Relations Ontology Module for GO Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/never_in_taxon.owl>) VersionIRI(<null>))) [Axioms: 18 Logical Axioms: 0] expand assertion to Class: ?X DisjointWith: RO_0002162 some ?Y RO:0002161 never_in_taxon true true never_in_taxon never_in_taxon 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 database_cross_reference shorthand a core relation that holds between a part and its whole part of a core relation that holds between a whole and its part has part 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. preceded by 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 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 [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 contains process a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence inheres in a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence bearer of a relation between a continuant and a process, in which the continuant is somehow involved in the process participates in a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence role of a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence has role a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity derives from a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity derives into a relation between two independent continuants, the location and the target, in which the target is entirely within the location location of contained in contains a relation between two independent continuants, the target and the location, in which the target is entirely within the location located in 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 bounding layer of A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. coincident with A relationship that holds between a process that regulates a transport process and the entity transported by that process. regulates transport of during which ends encompasses ends after immediately preceded by during which starts immediately precedes starts during happens during ends during x overlaps y if and only if there exists some z such that x has part z and z part of y overlaps true 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. only in taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. in taxon A is spatially_disjoint_from B if and only if they have no parts in common spatially disjoint from 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. 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 develops from inverse of develops from develops into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of y directly develops from inverse of directly develops from directly develops into x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y regulates x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y negatively regulates x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y positively regulates 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. capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. capable of part of true x adjacent to y if and only if x and y share a boundary. adjacent to temporally related to inverse of starts with starts x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y develops from part of x develops_in y if x is located in y whilst x is developing develops in inverse of ends with ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y has end location p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. has output x has developmental contribution from y iff x has some part z such that z develops from y has developmental contribution from inverse of has developmental contribution from developmentally contributes to 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 developmentally preceded by c involved in regulation of p if c enables 'p' and p' causally upstream of p acts upstream of c acts upstream of or within p if c is enables 'p' and p' causally upstream of or within p acts upstream of or within Inverse of developmentally preceded by developmentally succeeded by part of developmental precursor of p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). results in developmental progression of p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. results in development of results in formation of The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. results in morphogenesis of The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. results in maturation of causally upstream of, positive effect causally upstream of, negative effect Holds between p and c when p is a transportation or localization process and the outcome of this process is to regulate the location of c transports or maintains localization of q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. inheres in part of true The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity results in acquisition of features of A relationship that holds via some environmental process evolutionarily related to A mereological relationship or a topological relationship mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) developmentally related to enables functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p involved in p regulates levels of c if p regulates some amount (PATO:0000070) of c regulates levels of inverse of enables enabled by inverse of regulates regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by A relationship that holds via some process of localization related via localization to This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. has target start location This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. has target end location Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. imports Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l results in transport along Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. results in transport across results in growth of results in transport to from or in exports p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. results in commitment to p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. results in determination of inverse of has input input of inverse of has output output of formed as result of A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. results in structural organization of The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. results in specification of x spatially_coextensive_with y if and inly if x and y have the same location 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 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 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 directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q indirectly activates indirectly inhibits This relation groups causal relations between material entities and causal relations between processes causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. 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 involved in positive regulation of 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 involved in or involved in regulation of c executes activity in d if and only if c enables p and p occurs_in d enables activity in true A relationship that holds between two entities in which the processes executed by the two entities are causally connected. interacts with An interaction relationship in which the two partners are molecular entities and are executing molecular processes that are directly causally connected. molecularly interacts with Holds between molecular entities a and b when the execution of a activates or inhibits the activity of b molecularly controls helper property is symbiosis is commensalism is mutualism is parasitism 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 is ubiquitination 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 A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. causal relation between processes depends on causal relation between material entities causally influenced by interaction relation helper property molecular interaction relation helper property Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c results in movement of Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b causally influences p 'directly regulates' q if and only if p and q are processes, and p regulates q, and q directly follows from p directly regulates 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. causal relation between material entity and a process Holds between c and p if and only if c is capable of some activity a, and a regulates p. 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 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' has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. related via dependence to p 'directly positively regulates' q if and only if p and q are processes, and p positively regulates q, and q directly follows from p directly positively regulates p 'directly negatively regulates' q if and only if p and q are processes, and p negatively regulates q, and q directly follows from p directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. produces a produced_by b iff some process that occurs_in b has_output a. produced by