format-version: 1.2 date: 23:09:2005 14:37 saved-by: cjm idspace: snap http://www.ifomis.org/bfo/1.0/snap# "BFO SNAP ontology (continuants)" idspace: span http://www.ifomis.org/bfo/1.0/span# "BFO SPAN ontology (occurrents)" auto-generated-by: Obol default-namespace: relationship synonymtypedef: INFORMAL "Informal term to use when presenting to end-users" RELATED remark: This ontology consists of relation that are NOT YET finalized. Definitions may change without concomittant ID changes ! ++++++++++++++++++++++++++++++++++++++++ ! QUALITIES AND DEPENDENT CONTINUANTS ! ++++++++++++++++++++++++++++++++++++++++ ! in 1-01 [Typedef] id: OBO_REL:inheres_in alt_id: OBO_REL:0000026 name: inheres_in synonym: "has_bearer" EXACT [] def: "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] is_functional: true comment: 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 inverse_of: OBO_REL:bearer_of priority: 1-01 discussion: change to specifically_inheres_in discussion: name of inverse relation? discussion: can dependent continuants inhere in occurrents? discussion: is inherence a functional relation? Do we need to distinguish between specific inherence (functional) and generic/multiple inherence (non-functional) ! domain: snap:DependentContinuant [Typedef] id: OBO_REL:bearer_of alt_id: OBO_REL:0000027 name: bearer_of synonym: "has_inherent" EXACT [] synonym: "has_inherer" EXACT [] def: "A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in" [GOC:cjm] comment: Examples: red eye bearer_of redness inverse_of: OBO_REL:inheres_in ! range: snap:DependentContinuant [Typedef] id: OBO_REL:quality_of alt_id: OBO_REL:0000028 name: quality_of synonym: "is_quality_of" EXACT [] def: "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] is_a: OBO_REL:inheres_in inverse_of: OBO_REL:has_quality priority: 1-01 ! domain: snap:Quality [Typedef] id: OBO_REL:has_quality alt_id: OBO_REL:0000029 name: has_quality def: "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] is_a: OBO_REL:bearer_of discussion: can occurrents have qualities? inverse_of: OBO_REL:quality_of priority: 1-01 ! range: snap:DependentContinuant [Typedef] id: OBO_REL:function_of alt_id: OBO_REL:0000030 name: function_of def: "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] is_a: OBO_REL:inheres_in comment: Example: 'to blood pump' function_of 'heart' inverse_of: OBO_REL:has_function ! domain: snap:Function ! range: snap:IndependentContinuant [Typedef] id: OBO_REL:has_function alt_id: OBO_REL:0000031 name: has_function def: "Relation between an independent continuant and a function." [GOC:cjm] is_a: OBO_REL:bearer_of comment: heart has_function to-pump-blood inverse_of: OBO_REL:function_of ! domain: snap:IndependentContinuant ! range: snap:Function [Typedef] id: OBO_REL:role_of alt_id: OBO_REL:0000032 name: role_of def: "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] is_a: OBO_REL:inheres_in comment: Example: 'to blood pump' function_of 'heart' inverse_of: OBO_REL:has_role ! domain: snap:Role ! range: snap:IndependentContinuant [Typedef] id: OBO_REL:has_role alt_id: OBO_REL:0000033 name: has_role def: "A relation between a continuant C and a role R. The reciprocal relation of role_of." [GOC:cjm] is_a: OBO_REL:bearer_of ! domain: snap:IndependentContinuant ! range: snap:Role [Typedef] id: OBO_REL:realizes alt_id: OBO_REL:0000034 name: realizes def: "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] synonym: "executes" RELATED [] synonym: "involves_execution_of" RELATED [] synonym: "is_realization_of" EXACT [] synonym: "has_function_part" EXACT [] inverse_of: OBO_REL:realized_by ! domain: span:Process ! range: snap:Realizable comment: 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 priority: 1-01 [Typedef] id: OBO_REL:realized_by alt_id: OBO_REL:realized_as alt_id: OBO_REL:0000035 name: realized_by def: "Relation between a realizable and a process. Reciprocal relation of realizes" [GOC:cjm] synonym: "executed_during" RELATED [] synonym: "has_realization" EXACT [] inverse_of: OBO_REL:realizes ! domain: snap:Realizable ! range: span:Process comment: NOTE: there appears to be some consistency in usage as to whether processes or continuants realize priority: 1-01 [Typedef] id: OBO_REL:has_disposition name: has_disposition def: "" [] placement: BFO inverse_of: OBO_REL:disposition_of ! domain: snap:IndependentContinuant ! range: snap:DependentContinuant [Typedef] id: OBO_REL:disposition_of name: disposition_of def: "" [] placement: BFO inverse_of: OBO_REL:has_disposition ! domain: snap:DependentContinuant ! range: snap:IndependentContinuant [Typedef] id: OBO_REL:has_function_realized_as_process alt_id: OBO_REL:has_function_in name: has_function_realized_as_process def: "c has_function_realized_as_process some p <=> c has_function some (realized_as some p)" [ROC:alanr] ! domain: snap:IndependentContinuant ! range: span:Process xref: http://sourceforge.net/tracker/index.php?func=detail&aid=1825041&group_id=76834&atid=947684 comment: Example: chlorenchyma cell has_function_realized_as_process GO:photosynthesis; P53 has_function_in DNA_Repair [Typedef] id: OBO_REL:towards alt_id: OBO_REL:0000036 name: towards def: "A relation between a relational quality and an entity type. Q towards E iff: for any qQt, q towards E at t. " [GOC:cjm] synonym: "with respect to" RELATED [] synonym: "directed to" RELATED [] synonym: "to" RELATED [] synonym: "depends_on" RELATED [] status: in-use discussion: does this belong in an application ontology? In logical frameworks that support n-ary relations, this is an extra argument on the inherence relation (see Neuhaus paper, SQU). For frameworks with binary relations we need a way to indicate a linkage between the relational quality and the entity type it is directed 'towards' comment: Examples: sensitivity towards chlorine; the PATO:concentration of a liquid with respect to some chemical entity type ! domain: snap:DependentContinuant [Typedef] id: OBO_REL:has_phenotype alt_id: OBO_REL:0000037 name: has_phenotype def: "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] comment: Human has_phenotype shape-of-skull; Spider has_phenotype structure-of-web ! domain: CARO:0000003 ! anatomical structure ! range: snap:DependentContinuant [Typedef] id: OBO_REL:develops_from alt_id: OBO_REL:0000038 name: develops_from def: "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] comment: 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 is_transitive: true ! domain: snap:IndependentContinuant ! range: snap:IndependentContinuant !!! for 1-02 [Typedef] id: OBO_REL:generically_inheres_in alt_id: OBO_REL:multiply_inheres_in name: generically_inheres_in is_a: OBO_REL:inheres_in def: "" [] placement: BFO priority: 1-02 ! domain: snap:GenericallyDependentContinuant [Typedef] id: OBO_REL:specifically_inheres_in name: specifically_inheres_in is_a: OBO_REL:inheres_in def: "" [] placement: BFO priority: 1-02 is_obsolete: true replaced_by: OBO_REL:inheres_in ! domain: snap:SpecificallyDependentContinuant [Typedef] id: OBO_REL:depends_on name: depends_on def: "A depends_on B : all instances of A require B to exist" [] ! domain: snap:DependentContinuant [Typedef] id: OBO_REL:exemplifies name: exemplifies def: "A relation between an entity instance and a dependent entity type." [] comment: see Neuhaus et al Substances, Qualitiies Universals discussion: no OWL translation [Typedef] id: OBOL:towards is_obsolete: true replaced_by: OBO_REL:towards [Typedef] id: OBO_REL:lacks_part name: lacks_part def: "" [] [Typedef] id: OBO_REL:connected_to name: connected_to instance_level_is_symmetric: true def: "" [] [Typedef] id: OBO_REL:surrounded_by name: surrounded_by inverse_of: OBO_REL:surrounds !is_a: OBO_REL:part_of ! domain: snap:IndependentContinuant ! range: snap:IndependentContinuant [Typedef] id: OBO_REL:surrounds name: surrounds inverse_of: OBO_REL:surrounded_by !is_a: OBO_REL:part_of ! domain: snap:IndependentContinuant ! range: snap:IndependentContinuant [Typedef] id: OBO_REL:executed_in name: executed_in def: "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] ! ++++++++++++++++++++++++++++++++++++++++ ! TIME AND DEVELOPMENT ! ++++++++++++++++++++++++++++++++++++++++ [Typedef] id: OBO_REL:time_restricted_part_of name: time_restricted_part_of def: "" [] comment: get def from CARO chapter is_reflexive: true [Typedef] id: OBO_REL:arises_from name: arises_from alt_id: OBO_REL:derives_from transitive_over: OBO_REL:buds_from transitive_over: OBO_REL:succeeds comment: from CARO chapter [Typedef] id: OBO_REL:succeeds name: succeeds comment: not inverse of precedes? [Typedef] id: OBO_REL:buds_from name: buds_from comment: see CARO chapter ! From DavidOS and Fabian [Typedef] id: OBO_REL:simultaneous_with name: simultaneous_with def: "p1 simultaneous_with p1 iff start_of(p1) = start_of2(p2) & end_of(p1) = end_of(p2)" [] comment: Examples: [Typedef] id: OBO_REL:exists_during name: exists_during synonym: "during" EXACT [] def: "c exists_during p iff exists(t) & c exists-at t & start_of(p) <= t & t <= end_of(p)" [] comment: Examples: [Typedef] id: OBO_REL:starts_during name: starts_during synonym: "starts_to_exist_during" NARROW [] def: "p starts_during s iff start_of(s) <= start_of(p) & start_of(p) <= end_of(s)" [] comment: Examples (continuants): neural_tube starts_during Segmentation; Examples (processes): neural_tube_development starts_during Segmentation notes: Do we need separate relations for continuants and occurrents? Are there separate axioms? [Typedef] id: OBO_REL:ends_during name: ends_during def: "p ends_during s iff start_of(s) <= end_of(p) & end_of(p) <= end_of(s)" [] comment: Examples (continuants): neural_tube ends_during Pharyngula; Examples (processes): neural_tube_development ends_during Pharyngula [Typedef] id: OBO_REL:happens_during name: happens_during def: "p happens_during s iff start_of(s) <= start_of(p) & end_of(p) <= end_of(s)" [] rule: part_of(?x ?y) and process(?x) and process(?y) => happens_during(?x ?y) comment: Examples: formation of primary germ layer happens_during gastrulation. Distinct from part_of. part_of implies happens_during [Typedef] id: OBO_REL:begins_at_end_of name: begins_at_end_of def: "p1 begins_at_end_of p2 iff end_of(p2) = start_of(p1)" [] inverse_of: OBO_REL:ends_at_beginning_of comment: we already have preceded_by - this would just appear to be immediately_preceded_by? rule: begins_at_end_of => preceded_by [Typedef] id: OBO_REL:ends_at_beginning_of name: ends_at_beginning_of def: "p1 ends_at_beginning_of p2 iff end_of(p1) = start_of(p2)" [] inverse_of: OBO_REL:begins_at_end_of [Typedef] id: OBO_REL:starts_during_or_after name: starts_during_or_after synonym: "starts_after_beginning_of" EXACT [] synonym: "start" EXACT [ZFA:*] def: "p starts_during_or_after s iff start_of(s) <= start_of(p)" [] holds_over_chain: part_of * starts_during ! SubPart part_of SuperPart & SuperPart starts_during Stage => SubPart holds_over_chain: results_in_complete_development_of * starts_during_or_after ! SubPart part_of SuperPart & SuperPart starts_during Stage => SubPart rule: P results_in_formation_of C & C ends_during S => P part_of S rule: P results_in_complete_development_of C & C starts_during S => P part_of S [Typedef] id: OBO_REL:ends_during_or_before name: ends_during_or_before synonym: "ends_before_end_of" EXACT [] def: "p ends_before_end_of s iff end_of(p) <= end_of(s)" [] [Typedef] id: OBO_REL:starts_earlier_than name: starts_earlier_than def: "" [] [Typedef] id: OBO_REL:ends_earlier_than name: ends_earlier_than def: "" [] ! ++++++++++++++++++++++++++++++++++++++++ ! CAUSATION AND INFLUENCE ! ++++++++++++++++++++++++++++++++++++++++ [Typedef] id: OBO_REL:influences name: influences def: "" [] synonym: "disposes_bearer_towards" RELATED [] inverse_of: OBO_REL:influenced_by comment: mutated gene influences morphology; anxiety influences thigmotaxis rule: Gt influences P & Gt variant_of G => G influences P [Typedef] id: OBO_REL:influenced_by name: influenced_by def: "" [] inverse_of: OBO_REL:influences [Typedef] id: OBOL:gives_rise_to name: gives_rise_to comment: stronger version of influences? [Typedef] id: OBO_REL:occurs_with name: occurs_with comment: merge with OBO_REL:influences? ! ++++++++++++++++++++++++++++++++++++++++ ! FUNCTION, FUNCTIONING AND REALIZABLE ! ++++++++++++++++++++++++++++++++++++++++ ! ++++++++++++++++++++++++++++++++++++++++ ! PARTICIPATION ROLES ! ++++++++++++++++++++++++++++++++++++++++ !! these are to be deprecated [Typedef] id: OBOL:acts_on name: acts_on synonym: "unfolds_towards" RELATED [] synonym: "has_direct_participant" RELATED [] def: "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" [] comment: DEPRECATED Examples: Organismal growth acts_on organism; neuron migration acts_on neuron; [Typedef] id: OBOL:has_central_participant name: has_central_participant comment: DEPRECATED may be deprecated in favour of acts_on [Typedef] id: OBO_REL:acts_on_population_of !is_a: OBO_REL:has_participant name: acts_on_population_of def: "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" [] [Typedef] id: OBOL:has_result name: has_result synonym: "acts_towards" RELATED [] def: "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" [] comment: DEPRECATED discussion: differentiate between giving result a new entity (creation?) vs effecting change in an entity? should we reserve has_result for a P and a Q? [Typedef] id: OBOL:has_output_participant name: has_output_participant [Typedef] id: OBOL:has_input_participant name: has_input_participant [Typedef] id: OBOL:has_passive_participant name: has_passive_participant [Typedef] id: OBOL:has_specific_outcome name: has_specific_outcome [Typedef] id: OBO_REL:has_enabler name: has_enabler def: "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" [] synonym: "has_catalyst" RELATED [] !is_a: OBO_REL:has_participant comment: consider: OBO_REL:has_enabler xref: OBOL:has_enabler ! ++++++++++++++++++++++++++++++++++++++++ ! GENETIC INFORMATION ! ++++++++++++++++++++++++++++++++++++++++ [Typedef] id: OBO_REL:generically_specified_by name: specified_by def: "Instance level, between C/P and DC: x edf y iff x specified_by gx and gx transmitted_from gy and gy specifies y" [] synonym: "encoded_by" RELATED [] is_transitive: false priority: MEDIUM comment: Organism parts and organismal development is specified_by genetic information; !range: snap:DependentContinuant [Typedef] id: OBO_REL:generically_specifies name: specifies def: "Instance level: x edf y iff x specified_by gx and gx transmitted_from gy and gy specifies y" [] synonym: "derived_from" RELATED [] synonym: "evolved_from" RELATED [] is_transitive: false priority: MEDIUM comment: Hox genetic information species Development !domain: snap:DependentContinuant [Typedef] id: OBO_REL:generically_specifies name: specifies def: "Instance level: x edf y iff x specified_by gx and gx transmitted_from gy and gy specifies y" [] synonym: "derived_from" RELATED [] synonym: "evolved_from" RELATED [] is_transitive: false priority: MEDIUM comment: Hox genetic information species Development !domain: snap:DependentContinuant ! ++++++++++++++++++++++++++++++++++++++++ ! EVOLUTION & INFORMATION FLOW ! ++++++++++++++++++++++++++++++++++++++++ [Typedef] id: OBO_REL:direct_copy_of name: direct_copy_of def: "x dco y iff " [] synonym: "facsimile_of" RELATED [] comment: 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 Lamarkian!) discussion: do we also need relations for imperfect copy of etc? DNA copying involves cross-over, transposition etc is_transitive: false !domain: snap:IndependentContinuant !range: snap:IndependentContinuant [Typedef] id: OBO_REL:ancestral_copy_of name: ancestral_copy_of def: "x aco y iff x dco y OR x aco z and z aco y" [] is_transitive: true !domain: snap:IndependentContinuant !range: snap:IndependentContinuant [Typedef] id: OBO_REL:evolutionarily_derived_from name: evolutionarily_derived_from def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" [] synonym: "derived_from" RELATED [] synonym: "descended_from" RELATED [] synonym: "evolved_from" RELATED [] is_transitive: true priority: MEDIUM [Typedef] id: OBO_REL:variant_of name: variant_of !domain: snap:GenericallyDependentContinuant !range: snap:GenericallyDependentContinuant [Typedef] id: OBO_REL:contains_variant_of name: contains_variant_of comment: merge with variant_of? [Typedef] id: OBO_REL:homologous_to name: homologous_to is_metadata_tag: true is_symmetric: true ! ++++++++++++++++++++++++++++++++++++++++ ! TYPES TO SPECIES TAXONOMIES ! ++++++++++++++++++++++++++++++++++++++++ ! See Waclaw paper [Typedef] id: OBO_REL:valid_for_taxon name: valid_for_taxon def: "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] comment: 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 is_metadata: true [Typedef] id: OBO_REL:only_in_taxon name: only_in_taxon synonym: "specific_to" EXACT [] synonym: "specific_to_taxon" EXACT [] synonym: "never_outside_taxon" EXACT [] def: "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] comment: 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. is_metadata: true [Typedef] id: OBO_REL:applicable_to_taxon name: applicable_to_taxon synonym: "applicable_to" EXACT [] synonym: "relevant_for_taxon" EXACT [] synonym: "weakly_valid_for_taxon" EXACT [] def: "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] comment: 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 is_metadata: true ! ++++++++++++++++++++++++++++++++++++++++ ! SYSTEMS ! ++++++++++++++++++++++++++++++++++++++++ [Typedef] id: OBO_REL:has_output name: has_output def: "C has_output C'" [GOC:cjm] comment: Examples: secretory cells. Should this be has_function (export of ...) ! ++++++++++++++++++++++++++++++++++++++++ ! REGULATION ! ++++++++++++++++++++++++++++++++++++++++ [Typedef] id: OBO_REL:regulated_by name: regulated_by inverse_of: OBO_REL:regulates use_case: process in host regulated_by symbiont protein [Typedef] id: OBO_REL:regulates name: regulates def: "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" [] transitive_over: OBO_REL:part_of [Typedef] id: OBO_REL:positively_regulates name: positively_regulates def: "A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process" [] is_a: OBO_REL:regulates transitive_over: OBO_REL:part_of [Typedef] id: OBO_REL:negatively_regulates name: negatively_regulates def: "A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process" [] is_a: OBO_REL:regulates transitive_over: OBO_REL:part_of [Typedef] id: OBO_REL:regulates_timing_of name: regulates_timing_of [Typedef] id: OBO_REL:negatively_regulates_timing_of name: negatively_regulates_timing_of namespace: unassigned_relation [Typedef] id: OBO_REL:positively_regulates_timing_of name: positively_regulates_timing_of namespace: unassigned_relation [Typedef] id: OBO_REL:regulates_levels_of name: regulates_levels_of namespace: unassigned_relation comment: needs to be defined. Used in 15 xp defs [Typedef] id: OBO_REL:regulates_population_size_of name: regulates_population_size_of namespace: unassigned_relation comment: needs to be defined. Used in 7 xp defs [Typedef] id: OBO_REL:happens_in_response_to name: happens_in_response_to comment: Example: negative chemotaxis in response to octanol (see WBph) ! ++++++++++++++++++++++++++++++++++++++++ ! PROCESS-CONTINUANT SPECIFIC RELATIONS ! ++++++++++++++++++++++++++++++++++++++++ [Typedef] id: OBO_REL:dependent_on name: dependent_on namespace: unassigned_relation comment: needs to be defined. Used in 10 xp defs [Typedef] id: OBO_REL:depends_on name: depends_on namespace: unassigned_relation comment: needs to be defined. Used in 1 xp defs [Typedef] id: OBO_REL:has_input name: has_input namespace: unassigned_relation comment: needs to be defined. Used in 9 xp defs [Typedef] id: OBO_REL:increases_population_size_of name: increases_population_size_of namespace: unassigned_relation comment: needs to be defined. Used in 10 xp defs [Typedef] id: OBO_REL:mediated_by name: mediated_by namespace: unassigned_relation comment: needs to be defined. Used in 78 xp defs [Typedef] id: OBO_REL:occurs_in name: occurs_in namespace: unassigned_relation comment: DEPRECATED comment: consider: OBO_REL:unfolds_in [Typedef] id: OBO_REL:results_in_acquisition_of_features_of name: results_in_acquisition_of_features_of def: "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] comment: Example: Sertoli cell differentiation : The process whereby a relatively unspecialized cell acquires specialized structural and/or functional features of a Sertoli cell rule: results_in_acquisition_of_features_of(X) part_of results_in_formation_of(X) [Typedef] id: OBO_REL:results_in_binding_of name: results_in_binding_of namespace: unassigned_relation comment: needs to be defined. Used in 1 xp defs comment: consider: OBO_REL:results_in_connection_of [Typedef] id: OBO_REL:results_in_breakdown_of name: results_in_breakdown_of namespace: unassigned_relation [Typedef] id: OBO_REL:results_in_change_to name: results_in_change_to namespace: unassigned_relation synonym: "results_in_transformation_of" EXACT [] comment: TODO: define in terms of transformation_of [Typedef] id: OBO_REL:results_in_transformation_to name: results_in_transformation_to namespace: unassigned_relation comment: TODO: define in terms of transformation_of [Typedef] id: OBO_REL:results_in_creation_of name: results_in_creation_of comment: DEPRECATED comment: consider: OBO_REL:results_in_formation_of [Typedef] id: OBO_REL:results_in_creation_or_release_of name: results_in_creation_or_release_of namespace: unassigned_relation comment: needs to be defined. Used in 20 xp defs [Typedef] id: OBO_REL:results_in_commitment_to name: results_in_commitment_to comment: 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? [Typedef] id: OBO_REL:results_in_determination_of name: results_in_determination_of [Typedef] id: OBO_REL:results_in_specification_of name: results_in_specification_of [Typedef] id: OBO_REL:results_in_removal_of name: results_in_removal_of comment: Example: sperm nuclear envelope removal : Removal of the sperm nuclear envelope, allowing entry of maternal factors into the sperm nucleus [Typedef] id: OBO_REL:results_in_removal_from name: results_in_removal_from [Typedef] id: OBO_REL:results_in_addition_to name: results_in_addition_to comment: Example: mRNA polyadenylation results_in_addition_of polyAtail to mRNA [Typedef] id: OBO_REL:results_in_addition_of name: results_in_addition_of comment: Example: mRNA polyadenylation results_in_addition_of polyAtail to mRNA ! ++++++++++++++++++++++++++++++++++++++++ ! DEVELOPMENT ! ++++++++++++++++++++++++++++++++++++++++ ! super-property? [Typedef] id: OBO_REL:results_in_developmental_progression_of name: results_in_developmental_progression_of def: "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] comment: Example: nerve maturation = a developmental maturation that results in the developmental progression of a nerve. contrast with results_in_complete_development_of. holds_over_chain: OBO_REL:part_of * OBO_REL:results_in_complete_development_of ! any part of a process that results in the complete development of X necessarily results in a developmental progression of X ! x development [Typedef] id: OBO_REL:results_in_complete_development_of name: results_in_complete_development_of synonym: "results_in_development_of" EXACT [] def: "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] comment: 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 rule: P results_in_complete_development_of C & C develops_from C' & P' results_in_complete_development_of C' => P' precedes P ! x morphogenesis [Typedef] id: OBO_REL:results_in_morphogenesis_of name: results_in_morphogenesis_of is_a: OBO_REL:has_participant comment: x morphogenesis: The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form. rule: results_in_morphogenesis_of(X) part_of results_in_complete_development_of(X) ! x structural_organization [Typedef] id: OBO_REL:results_in_structural_organization_of name: results_in_structural_organization_of is_a: OBO_REL:has_participant comment: 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. rule: results_in_structural_organization_of(X) part_of results_in_morphogenesis_of(X) ! x formation [Typedef] id: OBO_REL:results_in_formation_of name: results_in_formation_of def: "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] synonym: "results_in_creation_of" EXACT [] synonym: "results_in_assembly_of" EXACT [] comment: 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 is_a: OBO_REL:results_in_developmental_progression_of rule: results_in_formation_of(X) part_of results_in_morphogenesis_of(X) ! x maturation [Typedef] id: OBO_REL:results_in_maturation_of name: results_in_maturation_of def: "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" [http://www.geneontology.org/GO.process.guidelines.shtml#mat, GOC:cjm, GOC:curators] is_a: OBO_REL:has_participant comment: A developmental process, independent of morphogenetic (shape) change, that is required for x to attain its fully functional state [Typedef] id: OBO_REL:results_in_division_of name: results_in_division_of def: "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] synonym: "results_in_fission_of" EXACT [] xref: UCDHSC:results_in_division_of comment: 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. [Typedef] id: OBO_REL:results_in_fusion_of name: results_in_fusion_of synonym: "results_in_joining_of" EXACT [] def: "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] xref: UCDHSC:results_in_division_of comment: 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. [Typedef] id: OBO_REL:results_in_remodeling_of name: results_in_remodeling_of comment: 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 [Typedef] id: OBO_REL:results_in_increase_in name: results_in_increase_in def: "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] comment: elevation of cytosolic calcium ion concentration results_in_increase_in concentration of calcium ions [Typedef] id: OBO_REL:results_in_decrease_in name: results_in_decrease_in def: "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] comment: reduction of cytosolic calcium ion concentration results_in_decrease_in concentration of calcium ions [Typedef] id: OBO_REL:results_in_increase_in_mass_of name: results_in_increase_in_mass_of def: "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] comment: DEPRECATED [Typedef] id: OBO_REL:results_in_increased_mass_of name: results_in_increased_mass_of is_obsolete: true replaced_by: OBO_REL:results_in_increase_in_mass_of comment: DEPRECATED [Typedef] id: OBO_REL:results_in_localization_of name: results_in_localization_of def: "P results_in_localization_of C : **TODO** - compare and contrast with maintenance of localization, and transportation" [GOC:cjm] comment: nuclear pore localization results_in_localization_of nuclear pore : The processes by which nuclear pores are transported to, or maintained in, a specific location. [Typedef] id: OBO_REL:results_in_movement_of name: results_in_movement_of def: "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] comment: Example: dendritic cell chemotaxis results_in_movement_of dendritic cell : The movement of a dendritic cell in response to an external stimulus [Typedef] id: OBO_REL:results_in_patterning_for name: results_in_patterning_for namespace: unassigned_relation comment: needs to be defined. Used in 17 xp defs [Typedef] id: OBO_REL:results_in_secretion_of_granules_from name: results_in_secretion_of_granules_from comment: replace with release_of/release_from using the GO term for secretory granules is_obsolete: true [Typedef] id: OBO_REL:results_in_selection_of name: results_in_selection_of comment: 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? [Typedef] id: OBO_REL:results_in_negative_selection_of name: results_in_negative_selection_of comment: 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? [Typedef] id: OBO_REL:results_in_positive_selection_of name: results_in_positive_selection_of comment: 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? [Typedef] id: OBO_REL:results_in_structural_change_to name: results_in_structural_change_to def: "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] comment: nuclear envelope disassembly results_in_structural_change_to nuclear envelope : The controlled breakdown of the nuclear envelope in the context of a normal process [Typedef] id: OBO_REL:results_in_transport_from name: results_in_transport_from def: "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] comment: 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 [Typedef] id: OBO_REL:results_in_transport_to name: results_in_transport_to def: "P results_in_transport_to C : forall pP, there exists some c' such that located_in C at end_of(p) and not(c' located_in C at start_of(p))" [GOC:cjm] comment: 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 [Typedef] id: OBO_REL:results_in_transport_through name: results_in_transport_through [Typedef] id: OBO_REL:unfolds_in name: unfolds_in def: "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] comment: Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte !transitive_over: part_of notes: stricter definition required, such that if P unfolds_in cell, then it does not unfold in the whole organism? [Typedef] id: OBO_REL:unfolds_around name: unfolds_around def: "P unfolds_around C : the execution of P spatially contains by C." [GOC:cjm] comment: Example: chromatin silencing at centromere unfolds_around centromere : Repression of transcription of centromeric DNA by the formation of heterochromatin. [Typedef] id: OBO_REL:results_in_closure_of name: results_in_closure_of def: "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] comment: Example: neural tube closure results_in_closure_of neural tube. [Typedef] id: OBO_REL:results_in_release_of name: results_in_release_of def: "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] comment: 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. [Typedef] id: OBO_REL:results_in_release_from name: results_in_release_from def: "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] comment: 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 [Typedef] id: OBO_REL:results_in_transport_of name: results_in_transport_of namespace: unassigned_relation comment: DEPRECATE? comment: consider: OBO_REL:results_in_movement_of [Typedef] id: OBO_REL:results_in_death_of name: results_in_death_of [Typedef] id: OBO_REL:results_in_attachment_of name: results_in_attachment_of comment: DEPRECATED comment: consider: OBO_REL:results_in_connection_of [Typedef] id: OBO_REL:results_in_adhesion_to name: results_in_adhesion_to comment: DEPRECATED comment: consider: OBO_REL:results_in_connection_of [Typedef] id: OBO_REL:results_in_connection_of name: results_in_connection_of def: "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] comment: 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 [Typedef] id: OBO_REL:activates name: activates is_a: OBO_REL:positively_regulates [Typedef] id: OBO_REL:inactivates name: inactivates is_a: OBO_REL:negatively_regulates [Typedef] id: OBO_REL:develops_into name: develops_into [Typedef] id: OBO_REL:costimulates_activation_of name: costimulates_activation_of comment: 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 [Typedef] id: OBO_REL:stimulates name: stimulates [Typedef] id: OBO_REL:subslice_of name: subslice_of comment: Necessary for 'time-sliced' representations. Examples: this eye at t1 subslice_of this eye during its entire existence [Typedef] id: OBO_REL:has_aggregate_part name: has_aggregate_part comment: Sourced from BIRN. Domain: bfo:ObjectAggregate [Typedef] id: OBO_REL:has_boundary name: has_boundary comment: Sourced from BIRN. Range: bfo:ObjectBoundary [Typedef] id: OBO_REL:has_duration name: has_duration def: "The relation that holds between a process or a processual entity and the length of the temporal interval between its beginning and its end." [] comment: Submitted by Liju Fan (OBI) !domain: span:Occurrent !range: span:TemporalInterval [Typedef] id: OBO_REL:has_qualifier name: has_qualifier comment: 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 [Typedef] id: OBO_REL:increased_in_magnitude_compared_to name: increased_in_magnitude_compared_to inverse_of: OBO_REL:decreased_in_magnitude_compared_to comment: 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). is_transitive: true [Typedef] id: OBO_REL:decreased_in_magnitude_compared_to name: decreased_in_magnitude_compared_to inverse_of: OBO_REL:increased_in_magnitude_compared_to is_transitive: true [Typedef] id: OBO_REL:relative_to name: relative_to comment: required for defining classes such as 'ratio of root length to root shoot' [Typedef] id: OBO_REL:overlaps name: overlaps def: "Two objects are connected if they share a fiat boundary" [] is_symmetric: true is_transitive: false implied_by: OBO_REL:located_in [Typedef] id: OBO_REL:interacts_with name: interacts_with ![Typedef] !id: OBO_REL:has_part_on_cell_surface