010257 6th arch mesenchyme from neural crest UBERON:0010258 mesenchyme from rhombencephalic neural crest UBERON:0010259 1st arch mesenchyme from neural crest UBERON:0010272 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 UBERON:0010273 zone of hyoid bone UBERON:0010285 midbrain basal plate UBERON:0010286 we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed midbrain neural tube UBERON:0010291 layer of sclera UBERON:0010294 scleral endothelium UBERON:0010295 substantia propria of sclera UBERON:0010299 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 UBERON:0010303 extraembryonic epithelium UBERON:0010304 non-keratinized stratified squamous epithelium UBERON:0010312 immature eye UBERON:0010313 Grouping term for query purposes neural crest-derived structure UBERON:0010314 Grouping term for query purposes structure with developmental contribution from neural crest UBERON:0010316 germ layer / neural crest UBERON:0010321 skeletal element of eye region UBERON:0010323 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 UBERON:0010328 limb bud mesenchyme UBERON:0010329 paired limb/fin bud mesenchyme UBERON:0010333 extraembryonic membrane mesenchyme UBERON:0010336 mandibular process mesenchyme from neural crest UBERON:0010337 mandibular process mesenchyme from head mesenchyme UBERON:0010339 1st arch mandibular mesenchyme from head mesenchyme UBERON:0010341 1st arch mesenchyme from head mesenchyme UBERON:0010343 2nd arch mesenchyme from head mesenchyme UBERON:0010344 3rd arch mesenchyme from head mesenchyme UBERON:0010345 4th arch mesenchyme from head mesenchyme UBERON:0010347 6th arch mesenchyme from head mesenchyme UBERON:0010359 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from neural crest UBERON:0010360 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from head mesenchyme UBERON:0010362 endoskeleton UBERON:0010363 endochondral element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern UBERON:0010364 This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO dermal skeleton UBERON:0010368 pulmonary lobule UBERON:0010371 ecto-epithelium UBERON:0010375 consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen') pancreas dorsal primordium UBERON:0010376 Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen') pancreas ventral primordium UBERON:0010377 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 UBERON:0010378 mesenchyme from splanchnopleure UBERON:0010390 lumen of urethra UBERON:0010409 ocular surface region UBERON:0010418 urethral opening UBERON:0010427 ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png UBERON:0010428 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 UBERON:0010498 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 UBERON:0010499 pseudostratified ciliated columnar epithelium UBERON:0010522 replacement element UBERON:0010523 microcirculatory vessel UBERON:0010527 cavity of bone organ UBERON:0010528 pneumatic cavity of bone UBERON:0010531 metanephros induced blastemal cells UBERON:0010532 primitive nephron UBERON:0010533 metanephros cortex UBERON:0010534 primitive mesonephric nephron UBERON:0010535 primitive metanephric nephron UBERON:0010536 nephron progenitor UBERON:0010537 mesonephric nephron progenitor UBERON:0010707 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 UBERON:0010708 pectoral complex UBERON:0010709 pelvic complex UBERON:0010712 note the distinction between this and skeleton of limb limb skeleton subdivision UBERON:0010719 girdle skeleton UBERON:0010740 bone of appendage girdle complex UBERON:0010741 considering adding pectoral and pelvic complex skeleton classes bone of pectoral complex UBERON:0010742 bone of pelvic complex UBERON:0010743 meningeal In some primitive organisms, the meningeal cluster includes only the primitive meninx meningeal cluster UBERON:0010881 limb cartilage element UBERON:0010882 limb bone pre-cartilage condensation UBERON:0010883 forelimb cartilage element UBERON:0010884 forelimb bone pre-cartilage condensation UBERON:0010885 hindlimb cartilage element UBERON:0010886 hindlimb pre-cartilage condensation UBERON:0010890 pelvic complex muscle UBERON:0010891 the MA class belongs here, based on its current child classes pectoral complex muscle UBERON:0010912 subdivision of skeleton UBERON:0010959 craniocervical muscle UBERON:0011004 pharyngeal arch cartilage UBERON:0011090 skeleton of right pelvic girdle UBERON:0011091 skeleton of left pelvic girdle UBERON:0011092 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right pelvic girdle region UBERON:0011093 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left pelvic girdle region UBERON:0011096 lacrimal nerve UBERON:0011107 synovial joint of pelvic girdle UBERON:0011108 synovial joint of pectoral girdle UBERON:0011120 laryngeal joint UBERON:0011134 nonsynovial joint UBERON:0011137 axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton UBERON:0011138 postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton UBERON:0011139 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. synovial limb joint UBERON:0011143 upper urinary tract UBERON:0011148 submucosal gland UBERON:0011156 facial skeleton http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg UBERON:0011158 primary subdivision of skull UBERON:0011159 primary subdivision of cranial skeletal system UBERON:0011164 neurocranium bone UBERON:0011185 gastrointestinal sphincter UBERON:0011189 lamina propria of large intestine UBERON:0011191 ophthalmic vein http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png UBERON:0011192 superior ophthalmic vein http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png UBERON:0011198 muscle layer of large intestine UBERON:0011201 muscle layer of small intestine UBERON:0011215 central nervous system cell part cluster UBERON:0011216 organ system subdivision UBERON:0011222 intra-ocular muscle UBERON:0011233 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 UBERON:0011234 fibrous membrane of synovial tendon sheath UBERON:0011249 appendicular skeletal system https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton UBERON:0011270 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 UBERON:0011272 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 UBERON:0011332 extrinsic tongue pre-muscle mass UBERON:0011362 cranial blood vasculature UBERON:0011565 lumen of gastrointestinal system UBERON:0011566 lumen of esophagus UBERON:0011574 mesonephric duct lumen UBERON:0011582 paired limb/fin skeleton UBERON:0011585 consider obsoleting, coordinate with VSAO cell condensation UBERON:0011595 jaw region http://eol.org/collections/11578 UBERON:0011596 future lower lip UBERON:0011642 oral epithelium from ectoderm UBERON:0011648 jaw muscle UBERON:0011676 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 UBERON:0011695 embryonic cardiovascular system UBERON:0011766 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 UBERON:0011767 right recurrent laryngeal nerve UBERON:0011772 lower jaw opening UBERON:0011775 vagus nerve nucleus UBERON:0011777 nucleus of spinal cord UBERON:0011779 nerve of head region UBERON:0011814 non-neurogenic ectodermal placode UBERON:0011820 atrioventricular region UBERON:0011821 irregular connective tissue UBERON:0011822 dense irregular connective tissue UBERON:0011823 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 UBERON:0011824 fibrous connective tissue UBERON:0011825 loose connective tissue UBERON:0011857 acinus of lacrimal gland UBERON:0011858 acinus of exocrine gland UBERON:0011860 collection of collagen fibrils UBERON:0011861 aorta collagen fibril UBERON:0011862 pulmonary collagen fibril UBERON:0011863 bone collagen fibril UBERON:0011864 tendon collagen fibril UBERON:0011865 corneal stroma collagen fibril UBERON:0011878 muscle layer of esophagus UBERON:0011892 anterior uvea UBERON:0011899 The Epimysium also protects muscles from friction against other muscles and bones epimysium UBERON:0011919 yolk sac blood island UBERON:0011953 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 UBERON:0011955 left hepatic vein UBERON:0011956 right hepatic vein UBERON:0011997 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 UBERON:0012054 myocoele UBERON:0012075 replacement bone UBERON:0012172 stomach primordium UBERON:0012180 head or neck skin UBERON:0012240 urethral meatus UBERON:0012254 abdominal aorta artery UBERON:0012274 columnar epithelium UBERON:0012275 meso-epithelium UBERON:0012292 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 UBERON:0012299 mucosa of urethra UBERON:0012314 embryonic facial prominence UBERON:0012320 cervical artery UBERON:0012321 deep cervical artery UBERON:0012324 transverse cervical artery UBERON:0012360 Do not manually classify under here - bones are automatically classified bone of jaw UBERON:0012361 internal anal region UBERON:0012367 muscle layer of intestine UBERON:0012375 Contains nerves, blood vessels, lymphatics and lymph nodes subserosa UBERON:0012378 muscle layer of urinary bladder UBERON:0012416 respiratory system arterial smooth muscle UBERON:0012418 respiratory system venous smooth muscle UBERON:0012423 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 UBERON:0012425 striated border microvillus layer UBERON:0012430 tunica fibrosa of eyeball UBERON:0012463 cloacal lumen UBERON:0012464 cloacal vent UBERON:0012465 includes the cloacal lumen, in species where this is present lumen of terminal part of digestive tract UBERON:0012466 extraembryonic cavity UBERON:0012467 enclosed anatomical space UBERON:0012469 external anal region UBERON:0012475 skeleton of pectoral complex UBERON:0012476 skeleton of pelvic complex UBERON:0012478 cloacal gland UBERON:0012480 cloacal mucosa UBERON:0012481 cloacal epithelium UBERON:0012482 submucosa of cloaca UBERON:0012483 serosa of cloaca UBERON:0012485 cloacal villus UBERON:0012486 muscle layer of cloaca UBERON:0012488 muscle layer of duodenum UBERON:0012489 muscle layer of colon UBERON:0012490 muscle layer of anal canal UBERON:0012504 adventitia of esophagus UBERON:0012650 gastroduodenal junction UBERON:0012651 mucosa of gastroduodenal junction UBERON:0013126 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 UBERON:0013136 vein of lip UBERON:0013140 systemic vein UBERON:0013156 1st arch mandibular endoderm UBERON:0013158 foregut-midgut junction gland UBERON:0013191 ovarian cortex UBERON:0013232 serous acinus UBERON:0013241 embryonic urethral groove UBERON:0013411 cranial cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg UBERON:0013479 lung endothelium UBERON:0013501 the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938). cloacal sphincter UBERON:0013514 space surrounding organism UBERON:0013522 subdivision of tube UBERON:0013525 stomach lumen UBERON:0013636 epithelium of intestinal villus UBERON:0013685 foramen of skull 2 UBERON:0013686 anatomical conduit space UBERON:0013694 brain endothelium UBERON:0013695 colon endothelium UBERON:0013697 exocrine pancreas epithelium UBERON:0013700 axial musculature UBERON:0013701 main body axis UBERON:0013702 body proper UBERON:0013704 notochordal canal UBERON:0013727 Distinct feature of coelocanths notochordal fluid UBERON:0013754 integumentary system layer UBERON:0013755 arterial blood UBERON:0013756 venous blood UBERON:0013757 capillary blood UBERON:0013765 digestive system element UBERON:0013768 Groupings may vary - typically pulmonary vessels and aorta and vena cavae great vessel of heart UBERON:0014387 mesenchyme derived from neural crest UBERON:0014388 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 UBERON:0014389 gustatory papilla of tongue UBERON:0014398 this class may be merged with 'respiratory system muscle'; check intercostals respiratory muscle UBERON:0014401 renal venous blood vessel UBERON:0014451 tongue taste bud UBERON:0014452 gustatory epithelium of tongue UBERON:0014454 visceral abdominal adipose tissue UBERON:0014455 subcutaneous abdominal adipose tissue UBERON:0014477 thoracic skeleton UBERON:0014703 anal membrane ectodermal component UBERON:0014705 median lingual swelling epithelium UBERON:0014706 primitive renal collecting duct system UBERON:0014716 interlobular duct UBERON:0014717 mucous acinus UBERON:0014719 intralobular duct UBERON:0014720 interlobar duct UBERON:0014776 midbrain neuromere UBERON:0014777 spinal neuromere UBERON:0014783 cloacal muscle UBERON:0014790 lingual septum UBERON:0014792 currently defined by location rather than attachment musculature of pelvic complex UBERON:0014793 currently defined by location rather than attachment musculature of pectoral complex UBERON:0014794 pectoral appendage muscle UBERON:0014795 pelvic appendage muscle UBERON:0014892 skeletal muscle organ UBERON:0014903 primordial vasculature UBERON:0014907 intersomitic vessel UBERON:0015021 forelimb endochondral element UBERON:0015022 hindlimb endochondral element UBERON:0015061 limb endochondral element UBERON:0015128 consider merging into myocardial compact layer subepicardial layer of epicardium UBERON:0015129 epicardial fat UBERON:0015152 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 UBERON:0015154 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 UBERON:0015165 multi-unit eye UBERON:0015178 somite border UBERON:0015179 somite boundary epithelium UBERON:0015203 non-connected functional system UBERON:0015204 glandular system UBERON:0015212 This class is primarily to implement taxon constraints. It may be removed in the future. lateral structure UBERON:0015228 circulatory organ UBERON:0015280 pancreas left lobe UBERON:0015281 pancreas right lobe UBERON:0015329 respiratory system basement membrane UBERON:0015410 heart plus pericardium UBERON:0015418 urethra mesenchymal layer UBERON:0015420 ureteral valve UBERON:0015480 proper hepatic artery UBERON:0015481 left hepatic artery UBERON:0015482 right hepatic artery UBERON:0015485 choledocho-duodenal junction UBERON:0015716 anal canal epithelium UBERON:0015783 smooth muscle layer in fatty layer of subcutaneous tissue UBERON:0015796 liver blood vessel UBERON:0015808 eye epithelium UBERON:0015833 foregut epithelium UBERON:0015834 duodenum lamina propria UBERON:0016405 pulmonary capillary UBERON:0016478 liver stroma UBERON:0016490 auditory system UBERON:0016509 cavity of right ventricle UBERON:0016512 lumen of duodenum UBERON:0016513 cavity of left atrium UBERON:0016514 cavity of left ventricle UBERON:0016520 epithelium of female urethra UBERON:0016522 cavity of right atrium UBERON:0016545 pharyngeal ectoderm UBERON:0016548 central nervous system gray matter layer UBERON:0016552 phlegm UBERON:0016553 respiratory system mucus UBERON:0016566 pit UBERON:0016570 lamina of gray matter of spinal cord UBERON:0016879 future central nervous system UBERON:0016880 future nervous system UBERON:0016885 epithelium of terminal part of digestive tract UBERON:0016886 muscle tissue of terminal part of digestive tract UBERON:0016887 entire extraembryonic component UBERON:0016888 transitional anatomical structure UBERON:0017635 paired venous dural sinus UBERON:0017649 dorsal body wall UBERON:0017650 developing mesenchymal structure UBERON:0017672 abdominal viscera UBERON:0018111 muscle layer of rectum UBERON:0018112 rectum smooth muscle tissue UBERON:0018115 left renal pelvis UBERON:0018116 right renal pelvis UBERON:0018135 fibrocollagenous connective tissue UBERON:0018150 skin of lower lip UBERON:0018234 stroma of pancreas UBERON:0018239 rhombomere boundary UBERON:0018251 In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault. meningeal vein UBERON:0018252 In humans, they begin in the deep veins of the penis which issue from the corpus cavernosum penis, accompany the internal pudendal artery, and unite to form a single vessel, which ends in the internal iliac vein. They receive the veins from the urethral bulb, and the perineal and inferior hemorrhoidal veins internal pudendal vein UBERON:0018254 Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104 skeletal musculature UBERON:0018256 lacrimal vein UBERON:0018257 submucosa of digestive tract UBERON:0018260 layer of muscle tissue UBERON:0018261 responsible for gut movement, such as peristalsis muscular coat of digestive tract UBERON:0018321 foramen for glossopharyngeal nerve UBERON:0018543 see notes in inclusivity in class 'intestine' lumen of intestine UBERON:0018544 trigeminal nerve muscle UBERON:0018649 cardiac muscle tissue of ventricle UBERON:0018674 heart vasculature UBERON:0018707 bladder organ UBERON:0019042 reproductive system mucosa UBERON:0019143 intramuscular adipose tissue UBERON:0019189 carotid artery endothelium UBERON:0019190 mucous gland of lung UBERON:0019204 skin epithelium UBERON:0019206 tongue papilla epithelium UBERON:0019207 chorioretinal region UBERON:0019263 gray matter of hindbrain UBERON:0019267 gray matter of midbrain UBERON:0019304 sensory organ epithelium UBERON:0019319 exocrine gland of integumental system UBERON:0020358 See also: Wikipedia:Spinal_accessory_nucleus accessory XI nerve nucleus UBERON:0022284 in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe lacrimal gland bud UBERON:0022288 surface of eyeball UBERON:0022292 splenic arteriole UBERON:0022293 reproductive gland secretion UBERON:0022303 this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer nervous system cell part layer UBERON:0022350 visceral serous membrane UBERON:0022351 parietal serous membrane UBERON:0022361 lung field UBERON:0034705 developing neuroepithelium UBERON:0034706 proliferating neuroepithelium UBERON:0034707 differentiating neuroepithelium UBERON:0034709 hindbrain marginal layer UBERON:0034710 spinal cord ventricular layer UBERON:0034713 cranial neuron projection bundle UBERON:0034717 integumental taste bud UBERON:0034719 lip taste bud UBERON:0034720 head taste bud UBERON:0034721 pharyngeal taste bud UBERON:0034724 esophageal taste bud UBERON:0034726 trunk taste bud UBERON:0034728 autonomic nerve UBERON:0034729 sympathetic nerve UBERON:0034873 bodily gas UBERON:0034874 air in respiratory system UBERON:0034878 prechordal mesoderm UBERON:0034903 left atrium endocardium UBERON:0034905 gland lumen UBERON:0034921 multi organ part structure UBERON:0034922 cell cluster 2 UBERON:0034923 disconnected anatomical group UBERON:0034925 resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected anatomical collection UBERON:0034929 external soft tissue zone UBERON:0034932 epithelium of biliary system UBERON:0034933 layer of smooth muscle tissue UBERON:0034940 venous sinus cavity UBERON:0034944 zone of organ UBERON:0034945 excreted gas UBERON:0034946 In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum gas excreted from digestive tract UBERON:0034947 gas in respiratory system UBERON:0034969 epithelial layer of duct UBERON:0034995 jaw mesenchyme UBERON:0035037 jaw epithelium UBERON:0035039 rectal artery UBERON:0035050 excretory duct UBERON:0035118 Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat material entity in digestive tract UBERON:0035159 entire surface of organism UBERON:0035237 branch of internal carotid artery UBERON:0035398 branch of external carotid artery UBERON:0035471 posterior surface of kidney UBERON:0035539 esophageal artery UBERON:0035546 uveal vein UBERON:0035548 colic artery UBERON:0035549 vasculature of integument UBERON:0035550 superficial vein UBERON:0035551 deep vasculature UBERON:0035552 deep vein UBERON:0035553 left cardiac chamber UBERON:0035554 right cardiac chamber UBERON:0035597 profundal placode UBERON:0035639 ocular adnexa UBERON:0035642 laryngeal nerve UBERON:0035763 cavity of cardiac chamber UBERON:0035767 intrapulmonary bronchus UBERON:0035804 future mouth UBERON:0035805 muscle layer of sigmoid colon UBERON:0035809 serous cavity UBERON:0035814 pericardial fat UBERON:0035815 paracardial fat UBERON:0035818 visceral fat UBERON:0035819 abdominopelvic cavity UBERON:0035820 peritoneal sac UBERON:0035965 wall of blood vessel UBERON:0036072 respiratory primordium epithelium UBERON:0036073 respiratory primordium mesenchyme UBERON:0036146 cardiopharyngeal field UBERON:0036186 fibroelastic connective tissue UBERON:0036214 rectosigmoid junction UBERON:0036215 anatomical surface region UBERON:0036217 he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid] coelomic fluid UBERON:0036225 respiratory system gland UBERON:0036242 post-embryonic notochord UBERON:0036244 secretion of serous membrane UBERON:0036253 orifice of skull UBERON:0036264 zygomaticotemporal nerve UBERON:0036268 pelvic vein UBERON:0036285 wall of left ventricle UBERON:0036286 wall of right ventricle UBERON:0036288 anterior wall of left ventricle UBERON:0036289 anterior wall of right ventricle UBERON:0036290 myocardium of anterior wall of left ventricle UBERON:0036291 myocardium of anterior wall of right ventricle UBERON:0036294 mucosa of lip UBERON:0036295 renal pelvis/ureter UBERON:0036301 vasculature of spleen UBERON:0036302 vasculature of central nervous system plus retina UBERON:0036303 vasculature of central nervous system UBERON:0036343 wall of gallbladder UBERON:0036351 wall of brachiocephalic artery UBERON:0036352 wall of subclavian artery UBERON:0036362 wall of anal canal UBERON:0036375 wall of right ureter UBERON:0036376 wall of left ureter UBERON:0036422 wall of pulmonary artery UBERON:0036521 wall of urethra UBERON:0036553 wall of synovial tendon sheath UBERON:0036925 wall of eyeball UBERON:0037094 wall of common carotid artery UBERON:0037144 wall of heart UBERON:0037455 wall of female urethra UBERON:0039222 cystic artery UBERON:0039228 sigmoid vein UBERON:0039261 pancreatic artery UBERON:0039355 urethral artery UBERON:0039377 urethral vein UBERON:0039856 right ovarian vein UBERON:0039857 left ovarian vein UBERON:1000021 skin of face UBERON:1000024 parenchyma of spleen UBERON:1100000 digestive tract junction UBERON:2001053 future internal carotid artery UBERON:2001457 postcranial axial cartilage UBERON:2007013 preplacodal ectoderm UBERON:3000961 Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 external integument structure UBERON:3000972 head external integument structure UBERON:3000977 body external integument structure UBERON:3000981 limb external integument structure UBERON:3010200 Modified from the original AAO source vasculature of respiratory integument UBERON:4200230 surface of bone UBERON:4300226 forelimb bud mesenchyme UBERON:4300227 hindlimb bud mesenchyme UBERON:6000004 panarthropod head UBERON:6001730 insect larval head UBERON:6002639 insect larval sense organ UBERON:6007240 insect embryonic/larval sensillum UBERON:6007242 insect embryonic/larval head sensillum UBERON:6007280 insect embryonic/larval head sense organ UBERON:8000006 left side of back UBERON:8000007 right side of back UBERON:8300001 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right forelimb UBERON:8300002 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left forelimb UBERON:8300003 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right hindlimb UBERON:8300004 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left hindlimb UBERON:8400021 liver serosa UBERON:8400023 liver subserosa UBERON:8410001 small intestine venule UBERON:8410004 small intestine arteriole UBERON:8410008 venule of anorectum UBERON:8410009 arteriole of anorectum UBERON:8410015 arteriole of colon UBERON:8410024 intestinal junction UBERON:8410043 bronchus submucosal gland UBERON:8410048 venule of colon UBERON:8410050 The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum. anorectal anorectum UBERON:8410056 capillary of anorectum UBERON:8410057 capillary of colon UBERON:8410068 capillary of small intestine UBERON:8410077 airway submucosal gland UBERON:8410081 microvascular blood microvessel https://github.com/obophenotype/uberon/issues/2186 UBERON:8440015 noradrenergic cell groups UBERON:8450002 excretory system UBERON:8480000 iliac vein smooth muscle tissue UBERON:8480001 capillary of brain UBERON:8480002 thoracic aorta smooth muscle tissue UBERON:8480004 iliac vein endothelium UBERON:8480025 skin of clavicle region UBERON:8480026 skin of iliac crest region UBERON:8480029 skin of external genitalia UBERON:8600004 visceral muscle tissue UBERON:8600006 visceral striated muscle tissue owl:Nothing owl:Thing 2023-07-04 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 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 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 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 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 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 David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) innervates X continuous_with Y if and only if X and Y share a fiat boundary. 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 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 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 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 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 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 inverse of starts with Chris Mungall Allen starts 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 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 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 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 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 has member is a mereological relation between a collection and an item. SIO has member 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 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 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 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 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 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 '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 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 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 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 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 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 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 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 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 An ontology of human and animal behaviours. Neuro Behaviour Ontology GO 2023-07-04 by_means has_participant in_response_to is_about GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).