23:09:2005 14:37 cjm relationship This ontology consists of relation that are NOT YET finalized. Definitions may change without concomittant ID changes relationship This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi inheres_in This relation links qualities, functions, dispositions and other dependent continuants to their bearers. Examples: A particular shape that inheres in a lung; The redness that ineres in a Drosophila eye; Catalytic activity function inheres_in catalytic molecule. Note that inherence is a functional relation: if x inheres_in y at t and x inheres_in z at t, then y=z. We leave open the possibility of a relation multiply_inheres_in, such as between a gene sequence and the multiple chromosomes it multiply inheres in. The super-relation of both inheres_in and multiply_inheres_in would be depends_on A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation. GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm has_bearer relationship OBO_REL:0000026 bearer_of Examples: red eye bearer_of redness A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm has_inherent has_inherer relationship OBO_REL:0000027 quality_of A relation between a quality Q and an entity E. Q quality_of E iff: Q inheres_in E and Q is a quality GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm is_quality_of relationship OBO_REL:0000028 has_quality A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship OBO_REL:0000029 function_of Example: 'to blood pump' function_of 'heart' A relation between a function F and an entity E. F function_of E iff: Q inheres_in E and Q is a function GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship OBO_REL:0000030 has_function heart has_function to-pump-blood Relation between an independent continuant and a function. GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship OBO_REL:0000031 role_of Example: 'to blood pump' function_of 'heart' A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship OBO_REL:0000032 has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship OBO_REL:0000033 realizes The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. NOTE: there appears to be some consistency in usage as to whether processes or continuants realize Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm executes involves_execution_of is_realization_of has_function_part relationship OBO_REL:0000034 realized_by NOTE: there appears to be some consistency in usage as to whether processes or continuants realize Relation between a realizable and a process. Reciprocal relation of realizes GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm executed_during has_realization relationship OBO_REL:realized_as OBO_REL:0000035 has_disposition relationship disposition_of relationship has_function_realized_as_process Example: chlorenchyma cell has_function_realized_as_process GO:photosynthesis; P53 has_function_in DNA_Repair c has_function_realized_as_process some p <=> c has_function some (realized_as some p) ROC:alanr http://purl.org/obo/owl/ROC#ROC_alanr relationship OBO_REL:has_function_in URL:http://sourceforge.net/tracker/index.php?func=detail&aid=1825041&group_id=76834&atid=947684 http://sourceforge.net/tracker/index.php?func=detail&aid=1825041&group_id=76834&atid=947684 towards Examples: sensitivity towards chlorine; the PATO:concentration of a liquid with respect to some chemical entity type A relation between a relational quality and an entity type. Q towards E iff: for any qQt, q towards E at t. GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm with respect to directed to to depends_on relationship OBO_REL:0000036 has_phenotype Human has_phenotype shape-of-skull; Spider has_phenotype structure-of-web A relation between an organism and a quality or collection of qualities, such that those qualities are influenced in whole or part by the expression of genes in that organism. The qualities may inhere in (a) the organism itself, (b) parts of that organism, (c) entities derived from that organism, or (d) entities in the environment under the influence of the organism. Instance level: c has_phenotype q iff: exists t such that c has_part_or_derivative p at t and p has_quality q at t. For types: C has_phenotype Q iff: for any cCt, exists qQt such that q inheres_in c at t. Here, c has_part_or_derivative p at t means that c has_part(reflexive) p at t, or p derives_from c or some part_of c, or p arises through the actions of c GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship OBO_REL:0000037 develops_from Examples: eye develops_from eye disc; erythrocyte develops_from reticulocyte. Note that ontologies should use either derives_from or transformation_of where appropriate, but the develops_from relation can be used where one does not want to differentiate between these 2 cases A relation between two continuants, C and D. C develops_from D if C derived_from D or C transformation_of D. On the class level: C develops from D if and only if, for any x and any time t, the following holds: if x instantiates C at time t, then 1. either for some time t1, x instantiates D at t1 and t1 precedes t, and there is no time interval t2 such that x instantiates C at t2 and x instantiates D at t2 ; 2. or for some time t1 , there is some y such that y instantiates D at t1 and x derived_from y. On the instance level: x develops_from y is indistinguishable from x derives_from y GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship OBO_REL:0000038 generically_inheres_in relationship OBO_REL:multiply_inheres_in specifically_inheres_in relationship depends_on A depends_on B : all instances of A require B to exist relationship exemplifies see Neuhaus et al Substances, Qualitiies Universals A relation between an entity instance and a dependent entity type. relationship relationship lacks_part relationship connected_to relationship surrounded_by relationship surrounds relationship executed_in Relation between a function and a continuant. F executed_in C iff forall p such that p realizes F, p unfolds_in some c, where c is an instance of C throughout p GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship time_restricted_part_of get def from CARO chapter relationship arises_from from CARO chapter relationship OBO_REL:derives_from succeeds not inverse of precedes? relationship buds_from see CARO chapter relationship simultaneous_with Examples: p1 simultaneous_with p1 iff start_of(p1) = start_of2(p2) & end_of(p1) = end_of(p2) relationship exists_during Examples: c exists_during p iff exists(t) & c exists-at t & start_of(p) <= t & t <= end_of(p) during relationship starts_during Examples (continuants): neural_tube starts_during Segmentation; Examples (processes): neural_tube_development starts_during Segmentation p starts_during s iff start_of(s) <= start_of(p) & start_of(p) <= end_of(s) starts_to_exist_during relationship ends_during Examples (continuants): neural_tube ends_during Pharyngula; Examples (processes): neural_tube_development ends_during Pharyngula p ends_during s iff start_of(s) <= end_of(p) & end_of(p) <= end_of(s) relationship happens_during Examples: formation of primary germ layer happens_during gastrulation. Distinct from part_of. part_of implies happens_during p happens_during s iff start_of(s) <= start_of(p) & end_of(p) <= end_of(s) relationship begins_at_end_of we already have preceded_by - this would just appear to be immediately_preceded_by? p1 begins_at_end_of p2 iff end_of(p2) = start_of(p1) relationship ends_at_beginning_of p1 ends_at_beginning_of p2 iff end_of(p1) = start_of(p2) relationship starts_during_or_after p starts_during_or_after s iff start_of(s) <= start_of(p) starts_after_beginning_of start ZFA:* http://purl.org/obo/owl/ZFA#ZFA_* relationship ends_during_or_before p ends_before_end_of s iff end_of(p) <= end_of(s) ends_before_end_of relationship starts_earlier_than relationship ends_earlier_than relationship influences mutated gene influences morphology; anxiety influences thigmotaxis disposes_bearer_towards relationship influenced_by relationship gives_rise_to stronger version of influences? relationship occurs_with merge with OBO_REL:influences? relationship acts_on DEPRECATED Examples: Organismal growth acts_on organism; neuron migration acts_on neuron; A relation between a process and a continuant, where the continuant plays the role of the entity that is changed by that process. Instance: p acts_on c: exists Quality q, Time t and q inheres_in c at t, such that the continual unfolding of p results_in changes in q or maintenance of q; Type: all pP, exists cCt such that p acts_on c unfolds_towards has_direct_participant relationship has_central_participant DEPRECATED may be deprecated in favour of acts_on relationship acts_on_population_of This is a class-level relation only. If P acts_on_population_of C, then: for all instances p of P, there exists some cp, t such that c instantiates CP at t, p has_central_participant cp, and CP is equivalent to population_of(C). For example: T-cell_proliferation acts_on_population_of T-cell - for all instances of T-cell_proliferation have a population of T-cells as central_participants relationship has_result DEPRECATED p has_result c iff exists c' such that c derives_form c', c' exists at end of p, c' does not exist at beginning of p, c' participates_in p. Type: P has_result C iff for all pP, exists c such that p has_result c acts_towards relationship has_output_participant relationship has_input_participant relationship has_passive_participant relationship has_specific_outcome relationship has_enabler consider: OBO_REL:has_enabler p has_enabler c iff c is required for the unfolding of p, and c is not consumed by p. Type: P has_enabler C iff for all pP, exists c such that p has_enabler c has_catalyst relationship OBOL:has_enabler http://purl.org/obo/owl/OBOL#OBOL_has_enabler specified_by Organism parts and organismal development is specified_by genetic information; Instance level, between C/P and DC: x edf y iff x specified_by gx and gx transmitted_from gy and gy specifies y encoded_by relationship specifies Hox genetic information species Development Instance level: x edf y iff x specified_by gx and gx transmitted_from gy and gy specifies y derived_from evolved_from relationship specifies Hox genetic information species Development Instance level: x edf y iff x specified_by gx and gx transmitted_from gy and gy specifies y derived_from evolved_from relationship direct_copy_of copies may be perfect, partial, incomplete, erroneous. Examples: the relation between two strands of DNA, post-mitosis; or between strand1 and strand2+strand3 post-meiosis. Counterexamples: A human hand and the hand of a direct progenitor (it is the physical specification of the hand that is copied - unless we are Lamarkia x dco y iff facsimile_of relationship ancestral_copy_of x aco y iff x dco y OR x aco z and z aco y relationship evolutionarily_derived_from Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y derived_from descended_from evolved_from relationship variant_of relationship contains_variant_of merge with variant_of? relationship homologous_to relationship valid_for_taxon Examples: sucking behavior valid_for Mammalia (and trivially valid for Metazoa, Eukaryota). Counter-examples: GO:0031987 locomotion during locomotory behavior is not valid for Viridiplantae, because there are species of green plants that never locomote during locomotory behavior U valid_for_taxon T: for ALL species in taxon T, U is a feature found in SOME organism of that species. up-propagates in U hierachy. down-propagates in T hierarchy (species taxonomy) ROC:Waclaw http://purl.org/obo/owl/ROC#ROC_Waclaw relationship only_in_taxon down-propagates. The original name for this in the paper is 'specific_to'. GO:0001967 suckling behavior is specific to the taxon Mammalia, because no organisms other than mammals suckle (we believe). (The term is also trivially specific to the taxon Metazoa, because no organisms other than animals suckle.) Likewise, GO:0048046 apoplast is specific to Viridiplantae, because only plant cells have apoplasts (as far as we know). On the other hand, the term GO:0042711 maternal behavior is not specific to the taxon Mammalia, because many animals other than mammals demonstrate maternal behavior. Likewise, GO:0005576 extracellular region (of which apoplast is a child term) is not specific to Viridiplantae, because many organisms other than green plants have extracellular regions within their bodies. U only_in T: U is a feature found in only in organisms of species of taxon T. the feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon ROC:Waclaw http://purl.org/obo/owl/ROC#ROC_Waclaw specific_to specific_to_taxon never_outside_taxon relationship applicable_to_taxon GO:0035188 hatching is relevant for the taxon Mammalia, because there are mammals that hatch - Monotremes (Monotremata, an order-ranked taxon under Mammalia) lay eggs, and presumably hatch as well. Hatching is neither valid for nor specific to Mammalia U relevant_for_taxon T: U is found in SOME organisms for SOME species in taxon T. up-propagates in U, up-propagates in T hierarchy ROC:Waclaw http://purl.org/obo/owl/ROC#ROC_Waclaw applicable_to relevant_for_taxon weakly_valid_for_taxon relationship has_output Examples: secretory cells. Should this be has_function (export of ...) C has_output C' GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship regulated_by relationship regulates A relation between a process and a process or quality. A regulates B if the unfolding of A affects the frequency, rate or extent of B. A is called the regulating process, B the regulates process relationship positively_regulates A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process relationship negatively_regulates A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process relationship regulates_timing_of relationship negatively_regulates_timing_of unassigned_relation positively_regulates_timing_of unassigned_relation regulates_levels_of needs to be defined. Used in 15 xp defs unassigned_relation regulates_population_size_of needs to be defined. Used in 7 xp defs unassigned_relation happens_in_response_to Example: negative chemotaxis in response to octanol (see WBph) relationship dependent_on needs to be defined. Used in 10 xp defs unassigned_relation depends_on needs to be defined. Used in 1 xp defs unassigned_relation has_input needs to be defined. Used in 9 xp defs unassigned_relation increases_population_size_of needs to be defined. Used in 10 xp defs unassigned_relation mediated_by needs to be defined. Used in 78 xp defs unassigned_relation occurs_in DEPRECATED consider: OBO_REL:unfolds_in unassigned_relation results_in_acquisition_of_features_of Example: Sertoli cell differentiation : The process whereby a relatively unspecialized cell acquires specialized structural and/or functional features of a Sertoli cell P results_in_acquisition_of_features_of C : P is_a process in which a participant acquires the qualities of a C. Formally: forall pP exists C' such that C transformation_of C', exists c such that c instantiates C' at start-of P and c instantiates C' at end-of P GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_binding_of needs to be defined. Used in 1 xp defs consider: OBO_REL:results_in_connection_of unassigned_relation results_in_breakdown_of unassigned_relation results_in_change_to TODO: define in terms of transformation_of results_in_transformation_of unassigned_relation results_in_transformation_to TODO: define in terms of transformation_of unassigned_relation results_in_creation_of DEPRECATED consider: OBO_REL:results_in_formation_of relationship results_in_creation_or_release_of needs to be defined. Used in 20 xp defs unassigned_relation results_in_commitment_to Example: eye photoreceptor cell fate commitment : The process whereby the developmental fate of a cell becomes restricted such that it will develop into an eye photoreceptor cell. A photoreceptor cell is a cell that responds to incident electromagnetic radiation. Different classes of photoreceptor have different spectral sensitivities and express different photosensitive pigments. NOTES: should we use specification_of instead? relationship results_in_determination_of relationship results_in_specification_of relationship results_in_removal_of Example: sperm nuclear envelope removal : Removal of the sperm nuclear envelope, allowing entry of maternal factors into the sperm nucleus relationship results_in_removal_from relationship results_in_addition_to Example: mRNA polyadenylation results_in_addition_of polyAtail to mRNA relationship results_in_addition_of Example: mRNA polyadenylation results_in_addition_of polyAtail to mRNA relationship results_in_developmental_progression_of Example: nerve maturation = a developmental maturation that results in the developmental progression of a nerve. contrast with results_in_complete_development_of. P results_in_developmental_progression_of C : any instance of P spans part of the development of some C. Formally: forall pP, p part_of some P', and P' results_in_complete_development_of C GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_complete_development_of Example: oenocyte development results_in_complete_development_of oenocyte. The process whose specific outcome is the progression of the oenocyte over time, from its formation to the mature structure. The oenocytes are large secretory cells found in clusters underlying the epidermis of larval abdominal segments. contrast with results_in_developmental_progression_of. P results_in_complete_development_of C only if a single instance of P *spans* the subprocesses formation of C through to maturation of C. each of those subprocesses results_in_developmental_progression_of C A relation between a process type P and a continuant type C, such that any instance of Pp has as outcome the progression of an instance of Cc, from the formation of c to the maturation of c GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm results_in_development_of relationship results_in_morphogenesis_of x morphogenesis: The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form. relationship results_in_structural_organization_of x structural_organization: The process that contributes to creating the structural organization of x. This process pertains to the physical shaping of a rudimentary structure. relationship results_in_biogenesis_of TODO def relationship results_in_organization_of The process that gives rise to the structural organization of an anatomical structure. This process pertains to the physical shaping of a rudimentary structure. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. [from GO:0048532] relationship results_in_formation_of Example: autophagic vacuole formation results_in_formation_of autophagic vacuole. macromolecular complex assembly results_in_formation_of a macromolecule. Note: essentially the same as biosynthesis, although in biosynthesis the assembly is via chemical reactions P results_in_formation_of C : any instance of P gives rise to a C from the parts of C. Formally: forall pP, exists some c such that c instantiates C at end-of p, and c has some parts c1, c2, ... such that the parts are connected at the end-of p and disconected at the start-of p GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm results_in_creation_of results_in_assembly_of relationship results_in_maturation_of A developmental process, independent of morphogenetic (shape) change, that is required for x to attain its fully functional state p results_in_maturation_of c : exists f such that f instantiates F, p instantiates P, c participates_in p and c lacks_function f at start_of(p) and c has_function(f) at end_of(p), and P has_function F URL:http://www.geneontology.org/GO.process.guidelines.shtml#mat http://www.geneontology.org/GO.process.guidelines.shtml#mat GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm GOC:curators http://purl.org/obo/owl/GOC#GOC_curators relationship results_in_division_of guard mother cell cytokinesis results_in_division_of guard mother cell : The stereotyped symmetric cell division by which guard mother cell give rise to stomatal guard cells. P results_in_division_of C : any instance of C (c1) divides giving rise to two continuants c2 and c3 of type C' and C''. C' derives_from C, C'' derives_from C GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm results_in_fission_of relationship UCDHSC:results_in_division_of http://purl.org/obo/owl/UCDHSC#UCDHSC_results_in_division_of results_in_fusion_of guard mother cell cytokinesis results_in_division_of guard mother cell : The stereotyped symmetric cell division by which guard mother cell give rise to stomatal guard cells. P results_in_fusion_of C : two instances of C (c1, c2) join together to become a single instance c of C' over the course of any P. C' derives_from C GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm results_in_joining_of relationship UCDHSC:results_in_division_of http://purl.org/obo/owl/UCDHSC#UCDHSC_results_in_division_of results_in_remodeling_of see: neuron remodeling, bone remodeling, tissue remodeling. This is a placeholder relation; defs that use this should be changed to state exactly what happens in the remodeling relationship results_in_increase_in elevation of cytosolic calcium ion concentration results_in_increase_in concentration of calcium ions P results_in_increase_in Q : any P has some participant cC, such that c has_quality qQ, and the magnitude of q at start_of p > magnitude of q at end of p GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_decrease_in reduction of cytosolic calcium ion concentration results_in_decrease_in concentration of calcium ions P results_in_decrease_in Q : any P has some participant cC, such that c has_quality qQ, and the magnitude of q at start_of p < magnitude of q at end of p GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_increase_in_mass_of DEPRECATED P results_in_increase_in_mass_of C : any P has some participant cC, such that c has_quality q and q instantiates PATO:mass, and the magnitude of q at start_of p < magnitude of q at end of p GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_increased_mass_of DEPRECATED relationship results_in_localization_of nuclear pore localization results_in_localization_of nuclear pore : The processes by which nuclear pores are transported to, or maintained in, a specific location. P results_in_localization_of C : **TODO** - compare and contrast with maintenance of localization, and transportation GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_movement_of Example: dendritic cell chemotaxis results_in_movement_of dendritic cell : The movement of a dendritic cell in response to an external stimulus P results_in_movement_of C : forall pP, there exists some cC such that location_of(c) at start_of(P) NOT= location_of(c) at end_of(P) GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_patterning_for needs to be defined. Used in 17 xp defs unassigned_relation results_in_secretion_of_granules_from replace with release_of/release_from using the GO term for secretory granules relationship results_in_selection_of Example: B cell selection : process dependent upon B cell antigen receptor signaling in response to self or foreign antigen through which B cells are selected for survival. Placeholder relation. Perhaps better done using a more basic genus term? relationship results_in_negative_selection_of Example: B cell selection : process dependent upon B cell antigen receptor signaling in response to self or foreign antigen through which B cells are selected for survival. Placeholder relation. Perhaps better done using a more basic genus term? relationship results_in_positive_selection_of Example: B cell selection : process dependent upon B cell antigen receptor signaling in response to self or foreign antigen through which B cells are selected for survival. Placeholder relation. Perhaps better done using a more basic genus term? relationship results_in_structural_change_to nuclear envelope disassembly results_in_structural_change_to nuclear envelope : The controlled breakdown of the nuclear envelope in the context of a normal process P results_in_structural_change_to C : forall pP, there is some instance c of C such that c has some structural quality at start_of p that changes over the course of p GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_transport_involving Directed movement to, from or across. Example: peroxisomal membrane transport - directed movement of substances to, from or across the peroxisomal membrane. Note: excludes targeting results_in_targeting_to_from_or_across relationship results_in_transport_from Example: ovarian nurse cell to oocyte transport : results_in_transport_from nurse cell. Transfer of constituents synthesized in the ovarian nurse cells to the oocyte, through the ring canals, as the egg chamber is growing. 'multi-stops' are counted as separate processes P results_in_transport_from C : forall pP, there exists some c' such that located_in C at start_of(p) and not(c' located_in C at end_of(p)) GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_transport_to Example: ovarian nurse cell to oocyte transport : results_in_transport_to oocyte. Transfer of constituents synthesized in the ovarian nurse cells to the oocyte, through the ring canals, as the egg chamber is growing. Note: a single process can only result_in_transport_to a single end location. 'multi-stops' are counted as separate processes P results_in_transport_to C : forall pP, there exists some c' such that c' located_in C at end_of(p) and not(c' located_in C at start_of(p)) GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_transport_along Example: GO:0047497 mitochondrion transport along microtubule. The transported continuant is adjacent_to the larger continuant for the duration of the process relationship results_in_transport_towards Example: GO:0006626 results_in_targeting_to relationship results_in_transport_across relationship unfolds_in Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte P unfolds_in C : the execution of P is spatially contained by C. forall pP, forall c' partipates_in p, c' located_in C at t, for some t in P GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship unfolds_around Example: chromatin silencing at centromere unfolds_around centromere : Repression of transcription of centromeric DNA by the formation of heterochromatin. P unfolds_around C : the execution of P spatially contains by C. GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_closure_of Example: neural tube closure results_in_closure_of neural tube. P results_in_closure_of C : forall pP exists cC such that a topological change occurs in c, whereby two parts of c, c1 and c2 become connected GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_release_of Example: basophil degranulation results_in_release_of secretory granule: The regulated exocytosis of secretory granules containing preformed mediators such as histamine, serotonin, and neutral proteases by a basophil. Serotonin secretion. Parturition. p results_in_release_of a : exists b, a located_in b at t1, and not(a located_in b) at t2, where start_of(p)=t1 and end_of(p)=t2 GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_release_from Example: basophil degranulation results_in_release_from basophil: The regulated exocytosis of secretory granules containing preformed mediators such as histamine, serotonin, and neutral proteases by a basophil p results_in_release_from b : exists a, a located_in b at t1, and not(a located_in b) at t2, where start_of(p)=t1 and end_of(p)=t2 GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship results_in_transport_of DEPRECATE? consider: OBO_REL:results_in_movement_of unassigned_relation results_in_death_of relationship results_in_attachment_of DEPRECATED consider: OBO_REL:results_in_connection_of relationship results_in_adhesion_to DEPRECATED consider: OBO_REL:results_in_connection_of relationship results_in_connection_of cell-matrix adhesion results_in_connection_of a cell AND results_in_connection_of a matrix. Note that it would be more convenient if we could make n-ary relations, cell-matrix adhesion results_in connection of matrix to cell; however, we must work with binary relations, so we create a single relation statement for every entity that becomes attached during the process P results_in_connection_of C1, P results_in_connection_of C2 : forall pP, at the end of p, there is some c1, c2 such that c1C1 and c2C2 and c1 connected_to c2, and c1 not connected_to c2 at the end of p GOC:cjm http://purl.org/obo/owl/GOC#GOC_cjm relationship activates relationship inactivates relationship develops_into relationship costimulates_activation_of Example: process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation. NOTES: this is a placeholder relation; GO should define the basic genus terms necessary here relationship stimulates relationship subslice_of Necessary for 'time-sliced' representations. Examples: this eye at t1 subslice_of this eye during its entire existence relationship has_aggregate_part Sourced from BIRN. Domain: bfo:ObjectAggregate relationship has_boundary Sourced from BIRN. Range: bfo:ObjectBoundary relationship has_duration Submitted by Liju Fan (OBI) The relation that holds between a process or a processual entity and the length of the temporal interval between its beginning and its end. relationship has_qualifier The requirements are for a relation between a quality and some kind of comparative modifiers. This could be seen as a reified relation; e.g. 'abnormal shape'. Currently the qualifier terms such as 'abnormal' live in PATO relationship increased_in_magnitude_compared_to a relation between two qualities. We assume a primitive magnitude function mg(q,U) => Number. q1 increased_in_magnitude_compared_to q2 at t <=> mg(q1,U) > mg(q2,U). relationship decreased_in_magnitude_compared_to relationship has_population_of relationship inheres_in_part_of relationship relationship relative_to required for defining classes such as 'ratio of root length to root shoot' relationship overlaps Two objects are connected if they share a fiat boundary relationship interacts_with relationship