This ontology combines RO together with GO-specific relations in the GOREL namespace, used for annotation extensions. See;
Huntley, R. P., Harris, M. a, Alam-Faruque, Y., et al (2014). A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics, 15(1), 155. doi:10.1186/1471-2105-15-155
Notes on release edition (gorel.owl):
This ontology is created by merging the relevant subset of RO together with GO-specific annotations of RO relations, and GOREL relations
Notes on editors version (gorel-edit.owl):
The editors version imports ro.owl, and allows addition of new relations (GOREL ID space) and annotation of existing RO relations. Note for editors: if an RO relation is to be made visible in the final gorel product, then make the relation a SubProperty of 'go annotation extension relation'. Anything with a logical axiom is included in the final module. Consult Makefile for details
external
Includes Ontology(OntologyID(Anonymous-3)) [Axioms: 1925 Logical Axioms: 480]
definition
term replaced by
If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL
is a defining property chain axiom
If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.
is a defining property chain axiom where second argument is reflexive
display label for users
GO biological process
cell or anatomical
GO cellular component
Chemical
Developmental stages
GO molecular function
Sequence feature
Protein, protein complex, gene or transcript identifier
subset_property
synonym_type_property
consider
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_synonym_type
in_subset
shorthand
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000001
CL:0000000 GO:0005575 GO:0008150 PO:0009012 PO:0025131 UBERON:0001062 ZFS:0100000 WBls:0000075 WBbt:0004017 WBbt:0005766 NCBITaxon:1
This relation has two uses in annotation extension. It may be used to relate a cellular component to some cellular component, cell or anatomical structure that it is part of. It may also be used to relate a molecular function or biological process to a biological process or developmental stage of which it is a part. It may not be used to relate cellular components to functions, processes or stages, or to relate processes or functions to cellular components, cells or anatomical structures.
BFO:0000050
part of
go/extensions/gorel
part_of
part of
http://www.obofoundry.org/ro/#OBO_REL:part_of
https://wiki.geneontology.org/Part_of
part of
PomBase:curators
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
has part
go/extensions/gorel
has_part
has part
has part
PomBase:curators
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
preceded_by
preceded by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
BFO:0000063
precedes
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
BFO:0000015
CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1 FBbt:10000000
Identifies the cell, tissue, cellular component or anatomical entity within which all parts of the molecular function or biological process occurs
BFO:0000066
go/extensions/gorel
in
occurs_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
Previous definition "p occurs_in c if and only if all of the participants of p are part_of c." [BFO:cjm]
occurs in
https://wiki.geneontology.org/Occurs_in
in
PomBase:curators
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
BFO:0000067
contains_process
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
GOREL:0000000
go_annotation_extension_relation
go annotation extension relation
BFO:0000015
BFO:0000007 WBls:0000075 ZFS:0100000
Identifies a process or life stage during which a molecular function or biological process occurs or a cellular component is present
GOREL:0000002
go/extensions/gorel
during
during
OBSOLETE. c localizes_to d if c executes some function when it is part_of d.
BFO:0000004
CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
OBSOLETE. c localizes_to d if c executes some function when it is part_of d.
GOREL:0000003
localization_destination
go/extensions/gorel
localizes_to
TODO : check this one. Note Pombe is using different variant.
obsolete localizes_to
true
OBSOLETE. c localizes_to d if c executes some function when it is part_of d.
BFO:cjm
localization_destination
GOC:mah
OBSOLETE. Identifies a requirement under which the ontology term is observed to apply to the annotated gene product.
Identifies a requirement under which the ontology term is observed to apply to the annotated gene product.
GOREL:0000004
dependent on
go/extensions/gorel
dependent_on
PomBase uses the more specific child relations, and avoids using dependent_on directly.
obsolete dependent_on
true
OBSOLETE. Identifies a requirement under which the ontology term is observed to apply to the annotated gene product.
GOC:rph
dependent on
PomBase:curators
OBSOLETE. Was not defined before obsoletion.
BFO:0000001
CL:0000000 WBbt:0004017
has_input
has_output
GOREL:0000006
go/extensions/gorel
has_target_cell
this relation has been obsoleted it was unclear whether the associated cell type id should correspond to the final mature or precursor cell. If the outcome of a process is a modified cell, then the relationships has_output or has_input along with a CL identifier respectively defining the precursor or mature cell type can be considered instead.
obsolete has_target_cell
true
OBSOLETE. Was not defined before obsoletion.
BFO:0000001
CARO:0000000
has_input
has_output
GOREL:0000007
go/extensions/gorel
has_target_anatomical_entity
this relation has been obsoleted it was unclear whether the associated anatomical entity id should correspond to the final form or precursor anatomical entity. If the outcome of a process is a modified anatomical entity, then relationships has_output or has_input along with a anatomy identifier respectively defining the precursor or mature anatomical entity id can be considered instead.
obsolete has_target_anatomical_entity
true
OBSOLETE. Identifies a requirement under which the gene product is located at the specified cellular component.
Identifies a requirement under which the gene product is located at the specified cellular component.
GOREL:0000009
localized by
go/extensions/gorel
localization_dependent_on
Previous definition "Located at CC only if (BP occurs) OR (feature is present in annotated gene product) OR (CC is present) OR (gene product is present)" [GOC:mah]
obsolete localization_dependent_on
true
OBSOLETE. Identifies a requirement under which the gene product is located at the specified cellular component.
GOC:rph
localized by
PomBase:curators
OBSOLETE. A sequence feature, such as a protein domain or motif, of the annotated gene product required for its participation in Molecular Function or Biological Process.
A sequence feature, such as a protein domain or motif, of the annotated gene product required for its participation in Molecular Function or Biological Process.
requires
requires_feature
GOREL:0000010
go/extensions/gorel
requires_sequence_feature
strictly speaking, these fall outside the scope of GO, even with extended annotations
obsolete requires_sequence_feature
true
OBSOLETE. A sequence feature, such as a protein domain or motif, of the annotated gene product required for its participation in Molecular Function or Biological Process.
GOC:mah
requires
PomBase:curators
requires_feature
GOC:mah
OBSOLETE. Annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process.
annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process
requires
GOREL:0000011
go/extensions/gorel
requires_regulator
obsolete requires_regulator
true
OBSOLETE. Annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process.
GOC:mah
requires
PomBase:curators
OBSOLETE. The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance
The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance
requires
GOREL:0000012
go/extensions/gorel
requires_substance
obsolete requires_substance
true
OBSOLETE. The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance
GOC:mah
requires
PomBase:curators
Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product.
BFO:0000001
CHEBI:24431 GO:0003674 GO:0005575 GO:0008150 GO:0032991 MI:0315 MOD:00000 PR:000000001 SO:0000110 SO:0000673 SO:0000704
Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product.
not_dependent_on
GOREL:0000013
independent_of
not dependent on
go/extensions/gorel
independent_of
DEPRECATION WARNING: The GO editors have agreed that this relation should be deprecated. There are two main reasons for this 1. The relation does not extend the meaning of the GO term, as annotation relations are meant to, but instead specifies conditions under which the annotation is true. This can not be expressed in OWL. Annotation extensions using this relation will never fold. 2. The relation includes a hidden negation. This is problematic for a number of reasons, the most important of which is that burying negations in otherwise positive relationships can cause serious problems for inference.
independent_of
Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product.
GOA:rph
independent_of
GOC:rph
not dependent on
PomBase:curators
OBSOLETE. Identifies a specific target of regulation of a MF
GO:0010466
PR:000000001 SO:0000673
OBSOLETE. Identifies a specific target of regulation of a MF
GOREL:0000014
go/extensions/gorel
inhibits_protease
This relation was made obsolete because it is undesirably specific and redundant with any GO term that would be used in col5. Annotations that used this might use a different, to-be-added, child of has_regulation_target that captures something about directness; this one would probably be direct.
obsolete inhibits_protease
true
OBSOLETE. Identifies a specific target of regulation of a MF
GOC:mah
GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697
Use this relationship to link a regulatory process or function to an entity that (such as a gene, gene product, or complex) participates in the regulated process. This is a very general relation. Use something more specific wherever possible, e.g. 'regulates expression of' or 'regulates transport of'.
regulates
GOREL:0000015
go/extensions/gorel
has_regulation_target
probably want to add one or two new subtypes that capture something about directness
has_regulation_target
regulates
OBSOLETE. Identifies a specific target of regulation of a MF
GO:0010952
PR:000000001 SO:0000673
OBSOLETE. Identifies a specific target of regulation of a MF
GOREL:0000017
go/extensions/gorel
protease_activator
This relation was made obsolete because it is undesirably specific and redundant with any GO term that would be used in col5. Annotations that used this might use a different, to-be-added, child of has_regulation_target that captures something about directness; this one would be direct.
obsolete protease_activator
true
OBSOLETE. Identifies a specific target of regulation of a MF
GOC:mah
OBSOLETE. Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)
GO:0031647
GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697
Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)
GOREL:0000018
stabilizes
go/extensions/gorel
stabilizes
Obsoleted, see https://github.com/geneontology/go-ontology/issues/18540.
obsolete stabilizes
true
OBSOLETE. Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)
GOC:mah
stabilizes
PomBase:curators
OBSOLETE. Was not defined before obsoletion.
GO:0008150
GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
GOREL:0000020
go/extensions/gorel
has_upstream_or_downstream_target
obsolete has_upstream_or_downstream_target
true
OBSOLETE. Was not defined before obsoletion.
GO:0008150
GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
GOREL:0000021
go/extensions/gorel
has_upstream_target
obsolete has_upstream_target
true
OBSOLETE. Was not defined before obsoletion.
GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
GOREL:0000022
go/extensions/gorel
has_downstream_target
obsolete has_downstream_target
true
OBSOLETE. Identifies gene whose transcription is regulated
has_regulation_target
GO:0006355
OBSOLETE. Identifies gene whose transcription is regulated
GOREL:0000023
go/extensions/gorel
transcriptionally_regulates
This relation was made obsolete because it is undesirably specific and redundant with any GO term that would be used in col5. Annotations that used this might use a different, to-be-added, child of has_regulation_target that captures something about directness; this one would be indirect.
obsolete transcriptionally_regulates
true
OBSOLETE. Identifies gene whose transcription is regulated
GOC:mah
OBSOLETE. A BP during which an annotation does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
BFO:0000001
BFO:0000007 WBls:0000075 ZFS:0100000
A BP during which an annotation does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
except during
GOREL:0000024
go/extensions/gorel
true
not_during
This relation was obsoleted because GO-CAM specifications does not allow negative relations.
domain can be any process or object or even quality
obsolete not_during
true
OBSOLETE. A BP during which an annotation does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
GOC:mah
except during
PomBase:curators
OBSOLETE. A Molecular Function or Biological Process during which an annotation to a Molecular Function or Biological Process does not apply, e.g. involvement in a process not observed during the specified cell cycle phase (but observed in other phases).
BFO:0000007
BFO:0000007 WBls:0000075 ZFS:0100000
A Molecular Function or Biological Process during which an annotation to a Molecular Function or Biological Process does not apply, e.g. involvement in a process not observed during the specified cell cycle phase (but observed in other phases).
except during
GOREL:0000025
does_not_happen_during
not_occurs_during
go/extensions/gorel
true
not_happens_during
This relation was obsoleted because GO-CAM specifications does not allow negative relations.
obsolete not_happens_during
true
OBSOLETE. A Molecular Function or Biological Process during which an annotation to a Molecular Function or Biological Process does not apply, e.g. involvement in a process not observed during the specified cell cycle phase (but observed in other phases).
GOC:mah
except during
PomBase:curators
does_not_happen_during
GOC:mah
not_occurs_during
GOC:mah
OBSOLETE. A Molecular Function or Biological Process during which an annotation to a Cellular Component does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
BFO:0000004
BFO:0000007 WBls:0000075 ZFS:0100000
A Molecular Function or Biological Process during which an annotation to a Cellular Component does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
except during
GOREL:0000026
does_not_exist_during
go/extensions/gorel
true
not_exists_during
This relation was obsoleted because GO-CAM specifications does not allow negative relations.
obsolete not_exists_during
true
OBSOLETE. A Molecular Function or Biological Process during which an annotation to a Cellular Component does not apply, e.g. a localization not observed at the specified cell cycle phase (but observed in other phases).
GOC:mah
except during
PomBase:curators
does_not_exist_during
GOC:mah
OBSOLETE. Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product.
BFO:0000001
CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product.
GOREL:0000027
in presence of
go/extensions/gorel
in_presence_of
This relation was obsoleted because it does not follow GO-CAM specifications.
obsolete in_presence_of
true
OBSOLETE. Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product.
GOC:mah
in presence of
PomBase:curators
OBSOLETE. The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component
The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component
GOREL:0000028
dependent_on_localization
only when located at
go/extensions/gorel
requires_localization
obsolete requires_localization
true
OBSOLETE. The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component
GOC:mah
dependent_on_localization
GOC:mah
only when located at
PomBase:curators
OBSOLETE. Was not defined before obsoletion. Annotated gene product participates in Biological Process or executes Molecular Function activity only if regulated by action of gene product; regulation is indirect (or unknown whether direct or indirect)
BFO:0000007
GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
annotated gene product participates in Biological Process or executes Molecular Function activity only if regulated by action of gene product; regulation is indirect (or unknown whether direct or indirect)
GOREL:0000029
requires regulation by
go/extensions/gorel
requires_regulation_by
obsolete requires_regulation_by
true
OBSOLETE. Was not defined before obsoletion. Annotated gene product participates in Biological Process or executes Molecular Function activity only if regulated by action of gene product; regulation is indirect (or unknown whether direct or indirect)
GOC:mah
requires regulation by
PomBase:curators
OBSOLETE. Identifies the gene product that catalyzes a modification on the annotated gene product
MOD:00000
GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
Identifies the gene product that catalyzes a modification on the annotated gene product
GOREL:0000030
modified by
go/extensions/gorel
modified_by
http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation
obsolete modified_by
true
OBSOLETE. Identifies the gene product that catalyzes a modification on the annotated gene product
GOC:mah
modified by
PomBase:curators
OBSOLETE. Identifies a condition under which the ontology term is observed to apply to the annotated gene product
Identifies a condition under which the ontology term is observed to apply to the annotated gene product
GOREL:0000031
assay_condition
under_condition
go/extensions/gorel
condition
obsolete condition
true
OBSOLETE. Identifies a condition under which the ontology term is observed to apply to the annotated gene product
GOC:mah
assay_condition
GOC:mah
under_condition
GOC:mah
BFO:0000004
GO:0008150 WBls:0000075 ZFS:0100000
Identifies a process or life stage during which a cellular component is present
during
GOREL:0000032
go/extensions/gorel
exists_during
Previous definition "c exists_during p if and only if the temporal extent bounded by the start and end of c is part_of the temporal extent of p." [BFO:cjm]
exists_during
during
PomBase:curators
Annotated gene product requires direct regulation by the gene product or complex identified in the extension. Includes cases where the annotated gene product is a catalytic subunit of a complex and requires a regulatory subunit for activity as well as cases where the regulator acts directly but interacts transiently.
Annotated gene product requires direct regulation by the gene product or complex identified in the extension. Includes cases where the annotated gene product is a catalytic subunit of a complex and requires a regulatory subunit for activity as well as cases where the regulator acts directly but interacts transiently.
GOREL:0000033
requires direct regulation by
go/extensions/gorel
requires_direct_regulator
the gene product in the extension should be annotated to a "regulator" MF (implying that it acts directly to regulate the annotated gp activity)
obsolete requires_direct_regulator
true
Annotated gene product requires direct regulation by the gene product or complex identified in the extension. Includes cases where the annotated gene product is a catalytic subunit of a complex and requires a regulatory subunit for activity as well as cases where the regulator acts directly but interacts transiently.
GOC:mah
requires direct regulation by
PomBase:curators
pg
2020-08-28T07:03:28Z
GOREL:0000038
regulates_o_transports_or_maintains_localization_of
regulates_o_transports_or_maintains_localization_of
Identifies the Cellular Component or sequence feature adjacent to or in the vicinity of which the Molecular Function or Biological Process is executed
GOREL:0000501
at
occurs_at
Previous definition "P occurs_at C : the execution of P is located at C." [GOC:cjm, GOC:mah] This relation is not constrained with respect to whether C completely surrounds, or is adjacent to, the location where P is executed. Example: chromatin silencing at centromere unfolds_around centromere : Repression of transcription of centromeric DNA by the formation of heterochromatin.
obsolete occurs at
true
at
PomBase:curators
OBSOLETE. Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process.
Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process.
GOREL:0000502
only with modification
go/extensions/gorel
requires_modification
Note this relation is not intended for use in GO annotation. Discussion about using PR ID in column 17 instead; if we agree on that, this relation will be made obsolete
obsolete requires_modification
true
OBSOLETE. Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process.
GOC:mah
only with modification
PomBase:curators
OBSOLETE. An entity (e.g. Cellular Component, cell type or anatomical entity) in which a Biological Process or Molecular Function does not occur. Opposite of occurs_in.
BFO:0000007
CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
An entity (e.g. Cellular Component, cell type or anatomical entity) in which a Biological Process or Molecular Function does not occur. Opposite of occurs_in.
GOREL:0000506
go/extensions/gorel
not in
true
not_occurs_in
This relation was obsoleted because GO-CAM specifications does not allow negative relations.
obsolete not_occurs_in
true
OBSOLETE. An entity (e.g. Cellular Component, cell type or anatomical entity) in which a Biological Process or Molecular Function does not occur. Opposite of occurs_in.
GOC:mah
not in
PomBase:curators
Identifies a chemical substance that increases the activity of the gene product.
GOREL:0000507
activated by
activated_by_chemical
activated_by_substance
activity_increased_by
go/extensions/gorel
activated_by
This relation should not be used to annotate one gene product regulating another's activity; a regulator MF or regulation BP should be used in such cases.
activated_by
activated by
PomBase:curators
activated_by_chemical
GOC:mah
activated_by_substance
GOC:mah
activity_increased_by
GOC:mah
Identifies a chemical substance that decreases the activity of the gene product.
Identifies a chemical substance that decreases the activity of the gene product.
GOREL:0000508
activity_decreased_by
inhibited by
inhibited_by_chemical
inhibited_by_substance
go/extensions/gorel
inhibited_by
This relation should not be used to annotate one gene product regulating another's activity; a regulator MF or regulation BP should be used in such cases.
inhibited_by
Identifies a chemical substance that decreases the activity of the gene product.
GOC:mah
activity_decreased_by
GOC:mah
inhibited by
PomBase:curators
inhibited_by_chemical
GOC:mah
inhibited_by_substance
GOC:mah
OBSOLETE. An entity (e.g. Cellular Component, cell type or anatomical entity) at which a Biological Process or Molecular Function does not occur. Opposite of occurs_at.
BFO:0000007
GO:0005575 SO:0000110
An entity (e.g. Cellular Component, sequence feature) at which a Biological Process or Molecular Function does not occur. Opposite of occurs_at.
GOREL:0000509
go/extensions/gorel
not at
true
not_occurs_at
This relation was obsoleted because GO-CAM specifications does not allow negative relations.
obsolete not_occurs_at
true
OBSOLETE. An entity (e.g. Cellular Component, cell type or anatomical entity) at which a Biological Process or Molecular Function does not occur. Opposite of occurs_at.
GOC:mah
not at
PomBase:curators
OBSOLETE. Was not defined before obsoletion.
BFO:0000007
CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
Identifies an entity indirectly affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in MF or BP.
GOREL:0000505
has_indirect_target
indirectly_localizes
GOREL:0000751
has_indirect_target
indirectly_localizes
go/extensions/gorel
has_indirect_input
If the entity is directly bound/acted upon by the gene product that is the subject of the annotation, then the relation: has_direct_input should be alternatively considered. [GOC:ecd]
obsolete has_indirect_input
true
has_indirect_target
GOC:ecd
indirectly_localizes
GOC:ecd
BFO:0000015
Identifies an entity directly affected (transported, modified, consumed or destroyed) by the gene product's participation in a molecular function or biological process. It is expected that the gene product and entity will physically interact, this can be determined either by a direct binding assay or inferred from the activity of the gene product, for example, a gene product with catalytic activity is inferred to bind its substrate.
GOREL:0000019
GOREL:0000504
directly_localizes
has_direct_target
has_substrate
GOREL:0000752
has_direct_target
directly_localizes
has_substrate
go/extensions/gorel
has_direct_input
If the entity is indirectly bound/acted upon by the gene product that is the subject of an annotation, then the relation: has_indirect_input should be considered [GOC:ecd]
This relation is part of the ShEx speficications.
obsolete has_direct_input
true
has_direct_target
GOC:ecd
directly_localizes
GOC:ecd
has_substrate
GOC:ecd
OBSOLETE. Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurance of the function or process
BFO:0000001
SO:0000110
Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurance of the function or process
GOREL:0000754
requires feature in target
go/extensions/gorel
requires_target_sequence_feature
obsolete requires_target_sequence_feature
true
OBSOLETE. Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurance of the function or process
GOC:ecd
requires feature in target
PomBase:curators
OBSOLETE. Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product.
BFO:0000001
CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704
Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product.
GOREL:0000755
go/extensions/gorel
in_absence_of
DEPRECATION WARNING: The GO editors have agreed that this relation should be deprecated. There are two main reasons for this 1. The relation does not extend the meaning of the GO term, as annotation relations are meant to, but instead specifies conditions under which the annotation is true. This can not be expressed in OWL. Annotation extensions using this relation will never fold. 2. The relation includes a hidden negation. This is problematic for a number of reasons, the most important of which is that burying negations in otherwise positive relationships can cause serious problems for inference.
This relation was obsoleted because it does not follow GO-CAM specifications.
obsolete in_absence_of
true
OBSOLETE. Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product.
GOC:rph
GOREL:0001000
go/extensions/gorel
axis_of
axis_of
This is the combination of the has_output relation with the axis_of relation
This is the combination of the has_output relation with the axis_of relation
GOREL:0001002
go/extensions/gorel
has_output_o_axis_of
Example of use: anterior/posterior pattern specification has_output_o_axis_of lateral plate mesoderm. Note that the output of this process is an *axis*, not the LPM itself. This relation chain allows us to use an anatomical structure as the slot value
has_output_o_axis_of
true
This is the combination of the has_output relation with the axis_of relation
GOC:cjm
GOC:dph
GOC:mtg_berkeley_2012_08_27
This is the combination of the regulates relation with the has_output relation
This is the combination of the regulates relation with the has_output relation
GOREL:0001003
regulates_o_has_output
regulates_o_has_output
true
This is the combination of the regulates relation with the has_output relation
GOC:cjm
GOC:dph
GOC:mtg_berkeley_2012_08_27
'negative regulation of chromosome segregation' that regulates_o_occurs_in some spermatocyte.
A relation that holds between a regulatory process and the entity which the regulated biological process or molecular function occurs in.
Use this relation to link a regulatory process or function to the structure that the regulated process or function occurs in.
GOREL:0001004
regulates_o_occurs_in
go/extensions/gorel
regulates_o_occurs_in
regulates process that occurs in
true
A relation that holds between a regulatory process and the entity which the regulated biological process or molecular function occurs in.
GOC:cjm
GOC:dph
GOC:mtg_berkeley_2012_08_27
A relation that holds between a process that regulates locomotion and the cell or organism whose locomotion is being regulated.
Use this relation to relate a process that regulates locomotion to the cell or organism whose locomotion is being regulated.
GOREL:0001005
regulates_o_results_in_movement_of
go/extensions/gorel
regulates_o_results_in_movement_of
This is the combination of the regulates relation with the results_in_movement_of relation. Example of use: an annotation of gene X to 'regulation of cell migration with 'regulates_o_results_in_movement_of(CL:0000653) in column 16 would mean that gene X is involved in the regulation of glomerular visceral epithelial cell migration.
regulates process that results in movement of
true
A relation that holds between a process that regulates locomotion and the cell or organism whose locomotion is being regulated.
GOC:cjm
GOC:dph
GOC:mtg_berkeley_2012_08_27
OBSOLETE. The relationship that links an entity with a process in which the process has more than one participant that is of the same entity type.
RO:0012003
GO:0008283
CL:0000000 WBbt:0004017
Use this relation to relate a process to a population of cells that it acts on. The main usage of this relations is to relate GO: cell proliferation to the proliferating cells type. (Individual cells divide, populations of cells proliferate.)
alters levels of
GOREL:0001006
RO:0012003
go/extensions/gorel
acts_on_population_of
Example of use: an annotation of gene X to cell proliferation with acts_on_population_of CL:0000057 means that gene X is involved in the proliferation of fibroblasts. Note that many annotation extensions use regulates_o_acts_on_population_of - should this be considered regulation of number of cells / cell homeostasis?
obsolete acts_on_population_of
true
OBSOLETE. The relationship that links an entity with a process in which the process has more than one participant that is of the same entity type.
GOC:mtg_berkeley_2013
pg
2019-11-21T19:16:04Z
GOREL:0001007
go/extensions/gorel
mediated_by
obsolete_mediated_by
obsolete mediated by
true
'positive regulation of cell proliferation' and 'regulates process that acts on population of' some 'stem cell'
A relation that applies between a regulatory process and a population of entities that a process it regulates acts on.
This is the combination of the regulates relation with the acts_on_population_of relation.
GOREL:0001008
regulates_o_acts_on_population_of
go/extensions/gorel
regulates_o_acts_on_population_of
obsolete regulates process that acts on population of
true
true
A relation that applies between a regulatory process and a population of entities that a process it regulates acts on.
GOC:mtg_berkeley_2013
This is the combination of the regulates relation with the results_in_acquisition_of_features_of relation.
Use this relation to relate a process that regulates the differentiation of a cell type or anatomical structure to the specific cell type or anatomical structure in question.
GOREL:0001010
regulates differentiation of
regulates_o_results_in_acquisition_of_features_of
go/extensions/gorel
regulates_o_results_in_acquisition_of_features_of
regulates acquisition of features of
true
This is the combination of the regulates relation with the results_in_acquisition_of_features_of relation.
GOC:mtg_berkeley_2013
A relationship between the regulation of a process and the agent that executes that process.
GOREL:0001011
regulates_o_has_agent
regulates_o_has_agent
regulates_o_has_agent
true
A relationship between the regulation of a process and the agent that executes that process.
GOC:dos
This is the combination of the regulates relation with the results_in_maturation_of relation.
This is the combination of the regulates relation with the results_in_maturation_of relation.
GOREL:0001012
regulates_o_results_in_maturation_of
regulates maturation of
true
This is the combination of the regulates relation with the results_in_maturation_of relation.
GOC:mtg_berkeley_2013
This is the combination of the regulates relation with the has_participant relation.
Use this relationship to link a regulatory process or function to an entity that participates in the regulated process.
GOREL:0001016
regulates_o_has_participant
regulates_o_has_participant
This is the combination of the regulates relation with the has_participant relation.
GOC:mtg_berkeley_2013
The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type.
BFO:0000015
CL:0000000 WBbt:0004017
The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type.
GOREL:0001019
go/extensions/gorel
results_in_division_of
Example of use: an annotation of gene X to cell division with results_in_division_of CL:0000057 (fibroblast) means that at the end of the process a single fibroblast has divided into two fibroblasts.
results_in_division_of
The relationship linking a entity and its participation in a process that results in the division of the entity into two entities of the same type.
GOC:mtg_berkeley_2013
A relation that applies between a process that regulates cell fate commitment and the cell type that the regulated process results in commitment to.
This is the combination of the regulates relation with the results_in_commitment_to relation.
GOREL:0001022
regulates_o_results_in_commitment_to
regulates_o_results_in_commitment_to
regulates commitment to
true
A relation that applies between a process that regulates cell fate commitment and the cell type that the regulated process results in commitment to.
GOC:mtg_berkeley_2013
This is the combination of the regulates relation with the results_in_development_of relation.
Use this relation to relate 'regulation of developmental process' or one of its subclasses to the structure that the regulated developmental process results in the development of.
GOREL:0001023
regulates_o_results_in_development_of
go/extensions/gorel
regulates_o_results_in_development_of
regulates development of
true
This is the combination of the regulates relation with the results_in_development_of relation.
GOC:mtg_berkeley_2013
This is the combination of the regulates relation with the results_in_division_of relation.
This is the combination of the regulates relation with the results_in_division_of relation.
GOREL:0001024
regulates_o_results_in_division_of
regulates division of
true
This is the combination of the regulates relation with the results_in_division_of relation.
GOC:mtg_berkeley_2013
This is the combination of the regulates relation with the results_in_formation_of relation.
This is the combination of the regulates relation with the results_in_formation_of relation.
GOREL:0001025
regulates_o_results_in_formation_of
regulates formation of
true
This is the combination of the regulates relation with the results_in_formation_of relation.
GOC:mtg_berkeley_2013
This is the combination of the regulates relation with the results_in_morphogenesis_of relation.
This is the combination of the regulates relation with the results_in_morphogenesis_of relation.
GOREL:0001026
regulates_o_results_in_morphogenesis_of
regulates morphogenesis of
true
This is the combination of the regulates relation with the results_in_morphogenesis_of relation.
GOC:mtg_berkeley_2013
A relation that applies between a process that regulates the specification of some cell type or structure and the specified cell type or structure.
Use this relation to link a process that regulates the specification of some cell type of anatomical structure, and the structure or cell type specified.
GOREL:0001027
regulates_o_results_in_specification_of
go/extensions/gorel
regulates_o_results_in_specification_of
regulates specification of
true
A relation that applies between a process that regulates the specification of some cell type or structure and the specified cell type or structure.
GOC:mtg_berkeley_2013
This is the combination of the has_output relation with the gene_product_of relation.
BFO:0000015
PR:000000001 SO:0000673
This is the combination of the has_output relation with the results_in_specification_of relation.
GOREL:0001029
go/extensions/gorel
has_output_o_product_of
has_output_o_product_of
true
This is the combination of the has_output relation with the gene_product_of relation.
GOC:mtg_berkeley_2013
This is the combination of the regulates relation with the has_input relation
This is the combination of the regulates relation with the has_input relation
GOREL:0001030
regulates_o_has_input
regulates_o_has_input
true
This is the combination of the regulates relation with the has_input relation
GOC:dph
pg
2019-11-21T16:32:15Z
GOREL:0002008
go/extensions/gorel
obsolete_has_intermediate
obsolete has_intermediate
true
pg
2019-11-21T18:00:03Z
GOREL:0002010
go/extensions/gorel
obsolete_results_in_transport_to_from_or_mediated_by
This relation was only used for one class, 'endosomal transport' (GO:0016197), which groups together disparate roles the participants can play - it was defined as 'The directed movement of substances into, out of *or mediated by* an endosome...' The term has been redefined and the logical definition changed accordingly.
obsolete results_in_transport_to_from_or_mediated_by
true
OBSOLETE. A relation that holds between the regulation of a molecular function and the agent that executes that function.
GO:0098772 GO:0065009
GO:0032991 SO:0000374 PR:000000001
Use this relation to link either a molecular function, or a biological process that regulates a molecular function, to the gene product or complex that executes the regulated function.
GOREL:0098702
regulates_activity_of
This relation has been obsoleted as it is not part of the GO ShEx specifications.
obsolete regulates activity of
true
OBSOLETE. A relationship that holds between a process and a gene whose transcription is regulated by that process.
Relates a regulatory process or function to the gene whose transcription it regulates.
GOREL:0098788
regulates_transcription_of
Usage of this relation has been deprecated in favor of 'has direct input'.
obsolete regulates transcription of
true
Relates a regulatory process or function to the gene whose transcription it regulates.
GOC:dos
OBSOLETE. A relationship that holds between a process and a gene whose expression is regulated by that process.
BFO:0000015
PR:000000001 SO:0000673 SO:0000704
Relates a regulatory process or function to the gene whose expression it regulates. Expression encompasses transcription, regulation and processing involved in maturation.
GOREL:0098789
regulates_expression_of
Usage of this relation has been deprecated in favor of 'has direct input'.
obsolete regulates expression of
true
Relates a regulatory process or function to the gene whose expression it regulates. Expression encompasses transcription, regulation and processing involved in maturation.
GOC:dos
OBSOLETE. A relationship that holds between a process and a protein coding gene whose translation is regulated by that process.
BFO:0000015
PR:000000001 SO:0000673 SO:0000704
Relates a regulatory process or function to the gene whose translation it regulates.
GOREL:0098790
regulates_translation_of
Regulation of translation includes processes that regulate the levels of mature mRNA available for translation, as well as direct regulation of the rate of translation.
Usage of this relation has been deprecated in favor of 'has direct input'.
obsolete regulates translation of
true
Relates a regulatory process or function to the gene whose translation it regulates.
GOC:dos
inheres in
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
inheres_in
RO:0000052
characteristic_of
Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.
characteristic of
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
has_characteristic
has characteristic
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
participates_in
participates in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
BFO:0000015
CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CARO:0000000
Identifies an entity affected by the gene product's participation in a molecular function or biological process
http://www.obofoundry.org/ro/#OBO_REL:has_participant
RO:0000057
go/extensions/gorel
has_participant
Do not use this relation directly
has participant
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
function_of
is function of
RO:0000079
function_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
is quality of
quality_of
RO:0000080
quality_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
is role of
role_of
RO:0000081
role_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
RO:0000085
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
RO:0000086
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
RO:0000087
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
RO:0000091
has_disposition
has disposition
inverse of has disposition
RO:0000092
disposition_of
This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.
disposition of
A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
Note from NCEAS meeting: consider changing primary label
GO:0005575
CHEBI:24431 SO:0000001 SO:0000704
Use this relation to link a region of chromosome or chromatin to the sequence region that it contains. The sequence region may be a specific gene or some generic region referred to by a SO term.
RO:0002008
coincident_with
Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
coincident with
A relationship that holds between a process that regulates a transport process and the entity transported by that process.
BFO:0000015
CHEBI:24431 PR:000000001 GO:0005575 SO:0000673 CHEBI:33697
Use this relation to link a process that regulates transport to the the entity being transported.
RO:0002011
regulates_transport_of
regulates transport of
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
2017-05-24T09:30:46Z
RO:0002013
has_regulatory_component_activity
has regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
2017-05-24T09:31:01Z
RO:0002014
has_negative_regulatory_component_activity
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
2017-05-24T09:31:17Z
RO:0002015
has_positive_regulatory_component_activity
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
2017-05-24T09:44:33Z
RO:0002017
has_component_activity
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
has component activity
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
2017-05-24T09:49:21Z
RO:0002018
has_component_process
has component process
Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
2017-07-20T17:11:08Z
RO:0002020
transports
transports
2017-09-17T13:52:24Z
RO:0002022
directly_regulated_by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
directly regulated by
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
2017-09-17T13:52:38Z
RO:0002023
directly_negatively_regulated_by
directly negatively regulated by
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
2017-09-17T13:52:47Z
RO:0002024
directly_positively_regulated_by
directly positively regulated by
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
2017-09-22T14:14:36Z
RO:0002025
has_effector_activity
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
has effector activity
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
David Osumi-Sutherland
RO:0002084
during_which_ends
Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which ends
di
RO:0002085
encompasses
Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
encompasses
David Osumi-Sutherland
RO:0002086
ends_after
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
David Osumi-Sutherland
starts_at_end_of
RO:0002087
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
David Osumi-Sutherland
RO:0002088
during_which_starts
Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range.
during which starts
David Osumi-Sutherland
ends_at_start_of
meets
RO:0002090
immediately_precedes
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
David Osumi-Sutherland
io
RO:0002091
starts_during
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
David Osumi-Sutherland
d
during
BFO:0000015
GO:0008150 WBls:0000075 ZFS:0100000 UBERON:0000105
Identifies a process or life stage during which a molecular function or biological process occurs. This is weaker than parthood. So, for example, various processes occur during gastrulation without being part of it.
during
RO:0002092
occurs_during
go/extensions/gorel
happens_during
Previous definition "p happens_during q if and only if the temporal extent of p is part_of the temporal extent of q." Note that part_of between processes implies happens_during (we must use OWL to express this), but happens_during does not imply part_of. Note also that this relation holds between two processes. To link a physical entity to a process by duration, use exists_during. [BFO:cjm] Note that in order to express that part_of between processes implies during, we must use OWL.
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
https://wiki.geneontology.org/Happens_during
during
PomBase:curators
occurs_during
GOC:mah
David Osumi-Sutherland
o
overlaps
RO:0002093
ends_during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
RO:0002131
overlaps
overlaps
true
A is spatially_disjoint_from B if and only if they have no parts in common
There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom.
Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy
BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
RO:0002163
spatially_disjoint_from
spatially disjoint from
https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO:0002180
has_component
has component
definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x"
We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.
BFO:0000004
BFO:0000002
x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x.
GOREL:0001028
RO:0002204
go/extensions/gorel
gene_product_of
gene product of
every HOTAIR lncRNA is the gene product of some HOXC gene
every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene
x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y
RO:0002205
has_gene_product
has gene product
p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
BFO:0000015
BFO:0000015
RO:0002211
regulates
regulates
p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q.
negatively regulates (process to process)
BFO:0000015
BFO:0000015
RO:0002212
negatively_regulates
negatively regulates
p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q.
positively regulates (process to process)
BFO:0000015
BFO:0000015
RO:0002213
positively_regulates
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
RO:0002215
capable_of
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
has function in
RO:0002216
capable_of_part_of
capable of part of
true
OBSOLETE x has participant y if and only if x realizes some active role that inheres in y
has agent
GO:0008150
CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
Use this relation to link a process to an entity that carries out that process. The entity may be a cellular component, a cell type or an anatomical structure. Examples include recording a vesicle type that mediates a transport process, a cell type that is the agent of a secretion process or a cell adhesion process. Do not use this to extend a molecular function: The agents of molecular functions are gene products and complexes. Use of this relation with a molecular function therefore consistutes reverse annotation.
GOREL:0001007
RO:0002218
has_agent
Example of use: an annotation of gene X to cytokine production with has_agent of CL:0000057 (fibroblast) means that the fibroblast is producing the cytokine.
obsolete has active participant
true
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
The epidermis layer of a vertebrate is adjacent to the dermis.
The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies.
The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used.
x adjacent to y if and only if x and y share a boundary.
This relation acts as a join point with BSPO
GO:0005575
GO:0005575 CL:0000000
RO:0002220
adjacent to
go/extensions/gorel
adjacent_to
adjacent to
A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts.
adjacent to
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
RO:0002222
temporally_related_to
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y
starts with process that occurs in
BFO:0000015
CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1
Use this relation to relate a biological process to its start location. Examples include recording the cell-type in which a cell-cell signaling process starts and recording a cellular compartment (such as post-synapse, presynapse or cilium) in which a signal transduction process starts. Note, if the entire process occurs in a particular location, use 'occurs in' instead.
RO:0002231
has_start_location
has start location
x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y
ends with process that occurs in
BFO:0000015
CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1
Use this relation to relate a biological process to the location (cell component, cell type, anatomical location) in which the process ends. Examples include recording the cell-type or cellular compartment in which a cell-cell signalling process ends. To record a location in which the entire process occurs, please use 'occurs in'.
RO:0002232
has_end_location
has end location
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
consumes
BFO:0000015
CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697 SO:0000839 SO:0001683 NCBITaxon:1
Use this relation to relate a biological process or molecular function to an entity that participates in the process/function, is present at the start of the process/function and whose state is affected by that process/function. Change of state includes being transported, modified, consumed or destroyed. An input may be any continuant: chemical; gene product; cell component; cells type; organism. For inputs to MFs that are bound by the gene product that executes the MF, the more specific relation 'has_direct_input' may be used.
GOREL:0000016
GOREL:0000503
GOREL:0000753
has_target
localizes
GOREL:0000753
RO:0002233
has_target
localizes
go/extensions/gorel
has_input
Previous definition "p has_input c if and only c participates_in p at the start of p and c is in some way bound, transported, modified, consumed or destroyed by p." If it is known whether the entity is directly or indirectly bound/acted upon by the gene product that is the subject of the annotation, then the relations has_direct_input or has_indirect_input should be alternatively considered.
has input
https://wiki.geneontology.org/Has_input
has_target
GOC:ecd
localizes
GOC:ecd
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
produces
BFO:0000015
CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697
Identifies an entity that is changed or created after participation in a molecular function or biological process
RO:0002234
go/extensions/gorel
has_output
Previous definition "p has_output c if c participates_in p at the end of p and c is in some way changed by p or created by p." []
has output
https://wiki.geneontology.org/Has_output
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
RO:0002263
acts_upstream_of
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
RO:0002264
affects
acts_upstream_of_or_within
acts upstream of or within
https://wiki.geneontology.org/Acts_upstream_of_or_within
p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
RO:0002295
results_in_developmental_progression_of
results in developmental progression of
every flower development (GO:0009908) results in development of some flower (PO:0009046)
p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
http://www.geneontology.org/GO.doc.development.shtml
BFO:0000015
CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
The relationship linking an entity and its participation in a process that changes it through time from the formation of the entity to the resultant mature state.
GOREL:0001009
RO:0002296
go/extensions/gorel
results_in_development_of
Example of use: an annotation of gene X to cell development with results_in_development_of CL:0000540 (neuron) means that gene x is involved in a process where a cell that has an identity of a neuron has gone through a progression from its formation to the resulting mature neuron.
results in development of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
The relationship linking a entity and its participation in a process whereby at the beginning of the process the entity does not exist and at the end of the process the entity exists.
GOC:mtg_berkeley_2013
GO:0008150
CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
The relationship linking a entity and its participation in a process whereby at the beginning of the process the entity does not exist and at the end of the process the entity exists.
GOREL:0001020
RO:0002297
go/extensions/gorel
results_in_formation_of
Example of use: an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
results in formation of
The relationship linking a entity and its participation in a process whereby at the beginning of the process the entity does not exist and at the end of the process the entity exists.
GOC:mtg_berkeley_2013
an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
GOC:mtg_berkeley_2013
BFO:0000015
CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
GOREL:0001015
RO:0002298
go/extensions/gorel
results_in_morphogenesis_of
Example of use: an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
results in morphogenesis of
an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
GOC:mtg_berkeley_2013
BFO:0000015
CL:0000000 GO:0005575 PO:0009012 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766
The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
GOREL:0001013
RO:0002299
go/extensions/gorel
results_in_maturation_of
Example of use: an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process.
results in maturation of
p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q.
RO:0002304
causally_upstream_of,_positive_effect
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
causally upstream of, positive effect
p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q.
RO:0002305
causally_upstream_of,_negative_effect
causally upstream of, negative effect
Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
regulates localization of
BFO:0000015
CHEBI:24431 PR:000000001 GO:0005575 SO:0000673 CHEBI:33697
Use to relate a process or molecular function to a substance that is transported, localized or whose localization is maintained by that process or function. The substance may be a chemical, gene product or cellular component. For the movement via locomotion of cells and anatomical structure please use results_in_movement_of.
RO:0002313
go/extensions/gorel
regulates location of
transports_or_maintains_localization_of
transports or maintains localization of
q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of characteristic of part of
inheres in part of
RO:0002314
characteristic_of_part_of
characteristic of part of
true
an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
GOC:mtg_berkeley_2013
GO:0030154
CL:0000000 PO:0009002 WBbt:0004017
Use this relation to link a cell differentiation process to the cell type that the process results in the differentiation of.
GOREL:0001014
RO:0002315
results in differentiation of
go/extensions/gorel
results_in_acquisition_of_features_of
Example of use: an annotation of gene X to cell differentiation with results_in_acquisition_of_features_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
results in acquisition of features of
A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)
Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions
RO:0002321
ecologically_related_to
ecologically related to
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
RO:0002323
mereotopologically_related_to
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
RO:0002324
developmentally_related_to
developmentally related to
Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)
a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].
In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]
RO:0002325
colocalizes_with
colocalizes with
ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
We would like to say
if and only if
exists c', p'
c part_of c' and c' capable_of p
and
c capable_of p' and p' part_of p
then
c contributes_to p
However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
RO:0002326
contributes_to
contributes to
https://wiki.geneontology.org/Contributes_to
a particular instances of akt-2 enables some instance of protein kinase activity
c enables p iff c is capable of p and c acts to execute p.
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
RO:0002327
enables
enables
https://wiki.geneontology.org/Enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
functionally_related_to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
false
RO:0002329
part_of_structure_that_is_capable_of
part of structure that is capable of
true
holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism
RO:0002330
genomically_related_to
genomically related to
c involved_in p if and only if c enables some process p', and p' is part of p
actively involved in
enables part of
RO:0002331
involved_in
involved in
https://wiki.geneontology.org/Involved_in
every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid
p regulates levels of c if p regulates some amount (PATO:0000070) of c
regulates levels of (process to entity)
GOREL:0000036
RO:0002332
go/extensions/gorel
regulates_level_of
regulates levels of
inverse of enables
RO:0002333
enabled_by
enabled by
https://wiki.geneontology.org/Enabled_by
inverse of regulates
regulated by (processual)
RO:0002334
regulated_by
regulated by
inverse of negatively regulates
RO:0002335
negatively_regulated_by
negatively regulated by
inverse of positively regulates
RO:0002336
positively_regulated_by
positively regulated by
A relationship that holds via some process of localization
Do not use this relation directly. It is a grouping relation.
RO:0002337
related_via_localization_to
related via localization to
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.
GO:0005575 CL:0000000 UBERON:0001062
Use to relate a transport or localization process to the starting location of the cargo.
RO:0002338
has_target_start_location
has target start location
This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.
GO:0005575 CL:0000000 UBERON:0001062
Use to relate a transport or localization process to the end location of the transported or localized cargo.
RO:0002339
has_target_end_location
has target end location
Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
GOREL:0000034
RO:0002340
go/extensions/gorel
imports
imports
'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)
RO:0002344
results_in_transport_to_from_or_in
results in transport to from or in
Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s.
GOREL:0000035
RO:0002345
go/extensions/gorel
exports
exports
an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type.
BFO:0000015
CL:0000000 WBbt:0004017
The relationship linking a cell and its participation in a process that results in the transition of a cell such that is can only develop into a single cell type.
GOREL:0001017
RO:0002348
go/extensions/gorel
results_in_commitment_to
Example of use: an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron.
results in commitment to
p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment.
BFO:0000015
CL:0000000 WBbt:0004017
The relationship linking a cell and its participation in a process that results in the transition of a cell such that it can only develop into a single cell type independent of its environment.
GOREL:0001018
RO:0002349
go/extensions/gorel
results_in_determination_of
Example of use: an annotation of gene X to cell determination with results_in_determination_of CL:0000540 (neuron) means that at the end of the process an unspecified cell will develop into a neuron with no additional input.
results in determination of
inverse of has input
RO:0002352
input_of
input of
inverse of has output
RO:0002353
output_of
output of
RO:0002354
formed_as_result_of
formed as result of
The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
GO:0008150
CL:0000000 WBbt:0004017
The relationship linking a cell and its participation in a process that results in the transition of a cell such that is can only develop into a single cell type when left in its environment.
GOREL:0001021
RO:0002356
go/extensions/gorel
results_in_specification_of
Example of use: an annotation of gene X to cell determination with results_in_determination_of CL:0000540 (neuron) means that at the end of the process an unspecified cell will develop into a neuron if left in its environment. If the cell is moved, it may develop into a cell type other than a neuron.
results in specification of
inverse of upstream of
RO:0002404
causally_downstream_of
causally downstream of
RO:0002405
immediately_causally_downstream_of
immediately causally downstream of
p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q.
indirectly activates
RO:0002407
indirectly_positively_regulates
indirectly positively regulates
https://wiki.geneontology.org/Indirectly_positively_regulates
p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q.
indirectly inhibits
RO:0002409
indirectly_negatively_regulates
indirectly negatively regulates
https://wiki.geneontology.org/Indirectly_negatively_regulates
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative?
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
RO:0002410
causally_related_to
causally related to
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
https://en.wikipedia.org/wiki/Causality
p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.
BFO:0000015
GO:0008150 GO:0003674
Process A is causally_upstream of process B if process A occurs first, and process A causes process B to happen. Processes A and B do not overlap.
RO:0002411
go/extensions/gorel
causally_upstream_of
causally upstream of
p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q.
RO:0002412
immediately_causally_upstream_of
immediately causally upstream of
p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
influences (processual)
RO:0002418
affects
causally_upstream_of_or_within
causally upstream of or within
inverse of causally upstream of or within
RO:0002427
causally_downstream_of_or_within
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
RO:0002428
involved_in_regulation_of
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
RO:0002429
involved_in_positive_regulation_of
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
RO:0002430
involved_in_negative_regulation_of
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or reguates
RO:0002431
involved_in_or_involved_in_regulation_of
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
executes activity in
RO:0002432
enables activity in
is_active_in
is active in
https://wiki.geneontology.org/Is_active_in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
RO:0002434
in pairwise interaction with
interacts_with
interacts with
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
http://purl.obolibrary.org/obo/MI_0914
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
binds
molecularly binds with
RO:0002436
molecularly_interacts_with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.
interacts with on organism level
RO:0002437
biotically_interacts_with
biotically interacts with
http://eol.org/schema/terms/interactsWith
A biotic interaction in which the two organisms live together in more or less intimate association.
http://www.ncbi.nlm.nih.gov/pubmed/19278549
We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism
RO:0002440
symbiotically_interacts_with
symbiotically interacts with
An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO).
http://www.ncbi.nlm.nih.gov/pubmed/19278549
This relation groups a pair of inverse relations, parasite of and parasitized by
RO:0002443
interacts_with_via_parasite-host_interaction
interacts with via parasite-host interaction
Pediculus humanus capitis parasite of human
parasitizes
RO:0002444
direct parasite of
parasite_of
parasite of
http://eol.org/schema/terms/parasitizes
has parasite
parasitised by
RO:0002445
directly parasitized by
parasitized_by
parasitized by
http://eol.org/schema/terms/hasParasite
Axiomatization to GO to be added later
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
RO:0002447
phosphorylates
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
RO:0002448
molecularly controls
directly_regulates_activity_of
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly inhibits
RO:0002449
molecularly decreases activity of
directly_negatively_regulates_activity_of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly activates
RO:0002450
molecularly increases activity of
directly_positively_regulates_activity_of
directly positively regulates activity of
The term host is usually used for the larger (macro) of the two members of a symbiosis (GO)
RO:0002453
host_of
host of
X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y
RO:0002454
has_host
has host
http://eol.org/schema/terms/hasHost
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
RO:0002464
helper_property_(not_for_use_in_curation)
helper property (not for use in curation)
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
RO:0002479
has_part_that_occurs_in
has part that occurs in
true
RO:0002481
is_kinase_activity
is kinase activity
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage.
RO:0002487
relation_between_physical_entity_and_a_process_or_stage
relation between physical entity and a process or stage
x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).
RO:0002488
existence_starts_during
existence starts during
x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))
BFO:0000004
GO:0008150 WBls:0000075 ZFS:0100000
Identifies a process or life stage during which a cellular component is present
RO:0002490
existence_overlaps
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence overlaps
x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)
BFO:0000004
GO:0008150 WBls:0000075 ZFS:0100000
Identifies a process or life stage during which a cellular component is present
RO:0002491
exists during
existence_starts_and_ends_during
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence starts and ends during
x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).
RO:0002492
existence_ends_during
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during
x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).
RO:0002496
existence_starts_during_or_after
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence starts during or after
x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.
RO:0002497
existence_ends_during_or_before
The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription.
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
RO:0002500
causal_agent_in_process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
RO:0002501
causal_relation_between_processes
causal relation between processes
RO:0002502
depends_on
depends on
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
RO:0002506
causal_relation_between_entities
causal relation between entities
x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y
Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism
http://eol.org/schema/terms/hyperparasitoidOf
https://en.wikipedia.org/wiki/Hyperparasite
RO:0002553
hyperparasitoid of
epiparasite of
hyperparasite_of
hyperparasite of
inverse of hyperparasite of
RO:0002554
has epiparasite
has hyperparasite
hyperparasitoidized by
hyperparasitized_by
hyperparasitized by
RO:0002556
pathogen_of
pathogen of
RO:0002557
has_pathogen
has pathogen
causally influenced by (entity-centric)
RO:0002559
causally_influenced_by
causally influenced by
RO:0002563
interaction_relation_helper_property
interaction relation helper property
http://purl.obolibrary.org/obo/ro/docs/interaction-relations/
RO:0002564
molecular_interaction_relation_helper_property
molecular interaction relation helper property
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
GO:0008150
CL:0000000 WBbt:0004017
Use this relation to link a locomotion process to the type of cell or anatomical structure or organism that the process results in locomotion of.
GOREL:0001001
RO:0002565
go/extensions/gorel
results_in_movement_of
For movement of chemicals or cell parts, please use transports_or_maintains_localization_of
results in movement of
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
causally influences (entity-centric)
RO:0002566
causally_influences
causally influences
RO:0002574
participates_in_a_biotic-biotic_interaction_with
participates in a biotic-biotic interaction with
p directly regulates q iff p is immediately causally upstream of q and p regulates q.
directly regulates (processual)
BFO:0000015
BFO:0000015
RO:0002578
directly_regulates
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
RO:0002584
has_part_structure_that_is_capable_of
has part structure that is capable of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
RO:0002595
causal_relation_between_material_entity_and_a_process
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
RO:0002596
capable_of_regulating
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
RO:0002597
capable_of_negatively_regulating
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
RO:0002598
capable_of_positively_regulating
capable of positively regulating
Inverse of 'causal agent in process'
RO:0002608
process_has_causal_agent
process has causal agent
p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q.
directly positively regulates (process to process)
BFO:0000015
BFO:0000015
RO:0002629
directly_positively_regulates
directly positively regulates
https://wiki.geneontology.org/Directly_positively_regulates
p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q.
directly negatively regulates (process to process)
BFO:0000015
BFO:0000015
RO:0002630
directly_negatively_regulates
directly negatively regulates
https://wiki.geneontology.org/Directly_negatively_regulates
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
RO:0003000
produces
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
a produced_by b iff some process that occurs_in b has_output a.
GO:0005575
CL:0000000
Use this relation to link a cell component that is the product of a cell, to the cell-type that produced it. Examples include recording the cell type that produces an exosome, an LDL, or a secreted ECM component.
RO:0003001
produced_by
produced by
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
2018-01-25T23:20:13Z
RO:0004031
enables_subfunction
enables subfunction
2018-01-26T23:49:30Z
RO:0004032
acts_upstream_of_or_within,_positive_effect
acts upstream of or within, positive effect
https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect
2018-01-26T23:49:51Z
RO:0004033
acts_upstream_of_or_within,_negative_effect
acts upstream of or within, negative effect
https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
2018-01-26T23:53:14Z
RO:0004034
acts_upstream_of,_positive_effect
acts upstream of, positive effect
https://wiki.geneontology.org/Acts_upstream_of,_positive_effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
2018-01-26T23:53:22Z
RO:0004035
acts_upstream_of,_negative_effect
acts upstream of, negative effect
https://wiki.geneontology.org/Acts_upstream_of,_negative_effect
2018-03-13T23:55:05Z
RO:0004046
causally_upstream_of_or_within,_negative_effect
causally upstream of or within, negative effect
https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect
2018-03-13T23:55:19Z
RO:0004047
causally_upstream_of_or_within,_positive_effect
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
RO:0011002
regulates_activity_of
regulates activity of
p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q.
2022-09-26T06:07:17Z
RO:0012011
indirectly_causally_upstream_of
indirectly causally upstream of
p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q.
2022-09-26T06:08:01Z
RO:0012012
indirectly_regulates
indirectly regulates
A diagnostic testing device utilizes a specimen.
X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
2021-11-08T12:00:00Z
utilizes
RO:0017001
device_utilizes_material
device utilizes material
A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.
RO:0019000
regulates_characteristic
regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.
RO:0019001
positively_regulates_characteristic
positively regulates characteristic
A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.
RO:0019002
negatively_regulates_characteristic
negatively regulates characteristic
p has anatomical participant c iff p has participant c, and c is an anatomical entity
2018-09-26T01:08:58Z
RO:0040036
results_in_changes_to_anatomical_or_cellular_structure
results in changes to anatomical or cellular structure
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
quality
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
specifically dependent continuant
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
generically dependent continuant
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CALOHA:TS-2035
FBbt:00007002
FMA:68646
GO:0005623
KUPO:0000002
MESH:D002477
VHOG:0001533
WBbt:0004017
XAO:0003012
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CARO:mah
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
molecular function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.
GOC:pdt
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
jl
2012-09-19T15:05:24Z
Wikipedia:Biological_process
biological process
physiological process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
true
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
curation status specification
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
PERSON:Bill Bug
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
curation status specification
organism
animal
fungus
plant
virus
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
GROUP: OBI Biomaterial Branch
WEB: http://en.wikipedia.org/wiki/Organism
organism
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
PATO:0001199
linear
A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel.
ISBN:0881923214
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
SCTID:362889002
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
http://dbpedia.org/ontology/AnatomicalStructure
biological structure
connected biological structure
UBERON:0000061
anatomical structure
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CARO:0000003
connected biological structure
CARO:0000003
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
UBERON:0000465
material anatomical entity
Anatomical entity that has mass.
http://orcid.org/0000-0001-9114-8737
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
AAO:0010841
AEO:0000000
BILA:0000000
BIRNLEX:6
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
UBERON:0001062
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
FMA:62955
http://orcid.org/0000-0001-9114-8737
UMLS:C1515976
ncithesaurus:Anatomic_Structure_System_or_Substance
example to be eventually removed
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
organizational term
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
to be replaced with external ontology term
Terms with this status should eventually replaced with a term from another ontology.
Alan Ruttenberg
group:OBI
to be replaced with external ontology term
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
requires discussion
OBSOLETE. Was not defined before obsoletion.
OBSOLETE. Was not defined before obsoletion.
OBSOLETE. Was not defined before obsoletion.
GO:0003674
GO:0003674
GO:0003674
GO:0003674
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).