homologous_to
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
has_direct_participant
unfolds_towards
gives_rise_to
has_central_participant
DEPRECATED may be deprecated in favour of acts_on
has_input_participant
has_output_participant
has_passive_participant
has_result
acts_towards
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
has_specific_outcome
activates
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
ancestral_copy_of
x aco y iff x dco y OR x aco z and z aco y
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
applicable_to
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
weakly_valid_for_taxon
relevant_for_taxon
arises_from
bearer_of
A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in
has_inherent
has_inherer
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)
buds_from
connected_to
contains_variant_of
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
decreased_in_magnitude_compared_to
dependent_on
depends_on
A depends_on B : all instances of A require B to exist
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
develops_into
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
facsimile_of
x dco y iff
disposition_of
ends_at_beginning_of
p1 ends_at_beginning_of p2 iff end_of(p1) = start_of(p2)
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)
ends_during_or_before
p ends_before_end_of s iff end_of(p) <= end_of(s)
ends_before_end_of
ends_earlier_than
evolutionarily_derived_from
evolved_from
descended_from
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
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
exemplifies
see Neuhaus et al Substances, Qualitiies Universals
A relation between an entity instance and a dependent entity type.
exists_during
during
c exists_during p iff exists(t) & c exists-at t & start_of(p) <= t & t <= end_of(p)
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
generically_inheres_in
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
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
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)
happens_in_response_to
Example: negative chemotaxis in response to octanol (see WBph)
has_aggregate_part
Sourced from BIRN. Domain: bfo:ObjectAggregate
has_boundary
Sourced from BIRN. Range: bfo:ObjectBoundary
has_disposition
has_duration
The relation that holds between a process or a processual entity and the length of the temporal interval between its beginning and its end.
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
has_function
Relation between an independent continuant and a function.
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)
has_input
has_output
Examples: secretory cells. Should this be has_function (export of ...)
C has_output C'
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
has_population_of
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
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
has_role
A relation between a continuant C and a role R. The reciprocal relation of role_of.
inactivates
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).
increases_population_size_of
influenced_by
influences
mutated gene influences morphology; anxiety influences thigmotaxis
disposes_bearer_towards
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
has_bearer
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.
inheres_in_part_of
interacts_with
lacks_part
mediated_by
negatively_regulates
A regulation relation in which the unfolding of the regulating process *decreases* the frequency, rate or extent of the regulated process
negatively_regulates_timing_of
occurs_in
occurs_with
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.
specific_to_taxon
never_outside_taxon
specific_to
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
overlaps
Two objects are connected if they share a fiat boundary
positively_regulates
A regulation relation in which the unfolding of the regulating process *increases* the frequency, rate or extent of the regulated process
positively_regulates_timing_of
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
is_quality_of
realized_by
NOTE: there appears to be some consistency in usage as to whether processes or continuants realize
executed_during
has_realization
Relation between a realizable and a process. Reciprocal relation of realizes
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
executes
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
is_realization_of
involves_execution_of
has_function_part
regulated_by
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
regulates_levels_of
regulates_population_size_of
regulates_timing_of
relative_to
required for defining classes such as 'ratio of root length to root shoot'
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
results_in_addition_of
Example: mRNA polyadenylation results_in_addition_of polyAtail to mRNA
results_in_addition_to
results_in_adhesion_to
consider: OBO_REL:results_in_connection_of
results_in_attachment_of
results_in_binding_of
results_in_biogenesis_of
results_in_breakdown_of
results_in_change_to
TODO: define in terms of transformation_of
results_in_transformation_of
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
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?
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
results_in_development_of
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
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
results_in_creation_of
consider: OBO_REL:results_in_formation_of
results_in_creation_or_release_of
results_in_death_of
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
results_in_determination_of
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
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.
results_in_fission_of
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
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
results_in_assembly_of
results_in_fusion_of
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
results_in_joining_of
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
results_in_increase_in_mass_of
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
results_in_increased_mass_of
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
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
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.
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)
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?
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]
results_in_patterning_for
results_in_positive_selection_of
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
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
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
results_in_removal_from
results_in_removal_of
Example: sperm nuclear envelope removal : Removal of the sperm nuclear envelope, allowing entry of maternal factors into the sperm nucleus
results_in_secretion_of_granules_from
replace with release_of/release_from using the GO term for secretory granules
results_in_selection_of
results_in_specification_of
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
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.
results_in_transformation_to
results_in_transport_across
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
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))
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
results_in_transport_of
consider: OBO_REL:results_in_movement_of
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))
results_in_transport_towards
results_in_targeting_to
role_of
A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role
simultaneous_with
p1 simultaneous_with p1 iff start_of(p1) = start_of2(p2) & end_of(p1) = end_of(p2)
specifically_inheres_in
starts_during
Examples (continuants): neural_tube starts_during Segmentation; Examples (processes): neural_tube_development starts_during Segmentation
starts_to_exist_during
p starts_during s iff start_of(s) <= start_of(p) & start_of(p) <= end_of(s)
starts_during_or_after
p starts_during_or_after s iff start_of(s) <= start_of(p)
start
starts_after_beginning_of
starts_earlier_than
stimulates
subslice_of
Necessary for 'time-sliced' representations. Examples: this eye at t1 subslice_of this eye during its entire existence
succeeds
surrounded_by
surrounds
time_restricted_part_of
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.
with respect to
directed to
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.
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
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)
variant_of