is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 part_of part of part of http://www.obofoundry.org/ro/#OBO_REL:part_of https://wiki.geneontology.org/Part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 has_part has part has part preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 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. BFO:0000063 precedes precedes 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 RO:0000052 characteristic_of Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 has_characteristic has characteristic has characteristic https://github.com/oborel/obo-relations/pull/284 participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 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 RO:0000079 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 RO:0000080 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 RO:0000081 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 RO:0000085 has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 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 RO:0000087 has_role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence RO:0000091 has_disposition has disposition inverse of has disposition RO:0000092 disposition_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. disposition of penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. RO:0001020 is_allergic_trigger_for is allergic trigger for A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. RO:0001021 is_autoimmune_trigger_for is autoimmune trigger for penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. RO:0001022 has_allergic_trigger has allergic trigger A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. RO:0001023 has_autoimmune_trigger has autoimmune trigger 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 RO:0002000 2D_boundary_of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary RO:0002002 has_2D_boundary has 2D boundary A relation that holds between two neurons that are electrically coupled via gap junctions. RO:0002003 electrically_synapsed_to electrically_synapsed_to RO:0002006 has_synaptic_terminal_of has synaptic terminal of 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 RO:0002007 bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of A 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. Note from NCEAS meeting: consider changing primary label RO:0002008 coincident_with Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. coincident with x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). RO:0002010 regulates in other organism regulates_in_another_organism regulates in another organism A part of relation that applies only between occurrents. RO:0002012 occurrent_part_of occurrent part 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. 2017-05-24T09:30:46Z RO:0002013 has_regulatory_component_activity 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. 2017-05-24T09:31:01Z RO:0002014 has_negative_regulatory_component_activity 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. 2017-05-24T09:31:17Z RO:0002015 has_positive_regulatory_component_activity 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 2017-05-24T09:36:08Z RO:0002016 has_necessary_component_activity A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. has necessary component activity 2017-05-24T09:44:33Z RO:0002017 has_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. 2017-05-24T09:49:21Z RO:0002018 has_component_process has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. 2017-07-19T17:30:36Z RO:0002019 has_ligand has ligand Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. 2017-07-20T17:11:08Z RO:0002020 transports transports A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. 2017-07-20T17:19:37Z RO:0002021 occurs_across occurs across 2017-09-17T13:52:24Z RO:0002022 directly_regulated_by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. 2017-09-17T13:52:38Z RO:0002023 directly_negatively_regulated_by directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. 2017-09-17T13:52:47Z RO:0002024 directly_positively_regulated_by directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. 2017-09-22T14:14:36Z RO:0002025 has_effector_activity This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. 2017-12-07T12:58:06Z RO:0002026 in_register_with in register with A relationship that holds between two images, A and B, where: A depicts X; B depicts Y; X and Y are both of type T' C is a 2 layer image consiting of layers A and B; A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. Note: A and B may be 2D or 3D. Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. David Osumi-Sutherland <= RO:0002081 before_or_simultaneous_with Primitive instance level timing relation between events before or simultaneous with x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), 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 and '=' indicates the same instance in time. David Osumi-Sutherland RO:0002082 simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with David Osumi-Sutherland RO:0002083 before t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before David Osumi-Sutherland RO:0002084 during_which_ends Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends di RO:0002085 encompasses Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses David Osumi-Sutherland RO:0002086 ends_after X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of RO:0002087 immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland RO:0002088 during_which_starts Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts David Osumi-Sutherland RO:0002089 starts_before starts before David Osumi-Sutherland ends_at_start_of meets RO:0002090 immediately_precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes David Osumi-Sutherland io RO:0002091 starts_during X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during RO:0002092 happens_during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during https://wiki.geneontology.org/Happens_during David Osumi-Sutherland o overlaps RO:0002093 ends_during X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during Relation between a neuron and a material anatomical entity that its soma is part of. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) RO:0002100 has_soma_location has soma location relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. fasciculates with (forall (?x ?y) (iff (fasciculates_with ?x ?y) (exists (?nps ?npbs) (and ("neuron ; CL_0000540" ?x) ("neuron projection bundle ; CARO_0001001" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500' " ?npbs) (part_of ?npbs ?y) (part_of ?nps ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) RO:0002101 fasciculates_with fasciculates with Relation between a neuron and some structure its axon forms (chemical) synapses in. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) RO:0002102 axon_synapses_in axon synapses in Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002103 synapsed_by synapsed by Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) RO:0002104 has_plasma_membrane_part has plasma membrane part A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002105 synapsed_via_type_Ib_bouton_to Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_Ib_bouton_to A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002106 synapsed_via_type_Is_bouton_to Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_Is_bouton_to A relation between a motor neuron and a muscle that it synapses to via a type II bouton. BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002107 synapsed_via_type_II_bouton_to Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_II_bouton_to Relation between a muscle and a motor neuron that synapses to it via a type II bouton. BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) RO:0002108 synapsed_by_via_type_II_bouton Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_II_bouton Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) RO:0002109 synapsed_by_via_type_Ib_bouton Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_Ib_bouton Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) RO:0002110 has_postsynaptic_terminal_in has postsynaptic terminal in Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) RO:0002112 synapsed_by_via_type_Is_bouton Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_Is_bouton Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) RO:0002113 has_presynaptic_terminal_in has presynaptic terminal in A relation between a motor neuron and a muscle that it synapses to via a type III bouton. BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) RO:0002114 synapsed_via_type_III_bouton_to Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) synapsed_via_type_III_bouton_to Relation between a muscle and a motor neuron that synapses to it via a type III bouton. BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) RO:0002115 synapsed_by_via_type_III_bouton Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) synapsed_by_via_type_III_bouton Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002120 synapsed_to N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) synapsed to Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) RO:0002121 dendrite_synapsed_in dendrite synapsed in A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. has synapse in <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?) RO:0002130 has_synaptic_terminal_in has synaptic terminal in 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) RO:0002131 overlaps overlaps The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. has fasciculating component (forall (?x ?y) (iff (has_fasciculating_neuron_projection ?x ?y) (exists (?nps ?npbs) (and ("neuron projection bundle ; CARO_0001001" ?x) ("neuron projection ; GO0043005" ?y) ("neuron projection segment ; CARO_0001502" ?nps) ("neuron projection bundle segment ; CARO_0001500" ?npbs) (part_of ?nps ?y) (part_of ?npbs ?x) (part_of ?nps ?npbs) (forall (?npbss) (if (and ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) (part_of ?npbss ?npbs) ) (overlaps ?nps ?npbss) )))))) RO:0002132 has_fasciculating_neuron_projection has fasciculating neuron projection 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) RO:0002150 continuous_with continuous with FMA:85972 x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom proper overlaps (forall (?x ?y) (iff (proper_overlaps ?x ?y) (and (overlaps ?x ?y) (not (part_of ?x ?y)) (not (part_of ?y ?x))))) RO:0002151 partially_overlaps partially overlaps 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) RO:0002163 spatially_disjoint_from spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 connected_to 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. RO:0002176 connects 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) RO:0002177 attached_to_part_of 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 RO:0002178 supplies 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 RO:0002179 drains drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 has_component has component A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). RO:0002200 has_phenotype has phenotype inverse of has phenotype RO:0002201 phenotype_of phenotype of 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 RO:0002202 develops_from This is the transitive form of the develops from relation develops from inverse of develops from RO:0002203 develops_into develops into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. FBbt RO:0002207 has developmental precursor directly_develops_from TODO - add child relations from DOS directly develops from A parasite that kills or sterilizes its host RO:0002208 parasitoid_of parasitoid of inverse of parasitoid of RO:0002209 has_parasitoid has parasitoid inverse of directly develops from developmental precursor of RO:0002210 directly_develops_into directly develops into p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 regulates 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) RO:0002212 negatively_regulates 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) RO:0002213 positively_regulates 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)". RO:0002215 capable_of 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 RO:0002216 capable_of_part_of 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 RO:0002219 surrounded_by 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 RO:0002220 adjacent_to adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by RO:0002221 surrounds surrounds Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 RO:0002222 temporally_related_to A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to inverse of starts with Chris Mungall Allen RO:0002223 starts starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 starts_with 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 RO:0002225 develops_from_part_of develops from part of x develops_in y if x is located in y whilst x is developing EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 develops_in develops in A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. RO:0002227 obligate_parasite_of obligate parasite of A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. RO:0002228 facultative_parasite_of facultative parasite of inverse of ends with Chris Mungall RO:0002229 ends 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 RO:0002230 ends_with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y starts with process that occurs in RO:0002231 has_start_location 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 RO:0002232 has_end_location 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 RO:0002233 has_input has input https://wiki.geneontology.org/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 RO:0002234 has_output has output https://wiki.geneontology.org/Has_output A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) RO:0002235 stem_parasite_of stem parasite of A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) RO:0002236 root_parasite_of root parasite of A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. RO:0002237 hemiparasite_of hemiparasite of X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. RO:0002238 has_component_participant has component participant A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. ExO:0000001 RO:0002240 has_exposure_receptor has exposure receptor A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. ExO:0000000 RO:0002241 has_exposure_stressor has exposure stressor A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor ExO:0000055 RO:0002242 has_exposure_route has exposure route A broad relationship between an exposure event or process and the course takes from the source to the target. http://purl.obolibrary.org/obo/ExO_0000004 RO:0002243 has_exposure_transport_path has exposure transport path Any relationship between an exposure event or process and any other entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. RO:0002244 related_via_exposure_to related via exposure to Any portion of roundup 'has active ingredient' some glyphosate A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. RO:0002248 has active substance has active pharmaceutical ingredient has_active_ingredient has active ingredient inverse of has active ingredient RO:0002249 active_ingredient_in active ingredient in In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. RO:0002252 connecting_branch_of connecting branch of inverse of connecting branch of RO:0002253 has_connecting_branch has connecting branch 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 RO:0002254 has_developmental_contribution_from has developmental contribution from inverse of has developmental contribution from RO:0002255 developmentally_contributes_to developmentally contributes to t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] RO:0002256 developmentally_induced_by developmentally induced by Inverse of developmentally induced by RO:0002257 developmentally_induces 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 RO:0002258 developmentally_preceded_by 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 c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) RO:0002260 has_biological_role has biological role c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) RO:0002261 has_application_role has application role c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) RO:0002262 has_chemical_role has chemical role 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. RO:0002263 acts_upstream_of 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. RO:0002264 affects acts_upstream_of_or_within acts upstream of or within https://wiki.geneontology.org/Acts_upstream_of_or_within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage replaces RO:0002285 developmentally_replaces developmentally replaces Inverse of developmentally preceded by RO:0002286 developmentally_succeeded_by developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue RO:0002287 part_of_developmental_precursor_of part of developmental precursor of p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity 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). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. RO:0002295 results_in_developmental_progression_of results in developmental progression of every flower development (GO:0009908) results in development of some flower (PO:0009046) 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. http://www.geneontology.org/GO.doc.development.shtml RO:0002296 results_in_development_of results in development of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) GOC:mtg_berkeley_2013 RO:0002297 results_in_formation_of_anatomical_entity results in formation of anatomical entity an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) 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. GOC:mtg_berkeley_2013 RO:0002298 results_in_morphogenesis_of results in morphogenesis of an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) 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. GOC:mtg_berkeley_2013 RO:0002299 results_in_maturation_of results in maturation of foramen ovale closure SubClassOf results in disappearance of foramen ovale May be merged into parent relation RO:0002300 results_in_disappearance_of results in disappearance of every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) May be merged into parent relation RO:0002301 results_in_developmental_regression_of results in developmental regression of Inverse of 'is substance that treats' RO:0002302 is_treated_by_substance is treated by substance Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. adapted for living in RO:0002303 has_habitat A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. has habitat 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. RO:0002304 causally_upstream_of,_positive_effect 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. RO:0002305 causally_upstream_of,_negative_effect causally upstream of, negative effect A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. 2017-06-05T17:35:04Z RO:0002309 has_exposure_stimulus has exposure stimulus Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. regulates localization of RO:0002313 transports_or_maintains_localization_of transports or maintains localization of 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 RO:0002314 characteristic_of_part_of characteristic of part of an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. 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 GOC:mtg_berkeley_2013 RO:0002315 results_in_acquisition_of_features_of results in acquisition of features of A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions RO:0002321 ecologically_related_to ecologically related to An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. adapted for RO:0002322 confers_advantage_in confers advantage in 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 RO:0002323 mereotopologically_related_to 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 RO:0002324 developmentally_related_to developmentally related to Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] RO:0002325 colocalizes_with colocalizes with ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. RO:0002326 contributes_to contributes to https://wiki.geneontology.org/Contributes_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. RO:0002327 enables enables https://wiki.geneontology.org/Enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 functionally_related_to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false RO:0002329 part_of_structure_that_is_capable_of part of structure that is capable of c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of RO:0002331 involved_in involved in https://wiki.geneontology.org/Involved_in every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c regulates levels of (process to entity) RO:0002332 regulates_levels_of regulates levels of inverse of enables RO:0002333 enabled_by enabled by enabled by https://wiki.geneontology.org/Enabled_by inverse of regulates regulated by (processual) RO:0002334 regulated_by regulated by inverse of negatively regulates RO:0002335 negatively_regulated_by negatively regulated by inverse of positively regulates RO:0002336 positively_regulated_by positively regulated by A relationship that holds via some process of localization Do not use this relation directly. It is a grouping relation. RO:0002337 related_via_localization_to 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. RO:0002338 has_target_start_location 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. RO:0002339 has_target_end_location 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. RO:0002340 imports 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 RO:0002341 results_in_transport_along 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. RO:0002342 results_in_transport_across results in transport across 'pollen tube growth' results_in growth_of some 'pollen tube' RO:0002343 results_in_growth_of results in growth of 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) RO:0002344 results_in_transport_to_from_or_in results in transport to from or in 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 end location of c is part of the region that surrounds s. RO:0002345 exports exports an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. 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. RO:0002348 results_in_commitment_to 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. RO:0002349 results_in_determination_of results in determination of 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 RO:0002350 member_of member of has member is a mereological relation between a collection and an item. SIO RO:0002351 has_member has member inverse of has input RO:0002352 input_of input of inverse of has output RO:0002353 output_of output of RO:0002354 formed_as_result_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. RO:0002355 results_in_structural_organization_of 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. RO:0002356 results_in_specification_of results in specification of p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. RO:0002357 results_in_developmental_induction_of results in developmental induction of http://neurolex.org/wiki/Property:DendriteLocation RO:0002360 has_dendrite_location has dendrite location 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) RO:0002371 attached_to 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) RO:0002372 has_muscle_origin has muscle origin We need to import uberon muscle to create a stricter domain constraint 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) RO:0002373 has_muscle_insertion has muscle insertion We need to import uberon muscle into RO to use as a stricter domain constraint 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) RO:0002375 in_branching_relationship_with in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) RO:0002376 tributary_of tributary of http://en.wikipedia.org/wiki/Tributary Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x branch of distributary channel of http://en.wikipedia.org/wiki/Distributary RO:0002377 distributary_of This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes distributary of x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. anastomoses with RO:0002378 anabranch_of anabranch of 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 RO:0002379 spatially_coextensive_with spatially coextensive with In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y RO:0002380 branching_part_of branching part of FMA:85994 In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. RO:0002381 main_stem_of main stem of x proper_distributary_of y iff x distributary_of y and x does not flow back into y RO:0002382 proper_distributary_of proper distributary of x proper_tributary_of y iff x tributary_of y and x does not originate from y RO:0002383 proper_tributary_of proper tributary of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). RO:0002384 has_developmental_potential_involving 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 RO:0002385 has_potential_to_developmentally_contribute_to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y RO:0002386 has_potential_to_developmentally_induce has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y RO:0002387 has_potential_to_develop_into 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 RO:0002388 has_potential_to_directly_develop_into has potential to directly develop into 'protein catabolic process' SubClassOf has_direct_input some protein 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. directly consumes This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' RO:0002400 has_direct_input has direct input inverse of upstream of RO:0002404 causally_downstream_of causally downstream of RO:0002405 immediately_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 RO:0002407 indirectly_positively_regulates indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits RO:0002409 indirectly_negatively_regulates indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. RO:0002410 causally_related_to causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. RO:0002411 causally_upstream_of 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. RO:0002412 immediately_causally_upstream_of immediately causally upstream of p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. directly provides input for directly provides input for (process to process) RO:0002413 provides_input_for provides input for https://wiki.geneontology.org/Provides_input_for transitive form of directly_provides_input_for This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. transitively provides input for (process to process) RO:0002414 transitively_provides_input_for transitively provides input for 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) RO:0002418 affects causally_upstream_of_or_within causally upstream of or within inverse of causally upstream of or within RO:0002427 causally_downstream_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 RO:0002428 involved_in_regulation_of involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p RO:0002429 involved_in_positive_regulation_of involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p RO:0002430 involved_in_negative_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 OWL does not allow defining object properties via a Union involved in or reguates RO:0002431 involved_in_or_involved_in_regulation_of involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. executes activity in RO:0002432 enables activity in is_active_in is active in https://wiki.geneontology.org/Is_active_in c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. 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. RO:0002433 contributes_to_morphology_of contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. RO:0002434 in pairwise interaction with interacts_with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) RO:0002435 genetically_interacts_with genetically interacts with http://purl.obolibrary.org/obo/MI_0208 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 RO:0002436 molecularly_interacts_with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. interacts with on organism level RO:0002437 biotically_interacts_with biotically interacts with http://eol.org/schema/terms/interactsWith An interaction relationship in which the partners are related via a feeding relationship. RO:0002438 trophically_interacts_with trophically interacts with A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] Baleen whale preys on krill An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members is subject of predation interaction with preys upon RO:0002439 preys_on preys on http://eol.org/schema/terms/preysUpon http://www.inaturalist.org/observations/2942824 A biotic interaction in which the two organisms live together in more or less intimate association. http://www.ncbi.nlm.nih.gov/pubmed/19278549 We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism RO:0002440 symbiotically_interacts_with symbiotically interacts with An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002441 commensually_interacts_with commensually interacts with An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). http://www.ncbi.nlm.nih.gov/pubmed/19278549 RO:0002442 mutualistically_interacts_with mutualistically interacts with An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). http://www.ncbi.nlm.nih.gov/pubmed/19278549 This relation groups a pair of inverse relations, parasite of and parasitized by RO:0002443 interacts_with_via_parasite-host_interaction interacts with via parasite-host interaction Pediculus humanus capitis parasite of human parasitizes RO:0002444 direct parasite of parasite_of parasite of http://eol.org/schema/terms/parasitizes has parasite parasitised by RO:0002445 directly parasitized by parasitized_by parasitized by http://eol.org/schema/terms/hasParasite Porifiera attaches to substrate A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. RO:0002446 semibiotically interacts with participates_in_a_abiotic-biotic_interaction_with participates in a abiotic-biotic interaction with 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. RO:0002447 phosphorylates 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. RO:0002448 molecularly controls directly_regulates_activity_of 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 RO:0002449 molecularly decreases activity of directly_negatively_regulates_activity_of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates RO:0002450 molecularly increases activity of directly_positively_regulates_activity_of directly positively regulates activity of all dengue disease transmitted by some mosquito A relationship that holds between a disease and organism Add domain and range constraints RO:0002451 transmitted_by transmitted by A relation that holds between a disease or an organism and a phenotype RO:0002452 has_symptom has symptom The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) RO:0002453 host_of host of X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y RO:0002454 has_host has host http://eol.org/schema/terms/hasHost Bees pollinate Flowers This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. is subject of pollination interaction with RO:0002455 pollinates pollinates http://eol.org/schema/terms/pollinates has polinator is target of pollination interaction with RO:0002456 pollinated_by pollinated by http://eol.org/schema/terms/hasPollinator Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. RO:0002457 acquires_nutrients_from acquires nutrients from inverse of preys on has predator is target of predation interaction with RO:0002458 preyed_upon_by preyed upon by http://eol.org/schema/terms/HasPredator http://polytraits.lifewatchgreece.eu/terms/PRED Anopheles is a vector for Plasmodium a is a vector for b if a carries and transmits an infectious pathogen b into another living organism RO:0002459 is_vector_for is vector for RO:0002460 has_vector has vector Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target RO:0002461 partner_in partner in Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002462 subject_participant_in subject participant in Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. RO:0002463 target_participant_in target participant in RO:0002469 provides_nutrients_for provides nutrients for is subject of eating interaction with RO:0002470 eats eats eaten by is target of eating interaction with RO:0002471 is_eaten_by is eaten by '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. RO:0002473 composed_primarily_of composed primarily of ABal nucleus child nucleus of ABa nucleus (in C elegans) c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. RO:0002476 child_nucleus_of child nucleus of A child nucleus relationship in which the cells are part of a hermaphroditic organism RO:0002477 child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite A child nucleus relationship in which the cells are part of a male organism RO:0002478 child_nucleus_of_in_male child nucleus of in male 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. RO:0002479 has_part_that_occurs_in has part that occurs in An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y Axiomatization to GO to be added later RO:0002480 ubiquitinates ubiquitinates See notes for inverse relation RO:0002485 receives_input_from receives input from This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. RO:0002486 sends_output_to sends output to x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships RO:0002494 transformation_of 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 RO:0002495 immediate_transformation_of immediate transformation of A relationship between a material entity and a process where the material entity has some causal role that influences the process RO:0002500 causal_agent_in_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. RO:0002501 causal_relation_between_processes causal relation between processes RO:0002502 depends_on 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. RO:0002503 towards towards 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c has intermediate product RO:0002505 has_intermediate has intermediate 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. RO:0002506 causal_relation_between_entities causal relation between entities A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future determined by (system to material entity) RO:0002507 determined_by determined by inverse of determined by determines (material entity to system) RO:0002508 determines determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. RO:0002509 determined_by_part_of determined by part of A relation that holds between two entities that have the property of being sequences or having sequences. http://www.ncbi.nlm.nih.gov/pubmed/20226267 Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. RO:0002514 sequentially_related_to sequentially related to Every UTR is adjacent to a CDS of the same transcript Two consecutive DNA residues are sequentially adjacent Two exons on a processed transcript that were previously connected by an intron are adjacent x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002515 sequentially_adjacent_to sequentially adjacent to Every CDS has as a start sequence the start codon for that transcript x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence started by http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002516 has_start_sequence has start sequence inverse of has start sequence starts http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002517 is_start_sequence_of is start sequence of Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence ended by http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002518 has_end_sequence has end sequence inverse of has end sequence ends http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002519 is_end_sequence_of is end sequence of x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. In the SO paper, this was defined as an instance-type relation http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002520 is_consecutive_sequence_of is consecutive sequence of Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering RO:0002521 is_sequentially_aligned_with is sequentially aligned with The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y RO:0002522 bounds_sequence_of bounds sequence of inverse of bounds sequence of RO:0002523 is_bound_by_sequence_of is bound by sequence of x has subsequence y iff all of the sequence parts of y are sequence parts of x contains http://www.ncbi.nlm.nih.gov/pubmed/20226267 RO:0002524 has_subsequence has subsequence inverse of has subsequence contained by RO:0002525 is_subsequence_of is subsequence of x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. RO:0002526 overlaps_sequence_of overlaps sequence of x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. disconnected from RO:0002527 does_not_overlap_sequence_of does not overlap sequence of inverse of downstream of sequence of RO:0002528 is_upstream_of_sequence_of is upstream of sequence of x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. RO:0002529 is_downstream_of_sequence_of is downstream of sequence of A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y RO:0002530 is_immediately_downstream_of_sequence_of is immediately downstream of sequence of A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript inverse of immediately downstream of RO:0002531 is_immediately_upstream_of_sequence_of is immediately upstream of sequence of 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). RO:0002551 has_skeleton has skeleton This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. RO:0002552 results_in_ending_of results in ending of x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism http://eol.org/schema/terms/hyperparasitoidOf https://en.wikipedia.org/wiki/Hyperparasite RO:0002553 hyperparasitoid of epiparasite of hyperparasite_of hyperparasite of inverse of hyperparasite of RO:0002554 has epiparasite has hyperparasite hyperparasitoidized by hyperparasitized_by hyperparasitized by http://en.wikipedia.org/wiki/Allelopathy RO:0002555 allelopath_of allelopath of http://eol.org/schema/terms/allelopathyYes x is an allelopath of y iff xis an organism produces one or more biochemicals that influence the growth, survival, and reproduction of y RO:0002556 pathogen_of pathogen of RO:0002557 has_pathogen has pathogen causally influenced by (entity-centric) RO:0002559 causally_influenced_by causally influenced by Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c RO:0002565 results_in_movement_of results in movement of 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) RO:0002566 causally_influences 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. RO:0002567 biomechanically_related_to biomechanically related to m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. Wikipedia:Antagonist_(muscle) RO:0002568 has_muscle_antagonist has muscle antagonist inverse of branching part of RO:0002569 has_branching_part has branching part x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. UBERON:cjm This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. RO:0002570 conduit_for conduit for x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. RO:0002571 lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity RO:0002572 luminal_space_of luminal space of RO:0002574 participates_in_a_biotic-biotic_interaction_with participates in a biotic-biotic interaction with inverse of has skeleton RO:0002576 skeleton_of skeleton of p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) RO:0002578 directly_regulates 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 RO:0002584 has_part_structure_that_is_capable_of has part structure that is capable of p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. RO:0002585 results_in_closure_of results in closure of p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p RO:0002586 results_in_breakdown_of results in breakdown of RO:0002587 results_in_synthesis_of results in synthesis of RO:0002588 results_in_assembly_of results in assembly of p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. RO:0002589 results_in_catabolism_of results in catabolism of RO:0002590 results_in_disassembly_of results in disassembly of RO:0002591 results_in_remodeling_of results in remodeling of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 results_in_organization_of results in organization 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. RO:0002595 causal_relation_between_material_entity_and_a_process 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. RO:0002596 capable_of_regulating capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. RO:0002597 capable_of_negatively_regulating 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. RO:0002598 capable_of_positively_regulating capable of positively regulating pazopanib -> pathological angiogenesis Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. treats The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. RO:0002599 capable_of_inhibiting_or_preventing_pathological_process capable of inhibiting or preventing pathological process treats Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship benzene -> cancer [CHEBI] Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. causes disease RO:0002600 capable_of_upregulating_or_causing_pathological_process capable of upregulating or causing pathological process c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. treats RO:0002606 is_substance_that_treats is substance that treats Inverse of 'causal agent in process' RO:0002608 process_has_causal_agent process has causal agent RO:0002618 visits visits https://github.com/oborel/obo-relations/issues/74 RO:0002619 visited_by visited by RO:0002622 visits_flowers_of visits flowers of RO:0002623 has_flowers_visited_by has flowers visited by RO:0002624 lays_eggs_in lays eggs in RO:0002625 has_eggs_laid_in_by has eggs laid in by https://github.com/jhpoelen/eol-globi-data/issues/143 RO:0002626 kills kills RO:0002627 is_killed_by is killed by p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) RO:0002629 directly_positively_regulates directly positively regulates https://wiki.geneontology.org/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) RO:0002630 directly_negatively_regulates directly negatively regulates https://wiki.geneontology.org/Directly_negatively_regulates A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host RO:0002632 ectoparasite_of ectoparasite of inverse of ectoparasite of RO:0002633 has_ectoparasite has ectoparasite A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system RO:0002634 lives inside of endoparasite_of endoparasite of RO:0002635 has_endoparasite has endoparasite A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite RO:0002636 mesoparasite_of mesoparasite of inverse of mesoparasite of RO:0002637 has_mesoparasite has mesoparasite A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. RO:0002638 intercellular_endoparasite_of intercellular endoparasite of inverse of intercellular endoparasite of RO:0002639 has_intercellular_endoparasite has intercellular endoparasite A sub-relation of endoparasite-of in which the parasite inhabits host cells. RO:0002640 intracellular_endoparasite_of intracellular endoparasite of inverse of intracellular endoparasite of RO:0002641 has_intracellular_endoparasite has intracellular endoparasite Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. RO:0002801 co-roosts_with co-roosts with An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. RO:0002802 reservoir_host_of A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. reservoir host of An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. inverse of reservoir host of RO:0002803 has_reservoir_host has reservoir host Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. RO:0003002 represses_expression_of represses expression of Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. RO:0003003 increases_expression_of increases expression of The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. RO:0003302 causes_or_contributes_to_condition Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. causes or contributes to condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. RO:0003303 causes_condition causes condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. RO:0003304 contributes_to_condition contributes to condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. contributes to expressivity of condition RO:0003305 contributes_to_severity_of_condition contributes to severity of condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. contributes to penetrance of condition RO:0003306 contributes_to_frequency_of_condition contributes to frequency of condition A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. is preventative for condition RO:0003307 ameliorates_condition Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. ameliorates condition A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. RO:0003309 exacerbates_condition exacerbates condition A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. RO:0003310 condition_ameliorated_by condition ameliorated by A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. RO:0003311 condition_exacerbated_by condition exacerbated by Do not use this relation directly. It is intended as a grouping for a more specific relations 2017-11-05T02:38:20Z RO:0004000 condition_has_genetic_basis_in condition has genetic basis in 2017-11-05T02:45:20Z RO:0004001 has_material_basis_in_gain_of_function_germline_mutation_in has material basis in gain of function germline mutation in 2017-11-05T02:45:37Z RO:0004002 has_material_basis_in_loss_of_function_germline_mutation_in has material basis in loss of function germline mutation in 2017-11-05T02:45:54Z RO:0004003 has_material_basis_in_germline_mutation_in has material basis in germline mutation in 2017-11-05T02:46:07Z RO:0004004 has_material_basis_in_somatic_mutation_in has material basis in somatic mutation in 2017-11-05T02:46:26Z RO:0004005 has_major_susceptibility_factor has major susceptibility factor 2017-11-05T02:46:57Z RO:0004006 has_partial_material_basis_in_germline_mutation_in has partial material basis in germline mutation in p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. 2018-12-13T11:26:17Z RO:0004007 has_primary_input_or_output has primary input or output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. 2018-12-13T11:26:32Z RO:0004008 has_primary_output has primary output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. GOC:dph GOC:kva GOC:pt PMID:27812932 p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. 2018-12-13T11:26:56Z RO:0004009 has_primary_input has primary input p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. GOC:dph GOC:kva GOC:pt PMID:27812932 Do not use this relation directly. It is intended as a grouping for a more specific relations 2017-11-05T02:53:08Z RO:0004010 is_genetic_basis_for_condition is genetic basis for condition Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. 2017-11-05T02:55:51Z RO:0004011 is_causal_gain_of_function_germline_mutation_of_in is causal gain of function germline mutation of in Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. 2017-11-05T02:56:06Z RO:0004012 is_causal_loss_of_function_germline_mutation_of_in is causal loss of function germline mutation of in Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. 2017-11-05T02:56:40Z RO:0004013 is_causal_germline_mutation_in is causal germline mutation in Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. 2017-11-05T02:57:07Z RO:0004014 is_causal_somatic_mutation_in is causal somatic mutation in Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. 2017-11-05T02:57:43Z RO:0004015 is_causal_susceptibility_factor_for is causal susceptibility factor for Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. 2017-11-05T02:58:43Z RO:0004016 is_causal_germline_mutation_partially_giving_rise_to is causal germline mutation partially giving rise to 2017-11-05T03:20:01Z RO:0004017 realizable_has_basis_in realizable has basis in 2017-11-05T03:20:29Z RO:0004018 is_basis_for_realizable is basis for realizable 2017-11-05T03:26:47Z RO:0004019 disease_has_basis_in disease has basis in A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. disease has basis in dysfunction of (disease to anatomical structure) 2017-11-05T03:29:32Z RO:0004020 disease_has_basis_in_dysfunction_of disease has basis in dysfunction of A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. disease has basis in disruption of (disease to process) 2017-11-05T03:37:52Z RO:0004021 disease_has_basis_in_disruption_of disease has basis in disruption of A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. 2017-11-05T03:46:07Z RO:0004022 disease_has_basis_in_feature disease has basis in feature Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. 2017-11-05T03:50:54Z RO:0004023 causal_relationship_with_disease_as_subject causal relationship with disease as subject A relationship between a disease and a process where the disease process disrupts the execution of the process. disease causes disruption of (disease to process) 2017-11-05T03:51:09Z RO:0004024 disease_causes_disruption_of disease causes disruption of disease causes dysfunction of (disease to anatomical entity) 2017-11-05T03:58:20Z RO:0004025 disease_causes_dysfunction_of disease causes dysfunction of A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. TODO: complete range axiom once more of CARO has been mireoted in to this ontology This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. 2017-11-05T04:06:02Z RO:0004026 disease_has_location disease has location A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity 2017-12-26T19:37:31Z RO:0004027 disease_has_inflammation_site disease has inflammation site A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. 2017-12-26T19:45:49Z RO:0004028 realized_in_response_to_stimulus realized in response to stimulus A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. 2017-12-26T19:50:53Z RO:0004029 disease_has_feature disease has feature A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. 2017-12-26T19:58:44Z RO:0004030 disease_arises_from_alteration_in_structure disease arises from alteration in structure Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z RO:0004031 enables_subfunction enables subfunction 2018-01-26T23:49:30Z RO:0004032 acts_upstream_of_or_within,_positive_effect acts upstream of or within, positive effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect 2018-01-26T23:49:51Z RO:0004033 acts_upstream_of_or_within,_negative_effect acts upstream of or within, negative effect https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive 2018-01-26T23:53:14Z RO:0004034 acts_upstream_of,_positive_effect acts upstream of, positive effect https://wiki.geneontology.org/Acts_upstream_of,_positive_effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative 2018-01-26T23:53:22Z RO:0004035 acts_upstream_of,_negative_effect acts upstream of, negative effect https://wiki.geneontology.org/Acts_upstream_of,_negative_effect 2018-03-13T23:55:05Z RO:0004046 causally_upstream_of_or_within,_negative_effect causally upstream of or within, negative effect https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect 2018-03-13T23:55:19Z RO:0004047 causally_upstream_of_or_within,_positive_effect causally upstream of or within, positive effect An interaction relationship wherein a plant or algae is living on the outside surface of another plant. https://en.wikipedia.org/wiki/Epiphyte RO:0008501 epiphyte_of epiphyte of inverse of epiphyte of RO:0008502 has_epiphyte has epiphyte A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material https://en.wikipedia.org/wiki/Kleptoparasitism RO:0008503 kleptoparasite_of kleptoparasite of inverse of kleptoparasite of RO:0008504 kleptoparasitized_by kleptoparasitized by An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. RO:0008505 creates_habitat_for creates habitat for An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. RO:0008506 ecologically_co-occurs_with ecologically co-occurs with An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. RO:0008507 lays_eggs_on lays eggs on inverse of lays eggs on RO:0008508 has_eggs_laid_on_by has eggs laid on by Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. 2023-01-18T14:28:21Z RO:0008509 has_roost A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. has roost A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. RO:0009501 triggered by process realized_in_response_to realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit triggered by process 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. RO:0011002 regulates_activity_of regulates activity of The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. RO:0011003 regulates_quantity_of regulates quantity of The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. RO:0011004 indirectly_regulates_activity_of indirectly regulates activity of The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. RO:0011007 decreases_by_repression_quantity_of decreases by repression quantity of The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. RO:0011008 increases_by_expression_quantity_of increases by expression quantity of The entity A has an activity that directly positively regulates the quantity of B. RO:0011009 directly_positively_regulates_quantity_of directly positively regulates quantity of The entity A has an activity that directly negatively regulates the quantity of B. RO:0011010 directly_negatively_regulates_quantity_of directly negatively regulates quantity of The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. indirectly activates RO:0011013 indirectly_positively_regulates_activity_of indirectly positively regulates activity of AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. RO:0011014 destabilizes_quantity_of destabilizes quantity of AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. RO:0011015 stabilizes_quantity_of stabilizes quantity of The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. indirectly inhibits RO:0011016 indirectly_negatively_regulates_activity_of indirectly negatively regulates activity of The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. RO:0011021 directly_regulates_quantity_of directly regulates quantity of The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. RO:0011022 indirectly_regulates_quantity_of indirectly regulates quantity of The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. RO:0011023 indirectly_negatively_regulates_quantity_of indirectly negatively regulates quantity of The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. RO:0011024 indirectly_positively_regulates_quantity_of indirectly positively regulates quantity of a relation between a process and a continuant, in which the process is regulated by the small molecule continuant 2020-04-22T20:27:26Z RO:0012000 has_small_molecule_regulator has small molecule regulator a relation between a process and a continuant, in which the process is activated by the small molecule continuant 2020-04-22T20:28:37Z RO:0012001 has_small_molecule_activator has small molecule activator a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant 2020-04-22T20:28:54Z RO:0012002 has_small_molecule_inhibitor has small molecule inhibitor p acts on population of c iff c' is a collection, has members of type c, and p has participant c 2020-06-08T17:21:33Z RO:0012003 acts_on_population_of acts on population of a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process 2020-06-24T13:15:17Z RO:0012004 is_small_molecule_regulator_of is small molecule regulator of a relation between a continuant and a process, in which the continuant is a small molecule that activates the process 2020-06-24T13:15:26Z RO:0012005 is_small_molecule_activator_of is small molecule activator of https://wiki.geneontology.org/Is_small_molecule_activator_of a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process 2020-06-24T13:15:35Z RO:0012006 is_small_molecule_inhibitor_of is small molecule inhibitor of https://wiki.geneontology.org/Is_small_molecule_inhibitor_of The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. 2020-08-27T08:13:59Z RO:0012007 results_in_adhesion_of results in adhesion of 2021-02-26T07:28:29Z RO:0012008 results_in_fusion_of results in fusion of p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. 2022-09-26T06:01:01Z RO:0012009 constitutively_upstream_of constitutively upstream of https://wiki.geneontology.org/Constitutively_upstream_of p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. 2022-09-26T06:06:20Z RO:0012010 removes_input_for removes input for https://wiki.geneontology.org/Removes_input_for 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. 2022-09-26T06:07:17Z RO:0012011 indirectly_causally_upstream_of indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. 2022-09-26T06:08:01Z RO:0012012 indirectly_regulates indirectly regulates x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). 2023-10-12T10:02:28Z RO:0012013 positively regulates in other organism positively_regulates_in_another_organism positively regulates in another organism x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). 2023-10-12T10:02:42Z RO:0012014 negatively regulates in other organism negatively_regulates_in_another_organism negatively regulates in another organism A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. 2020-07-17T09:26:52Z RO:0013001 has synaptic input or output in has_synaptic_IO_in_region has synaptic IO in region A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. 2020-07-17T09:42:23Z RO:0013002 receives_synaptic_input_in_region receives synaptic input in region A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. 2020-07-17T09:45:06Z RO:0013003 sends_synaptic_output_to_region sends synaptic output to region A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). 2020-07-17T09:52:19Z RO:0013004 has_synaptic_IO_throughout has synaptic IO throughout A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). 2020-07-17T09:55:36Z RO:0013005 receives_synaptic_input_throughout receives synaptic input throughout A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). 2020-07-17T09:57:27Z RO:0013006 sends_synaptic_output_throughout sends synaptic output throughout Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. 2020-07-20T12:10:09Z RO:0013007 has sensory dendrite location has sensory terminal in has sensory terminal location has_sensory_dendrite_in has sensory dendrite in A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. 2021-05-26T08:40:18Z RO:0013008 receives_synaptic_input_from_neuron receives synaptic input from neuron A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. 2021-05-26T08:41:07Z RO:0013009 sends_synaptic_output_to_cell Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. sends synaptic output to cell A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. RO:0014001 disease_has_infectious_agent disease has infectious agent A relation between a group and another group it is part of but does not fully constitute. X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. RO:0015003 subcluster_of subcluster of 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. RO:0015015 has_high_plasma_membrane_amount has high plasma membrane amount A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. PMID:19243617 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. RO:0015016 has_low_plasma_membrane_amount has low plasma membrane amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. PMID:19243617 Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. 2021-11-05T17:30:14Z RO:0016001 has_phenotype_or_disease has phenotype or disease https://github.com/oborel/obo-relations/issues/478 A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. 2021-11-05T17:30:44Z RO:0016002 has_disease has disease https://github.com/oborel/obo-relations/issues/478 X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. ExO:0000083 2021-12-14T20:41:45Z RO:0016004 has_exposure_medium has exposure medium A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input RO:0018002 myristoylates myristoylates inverse of myristoylates RO:0018003 myristoylated_by myristoylated by mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor RO:0018027 is_agonist_of is agonist of pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level RO:0018028 is_inverse_agonist_of is inverse agonist of tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level RO:0018029 is_antagonist_of is antagonist of 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. RO:0019000 regulates_characteristic 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. RO:0019001 positively_regulates_characteristic 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. RO:0019002 negatively_regulates_characteristic negatively regulates characteristic Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. RO:0019501 confers_susceptibility_to_condition confers susceptibility to condition brachial artery vessel supplies blood to brachialis muscle x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. 2024-02-01T10:09:22Z RO:0020101 vessel_supplies_blood_to vessel supplies blood to cystic vein vessel drains blood from gallbladder x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. 2024-02-01T10:09:41Z RO:0020102 vessel_drains_blood_from vessel drains blood from alveolar capillary directly supplies and drains some alveolus x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. 2024-02-01T10:09:59Z RO:0020103 directly_supplies_and_drains directly supplies and drains This relation groups relations between diseases and any other kind of entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. 2018-09-26T00:00:32Z RO:0040035 disease_relationship disease relationship p has anatomical participant c iff p has participant c, and c is an anatomical entity 2018-09-26T01:08:58Z RO:0040036 results_in_changes_to_anatomical_or_cellular_structure results in changes to anatomical or cellular structure