Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) Prefix(rdfs:=) Ontology( Import() Annotation( "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") Annotation( "external") Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty(owl:deprecated)) ############################ # Annotation Properties ############################ # Annotation Property: (definition) AnnotationAssertion(rdfs:label "definition") # Annotation Property: (term replaced by) AnnotationAssertion(rdfs:label "term replaced by") # Annotation Property: (display label for users) AnnotationAssertion(rdfs:label "display label for users") SubAnnotationPropertyOf( ) # Annotation Property: () AnnotationAssertion(rdfs:comment "GO biological process") SubAnnotationPropertyOf( ) # Annotation Property: () AnnotationAssertion(rdfs:comment "cell or anatomical") SubAnnotationPropertyOf( ) # Annotation Property: () AnnotationAssertion(rdfs:comment "GO cellular component") SubAnnotationPropertyOf( ) # Annotation Property: () AnnotationAssertion(rdfs:comment "Chemical") SubAnnotationPropertyOf( ) # Annotation Property: () AnnotationAssertion(rdfs:comment "Developmental stages") SubAnnotationPropertyOf( ) # Annotation Property: () AnnotationAssertion(rdfs:comment "GO molecular function") SubAnnotationPropertyOf( ) # Annotation Property: () AnnotationAssertion(rdfs:comment "Sequence feature") SubAnnotationPropertyOf( ) # Annotation Property: () AnnotationAssertion(rdfs:comment "Protein, protein complex, gene or transcript identifier") SubAnnotationPropertyOf( ) # Annotation Property: () SubAnnotationPropertyOf( ) # Annotation Property: () SubAnnotationPropertyOf( ) # Annotation Property: () SubAnnotationPropertyOf( ) # Annotation Property: (subset_property) AnnotationAssertion(rdfs:label "subset_property") # Annotation Property: (synonym_type_property) AnnotationAssertion(rdfs:label "synonym_type_property") # Annotation Property: (consider) AnnotationAssertion(rdfs:label "consider") # Annotation Property: (has_alternative_id) AnnotationAssertion(rdfs:label "has_alternative_id") # Annotation Property: (has_broad_synonym) AnnotationAssertion(rdfs:label "has_broad_synonym") # Annotation Property: (database_cross_reference) AnnotationAssertion(rdfs:label "database_cross_reference") # Annotation Property: (has exact synonym) AnnotationAssertion(rdfs:label "has_exact_synonym") # Annotation Property: (has narrow synonym) AnnotationAssertion(rdfs:label "has_narrow_synonym") # Annotation Property: (has_obo_format_version) AnnotationAssertion(rdfs:label "has_obo_format_version") # Annotation Property: (has_obo_namespace) AnnotationAssertion(rdfs:label "has_obo_namespace") # Annotation Property: (has_related_synonym) AnnotationAssertion(rdfs:label "has_related_synonym") # Annotation Property: (has_synonym_type) AnnotationAssertion(rdfs:label "has_synonym_type") # Annotation Property: (in_subset) AnnotationAssertion(rdfs:label "in_subset") # Annotation Property: (shorthand) AnnotationAssertion(rdfs:label "shorthand") ############################ # Object Properties ############################ # Object Property: (part of) AnnotationAssertion( "BFO:0000001") AnnotationAssertion( "CL:0000000 GO:0005575 GO:0008150 PO:0009012 PO:0025131 UBERON:0001062 ZFS:0100000 WBls:0000075 WBbt:0004017 WBbt:0005766 NCBITaxon:1") AnnotationAssertion( "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.") AnnotationAssertion( "BFO:0000050") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "part of") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "part_of") SubObjectPropertyOf( ) # Object Property: (occurs in) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1 FBbt:10000000") AnnotationAssertion( "Identifies the cell, tissue, cellular component or anatomical entity within which all parts of the molecular function or biological process occurs") AnnotationAssertion( "BFO:0000066") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "in") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "occurs_in") AnnotationAssertion(rdfs:comment "Previous definition \"p occurs_in c if and only if all of the participants of p are part_of c.\" [BFO:cjm]") SubObjectPropertyOf( ) # Object Property: (go annotation extension relation) AnnotationAssertion(rdfs:label "go annotation extension relation") # Object Property: (during) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "BFO:0000007 WBls:0000075 ZFS:0100000") AnnotationAssertion( "Identifies a process or life stage during which a molecular function or biological process occurs or a cellular component is present") AnnotationAssertion( "GOREL:0000002") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "during") AnnotationAssertion(rdfs:label "during") TransitiveObjectProperty() ObjectPropertyRange( ) # Object Property: (obsolete localizes_to) AnnotationAssertion(Annotation( "BFO:cjm") "OBSOLETE. c localizes_to d if c executes some function when it is part_of d.") AnnotationAssertion( "BFO:0000004") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766") AnnotationAssertion( "OBSOLETE. c localizes_to d if c executes some function when it is part_of d.") AnnotationAssertion( "GOREL:0000003") AnnotationAssertion(Annotation( "GOC:mah") "localization_destination") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "localizes_to") AnnotationAssertion(rdfs:comment "TODO : check this one. Note Pombe is using different variant.") AnnotationAssertion(rdfs:label "obsolete localizes_to") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (obsolete dependent_on) AnnotationAssertion(Annotation( "GOC:rph") "OBSOLETE. Identifies a requirement under which the ontology term is observed to apply to the annotated gene product.") AnnotationAssertion( "Identifies a requirement under which the ontology term is observed to apply to the annotated gene product.") AnnotationAssertion( "GOREL:0000004") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "dependent on") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "dependent_on") AnnotationAssertion(rdfs:comment "PomBase uses the more specific child relations, and avoids using dependent_on directly.") AnnotationAssertion(rdfs:label "obsolete dependent_on") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete has_target_cell) AnnotationAssertion( "OBSOLETE. Was not defined before obsoletion.") AnnotationAssertion( "BFO:0000001") AnnotationAssertion( "CL:0000000 WBbt:0004017") AnnotationAssertion( "has_input") AnnotationAssertion( "has_output") AnnotationAssertion( "GOREL:0000006") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_target_cell") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "obsolete has_target_cell") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (obsolete has_target_anatomical_entity) AnnotationAssertion( "OBSOLETE. Was not defined before obsoletion.") AnnotationAssertion( "BFO:0000001") AnnotationAssertion( "CARO:0000000") AnnotationAssertion( "has_input") AnnotationAssertion( "has_output") AnnotationAssertion( "GOREL:0000007") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_target_anatomical_entity") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "obsolete has_target_anatomical_entity") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (obsolete localization_dependent_on) AnnotationAssertion(Annotation( "GOC:rph") "OBSOLETE. Identifies a requirement under which the gene product is located at the specified cellular component.") AnnotationAssertion( "Identifies a requirement under which the gene product is located at the specified cellular component.") AnnotationAssertion( "GOREL:0000009") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "localized by") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "localization_dependent_on") AnnotationAssertion(rdfs:comment "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]") AnnotationAssertion(rdfs:label "obsolete localization_dependent_on") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (obsolete requires_sequence_feature) AnnotationAssertion(Annotation( "GOC:mah") "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.") AnnotationAssertion( "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.") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "requires") AnnotationAssertion(Annotation( "GOC:mah") "requires_feature") AnnotationAssertion( "GOREL:0000010") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "requires_sequence_feature") AnnotationAssertion(rdfs:comment "strictly speaking, these fall outside the scope of GO, even with extended annotations") AnnotationAssertion(rdfs:label "obsolete requires_sequence_feature") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (obsolete requires_regulator) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. Annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process.") AnnotationAssertion( "annotated gene product requires regulation by the gene product or complex for its participation in the Molecular Function or Biological Process") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "requires") AnnotationAssertion( "GOREL:0000011") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "requires_regulator") AnnotationAssertion(rdfs:label "obsolete requires_regulator") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (obsolete requires_substance) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance") AnnotationAssertion( " The annotated gene product participates in a Biological Process or executes a Molecular Function only in the presence of a substance") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "requires") AnnotationAssertion( "GOREL:0000012") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "requires_substance") AnnotationAssertion(rdfs:label "obsolete requires_substance") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (independent_of) AnnotationAssertion(Annotation( "GOA:rph") "Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product.") AnnotationAssertion( "BFO:0000001") AnnotationAssertion( "CHEBI:24431 GO:0003674 GO:0005575 GO:0008150 GO:0032991 MI:0315 MOD:00000 PR:000000001 SO:0000110 SO:0000673 SO:0000704") AnnotationAssertion( "Identifies an entity that was shown not to be required for the ontology term to apply to the annotated gene product.") AnnotationAssertion( "not_dependent_on") AnnotationAssertion( "GOREL:0000013") AnnotationAssertion(Annotation( "GOC:rph") "independent_of") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "not dependent on") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "independent_of") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "independent_of") ObjectPropertyDomain( ) # Object Property: (obsolete inhibits_protease) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. Identifies a specific target of regulation of a MF") AnnotationAssertion( "GO:0010466") AnnotationAssertion( "PR:000000001 SO:0000673") AnnotationAssertion( "OBSOLETE. Identifies a specific target of regulation of a MF") AnnotationAssertion( "GOREL:0000014") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "inhibits_protease") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "obsolete inhibits_protease") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (has_regulation_target) AnnotationAssertion( "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697") AnnotationAssertion( "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'.") AnnotationAssertion(Annotation( ) "regulates") AnnotationAssertion( "GOREL:0000015") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_regulation_target") AnnotationAssertion(rdfs:comment "probably want to add one or two new subtypes that capture something about directness") AnnotationAssertion(rdfs:label "has_regulation_target") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (obsolete protease_activator) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. Identifies a specific target of regulation of a MF") AnnotationAssertion( "GO:0010952") AnnotationAssertion( "PR:000000001 SO:0000673") AnnotationAssertion( "OBSOLETE. Identifies a specific target of regulation of a MF") AnnotationAssertion( "GOREL:0000017") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "protease_activator") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "obsolete protease_activator") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (obsolete stabilizes) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)") AnnotationAssertion( "GO:0031647") AnnotationAssertion( "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697") AnnotationAssertion( "Identifies specific gene product stabilized in a protein stabilization process (or regulation thereof)") AnnotationAssertion( "GOREL:0000018") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "stabilizes") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "stabilizes") AnnotationAssertion(rdfs:comment "Obsoleted, see https://github.com/geneontology/go-ontology/issues/18540.") AnnotationAssertion(rdfs:label "obsolete stabilizes") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete has_upstream_or_downstream_target) AnnotationAssertion( "OBSOLETE. Was not defined before obsoletion.") AnnotationAssertion( "GO:0008150") AnnotationAssertion( "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion( "GOREL:0000020") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_upstream_or_downstream_target") AnnotationAssertion(rdfs:label "obsolete has_upstream_or_downstream_target") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (obsolete has_upstream_target) AnnotationAssertion( "OBSOLETE. Was not defined before obsoletion.") AnnotationAssertion( "GO:0008150") AnnotationAssertion( "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion( "GOREL:0000021") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_upstream_target") AnnotationAssertion(rdfs:label "obsolete has_upstream_target") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (obsolete has_downstream_target) AnnotationAssertion( "OBSOLETE. Was not defined before obsoletion.") AnnotationAssertion( "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion( "GOREL:0000022") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_downstream_target") AnnotationAssertion(rdfs:label "obsolete has_downstream_target") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete transcriptionally_regulates) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. Identifies gene whose transcription is regulated") AnnotationAssertion( "has_regulation_target") AnnotationAssertion( "GO:0006355") AnnotationAssertion( "OBSOLETE. Identifies gene whose transcription is regulated") AnnotationAssertion( "GOREL:0000023") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "transcriptionally_regulates") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "obsolete transcriptionally_regulates") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (obsolete not_during) AnnotationAssertion(Annotation( "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).") AnnotationAssertion( "BFO:0000001") AnnotationAssertion( "BFO:0000007 WBls:0000075 ZFS:0100000") AnnotationAssertion( "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).") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "except during") AnnotationAssertion( "GOREL:0000024") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "not_during") AnnotationAssertion(rdfs:comment "This relation was obsoleted because GO-CAM specifications does not allow negative relations.") AnnotationAssertion(rdfs:comment "domain can be any process or object or even quality") AnnotationAssertion(rdfs:label "obsolete not_during") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete not_happens_during) AnnotationAssertion(Annotation( "GOC:mah") "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).") AnnotationAssertion( "BFO:0000007") AnnotationAssertion( "BFO:0000007 WBls:0000075 ZFS:0100000") AnnotationAssertion( "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).") AnnotationAssertion(Annotation( "PomBase:curators") "except during") AnnotationAssertion( "GOREL:0000025") AnnotationAssertion(Annotation( "GOC:mah") "does_not_happen_during") AnnotationAssertion(Annotation( "GOC:mah") "not_occurs_during") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "not_happens_during") AnnotationAssertion(rdfs:comment "This relation was obsoleted because GO-CAM specifications does not allow negative relations.") AnnotationAssertion(rdfs:label "obsolete not_happens_during") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete not_exists_during) AnnotationAssertion(Annotation( "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).") AnnotationAssertion( "BFO:0000004") AnnotationAssertion( "BFO:0000007 WBls:0000075 ZFS:0100000") AnnotationAssertion( "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).") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "except during") AnnotationAssertion( "GOREL:0000026") AnnotationAssertion(Annotation( "GOC:mah") "does_not_exist_during") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "not_exists_during") AnnotationAssertion(rdfs:comment "This relation was obsoleted because GO-CAM specifications does not allow negative relations.") AnnotationAssertion(rdfs:label "obsolete not_exists_during") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete in_presence_of) AnnotationAssertion(Annotation( "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.") AnnotationAssertion( "BFO:0000001") AnnotationAssertion( "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion( "Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product.") AnnotationAssertion( "GOREL:0000027") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "in presence of") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "in_presence_of") AnnotationAssertion(rdfs:comment "This relation was obsoleted because it does not follow GO-CAM specifications.") AnnotationAssertion(rdfs:label "obsolete in_presence_of") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete requires_localization) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component") AnnotationAssertion( "The annotated gene product participates in a Biological Process only if the gene product is located at a Cellular Component") AnnotationAssertion( "GOREL:0000028") AnnotationAssertion(Annotation( "GOC:mah") "dependent_on_localization") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "only when located at") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "requires_localization") AnnotationAssertion(rdfs:label "obsolete requires_localization") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (obsolete requires_regulation_by) AnnotationAssertion(Annotation( "GOC:mah") "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)") AnnotationAssertion( "BFO:0000007") AnnotationAssertion( "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion( "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)") AnnotationAssertion( "GOREL:0000029") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "requires regulation by") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "requires_regulation_by") AnnotationAssertion(rdfs:label "obsolete requires_regulation_by") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (obsolete modified_by) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. Identifies the gene product that catalyzes a modification on the annotated gene product") AnnotationAssertion( "MOD:00000") AnnotationAssertion( "GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion( "Identifies the gene product that catalyzes a modification on the annotated gene product") AnnotationAssertion( "GOREL:0000030") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "modified by") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "modified_by") AnnotationAssertion(rdfs:comment "http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation") AnnotationAssertion(rdfs:label "obsolete modified_by") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete condition) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. Identifies a condition under which the ontology term is observed to apply to the annotated gene product") AnnotationAssertion( "Identifies a condition under which the ontology term is observed to apply to the annotated gene product") AnnotationAssertion( "GOREL:0000031") AnnotationAssertion(Annotation( "GOC:mah") "assay_condition") AnnotationAssertion(Annotation( "GOC:mah") "under_condition") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "condition") AnnotationAssertion(rdfs:label "obsolete condition") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (exists_during) AnnotationAssertion( "BFO:0000004") AnnotationAssertion( "GO:0008150 WBls:0000075 ZFS:0100000") AnnotationAssertion( "Identifies a process or life stage during which a cellular component is present") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "during") AnnotationAssertion( "GOREL:0000032") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "exists_during") AnnotationAssertion(rdfs:comment "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]") AnnotationAssertion(rdfs:label "exists_during") SubObjectPropertyOf( ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (obsolete requires_direct_regulator) AnnotationAssertion(Annotation( "GOC:mah") "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.") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0000033") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "requires direct regulation by") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "requires_direct_regulator") AnnotationAssertion(rdfs:comment "the gene product in the extension should be annotated to a \"regulator\" MF (implying that it acts directly to regulate the annotated gp activity)") AnnotationAssertion(rdfs:label "obsolete requires_direct_regulator") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) # Object Property: (regulates_o_transports_or_maintains_localization_of) AnnotationAssertion( "pg") AnnotationAssertion( "2020-08-28T07:03:28Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "regulates_o_transports_or_maintains_localization_of"@en) ObjectPropertyRange( ) # Object Property: (obsolete occurs at) AnnotationAssertion( "Identifies the Cellular Component or sequence feature adjacent to or in the vicinity of which the Molecular Function or Biological Process is executed") AnnotationAssertion( "GOREL:0000501") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "at") AnnotationAssertion( "occurs_at") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "obsolete occurs at") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete requires_modification) AnnotationAssertion(Annotation( "GOC:mah") "OBSOLETE. Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process.") AnnotationAssertion( "Annotated gene product must be modified as described by extension to participate in the Molecular Function or Biological Process.") AnnotationAssertion( "GOREL:0000502") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "only with modification") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "requires_modification") AnnotationAssertion(rdfs:comment "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") AnnotationAssertion(rdfs:label "obsolete requires_modification") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (obsolete not_occurs_in) AnnotationAssertion(Annotation( "GOC:mah") "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.") AnnotationAssertion( "BFO:0000007") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0000506") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "not in") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "not_occurs_in") AnnotationAssertion(rdfs:comment "This relation was obsoleted because GO-CAM specifications does not allow negative relations.") AnnotationAssertion(rdfs:label "obsolete not_occurs_in") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (activated_by) AnnotationAssertion( "Identifies a chemical substance that increases the activity of the gene product.") AnnotationAssertion( "GOREL:0000507") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "activated by") AnnotationAssertion(Annotation( "GOC:mah") "activated_by_chemical") AnnotationAssertion(Annotation( "GOC:mah") "activated_by_substance") AnnotationAssertion(Annotation( "GOC:mah") "activity_increased_by") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "activated_by") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "activated_by") # Object Property: (inhibited_by) AnnotationAssertion(Annotation( "GOC:mah") "Identifies a chemical substance that decreases the activity of the gene product.") AnnotationAssertion( "Identifies a chemical substance that decreases the activity of the gene product.") AnnotationAssertion( "GOREL:0000508") AnnotationAssertion(Annotation( "GOC:mah") "activity_decreased_by") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "inhibited by") AnnotationAssertion(Annotation( "GOC:mah") "inhibited_by_chemical") AnnotationAssertion(Annotation( "GOC:mah") "inhibited_by_substance") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "inhibited_by") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "inhibited_by") # Object Property: (obsolete not_occurs_at) AnnotationAssertion(Annotation( "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.") AnnotationAssertion( "BFO:0000007") AnnotationAssertion( "GO:0005575 SO:0000110") AnnotationAssertion( "An entity (e.g. Cellular Component, sequence feature) at which a Biological Process or Molecular Function does not occur. Opposite of occurs_at.") AnnotationAssertion( "GOREL:0000509") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "not at") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "not_occurs_at") AnnotationAssertion(rdfs:comment "This relation was obsoleted because GO-CAM specifications does not allow negative relations.") AnnotationAssertion(rdfs:label "obsolete not_occurs_at") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete has_indirect_input) AnnotationAssertion( "OBSOLETE. Was not defined before obsoletion.") AnnotationAssertion( "BFO:0000007") AnnotationAssertion( "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion( "Identifies an entity indirectly affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in MF or BP.") AnnotationAssertion( "GOREL:0000505") AnnotationAssertion( "has_indirect_target") AnnotationAssertion( "indirectly_localizes") AnnotationAssertion( "GOREL:0000751") AnnotationAssertion(Annotation( "GOC:ecd") "has_indirect_target") AnnotationAssertion(Annotation( "GOC:ecd") "indirectly_localizes") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_indirect_input") AnnotationAssertion(rdfs:comment "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]") AnnotationAssertion(rdfs:label "obsolete has_indirect_input") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete has_direct_input) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0000019") AnnotationAssertion( "GOREL:0000504") AnnotationAssertion( "directly_localizes") AnnotationAssertion( "has_direct_target") AnnotationAssertion( "has_substrate") AnnotationAssertion( "GOREL:0000752") AnnotationAssertion(Annotation( "GOC:ecd") "has_direct_target") AnnotationAssertion(Annotation( "GOC:ecd") "directly_localizes") AnnotationAssertion(Annotation( "GOC:ecd") "has_substrate") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_direct_input") AnnotationAssertion(rdfs:comment "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]") AnnotationAssertion(rdfs:comment "This relation is part of the ShEx speficications.") AnnotationAssertion(rdfs:label "obsolete has_direct_input") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete requires_target_sequence_feature) AnnotationAssertion(Annotation( "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") AnnotationAssertion( "BFO:0000001") AnnotationAssertion( "SO:0000110") AnnotationAssertion( "Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurance of the function or process") AnnotationAssertion( "GOREL:0000754") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "requires feature in target") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "requires_target_sequence_feature") AnnotationAssertion(rdfs:label "obsolete requires_target_sequence_feature") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (obsolete in_absence_of) AnnotationAssertion(Annotation( "GOC:rph") "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.") AnnotationAssertion( "BFO:0000001") AnnotationAssertion( "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion( "Identifies a chemical, gene product or complex in the absence of which an ontology term is observed to apply to the annotated gene product.") AnnotationAssertion( "GOREL:0000755") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "in_absence_of") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:comment "This relation was obsoleted because it does not follow GO-CAM specifications.") AnnotationAssertion(rdfs:label "obsolete in_absence_of") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (axis_of) AnnotationAssertion( "GOREL:0001000") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "axis_of") AnnotationAssertion(rdfs:label "axis_of") # Object Property: (has_output_o_axis_of) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:mtg_berkeley_2012_08_27") "This is the combination of the has_output relation with the axis_of relation") AnnotationAssertion( "This is the combination of the has_output relation with the axis_of relation") AnnotationAssertion( "GOREL:0001002") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_output_o_axis_of") AnnotationAssertion(rdfs:comment "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") AnnotationAssertion(rdfs:label "has_output_o_axis_of") # Object Property: (regulates_o_has_output) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:mtg_berkeley_2012_08_27") "This is the combination of the regulates relation with the has_output relation") AnnotationAssertion( "This is the combination of the regulates relation with the has_output relation") AnnotationAssertion( "GOREL:0001003") AnnotationAssertion( "regulates_o_has_output") AnnotationAssertion(rdfs:label "regulates_o_has_output") # Object Property: (regulates process that occurs in) AnnotationAssertion( "'negative regulation of chromosome segregation' that regulates_o_occurs_in some spermatocyte.") AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dph") Annotation( "GOC:mtg_berkeley_2012_08_27") "A relation that holds between a regulatory process and the entity which the regulated biological process or molecular function occurs in.") AnnotationAssertion( "Use this relation to link a regulatory process or function to the structure that the regulated process or function occurs in.") AnnotationAssertion( "GOREL:0001004") AnnotationAssertion( "regulates_o_occurs_in") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "regulates_o_occurs_in") AnnotationAssertion(rdfs:label "regulates process that occurs in") # Object Property: (regulates process that results in movement of) AnnotationAssertion(Annotation( "GOC:cjm") Annotation( "GOC:dph") Annotation( "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.") AnnotationAssertion( "Use this relation to relate a process that regulates locomotion to the cell or organism whose locomotion is being regulated.") AnnotationAssertion( "GOREL:0001005") AnnotationAssertion( "regulates_o_results_in_movement_of") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "regulates_o_results_in_movement_of") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "regulates process that results in movement of") ObjectPropertyDomain( ) # Object Property: (obsolete acts_on_population_of) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "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.") AnnotationAssertion( "RO:0012003") AnnotationAssertion( "GO:0008283") AnnotationAssertion( "CL:0000000 WBbt:0004017") AnnotationAssertion( "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.)") AnnotationAssertion( "alters levels of") AnnotationAssertion( "GOREL:0001006") AnnotationAssertion( "RO:0012003") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "acts_on_population_of") AnnotationAssertion(rdfs:comment "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?") AnnotationAssertion(rdfs:label "obsolete acts_on_population_of") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) SubObjectPropertyOf( ) ObjectPropertyDomain( ) # Object Property: (obsolete mediated by) AnnotationAssertion( ) AnnotationAssertion( "pg") AnnotationAssertion( "2019-11-21T19:16:04Z"^^xsd:dateTime) AnnotationAssertion( "GOREL:0001007") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "mediated_by") AnnotationAssertion(rdfs:label "obsolete mediated by"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete regulates process that acts on population of) AnnotationAssertion( "'positive regulation of cell proliferation' and 'regulates process that acts on population of' some 'stem cell'") AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "A relation that applies between a regulatory process and a population of entities that a process it regulates acts on.") AnnotationAssertion( "This is the combination of the regulates relation with the acts_on_population_of relation.") AnnotationAssertion( "GOREL:0001008") AnnotationAssertion( "regulates_o_acts_on_population_of") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "regulates_o_acts_on_population_of") AnnotationAssertion(rdfs:label "obsolete regulates process that acts on population of") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (regulates acquisition of features of) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "This is the combination of the regulates relation with the results_in_acquisition_of_features_of relation.") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001010") AnnotationAssertion( "regulates differentiation of") AnnotationAssertion( "regulates_o_results_in_acquisition_of_features_of") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "regulates_o_results_in_acquisition_of_features_of") AnnotationAssertion(rdfs:label "regulates acquisition of features of") # Object Property: (regulates_o_has_agent) AnnotationAssertion(Annotation( "GOC:dos") "A relationship between the regulation of a process and the agent that executes that process.") AnnotationAssertion( "GOREL:0001011") AnnotationAssertion( "regulates_o_has_agent") AnnotationAssertion(rdfs:label "regulates_o_has_agent") ObjectPropertyRange( ) # Object Property: (regulates maturation of) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "This is the combination of the regulates relation with the results_in_maturation_of relation.") AnnotationAssertion( "This is the combination of the regulates relation with the results_in_maturation_of relation.") AnnotationAssertion( "GOREL:0001012") AnnotationAssertion( "regulates_o_results_in_maturation_of") AnnotationAssertion(rdfs:label "regulates maturation of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) # Object Property: (regulates_o_has_participant) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "This is the combination of the regulates relation with the has_participant relation.") AnnotationAssertion( "Use this relationship to link a regulatory process or function to an entity that participates in the regulated process.") AnnotationAssertion( "GOREL:0001016") AnnotationAssertion( "regulates_o_has_participant") AnnotationAssertion(rdfs:label "regulates_o_has_participant") # Object Property: (results_in_division_of) AnnotationAssertion(Annotation( "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.") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CL:0000000 WBbt:0004017") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001019") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_division_of") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "results_in_division_of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (regulates commitment to) AnnotationAssertion(Annotation( "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.") AnnotationAssertion( "This is the combination of the regulates relation with the results_in_commitment_to relation.") AnnotationAssertion( "GOREL:0001022") AnnotationAssertion( "regulates_o_results_in_commitment_to") AnnotationAssertion( "regulates_o_results_in_commitment_to") AnnotationAssertion(rdfs:label "regulates commitment to") ObjectPropertyRange( ) # Object Property: (regulates development of) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "This is the combination of the regulates relation with the results_in_development_of relation.") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001023") AnnotationAssertion( "regulates_o_results_in_development_of") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "regulates_o_results_in_development_of") AnnotationAssertion(rdfs:label "regulates development of") # Object Property: (regulates division of) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "This is the combination of the regulates relation with the results_in_division_of relation.") AnnotationAssertion( "This is the combination of the regulates relation with the results_in_division_of relation.") AnnotationAssertion( "GOREL:0001024") AnnotationAssertion( "regulates_o_results_in_division_of") AnnotationAssertion(rdfs:label "regulates division of") # Object Property: (regulates formation of) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "This is the combination of the regulates relation with the results_in_formation_of relation.") AnnotationAssertion( "This is the combination of the regulates relation with the results_in_formation_of relation.") AnnotationAssertion( "GOREL:0001025") AnnotationAssertion( "regulates_o_results_in_formation_of") AnnotationAssertion(rdfs:label "regulates formation of") # Object Property: (regulates morphogenesis of) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "This is the combination of the regulates relation with the results_in_morphogenesis_of relation.") AnnotationAssertion( "This is the combination of the regulates relation with the results_in_morphogenesis_of relation.") AnnotationAssertion( "GOREL:0001026") AnnotationAssertion( "regulates_o_results_in_morphogenesis_of") AnnotationAssertion(rdfs:label "regulates morphogenesis of") ObjectPropertyDomain( ) # Object Property: (regulates specification of) AnnotationAssertion(Annotation( "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.") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001027") AnnotationAssertion( "regulates_o_results_in_specification_of") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "regulates_o_results_in_specification_of") AnnotationAssertion(rdfs:label "regulates specification of") # Object Property: (has_output_o_product_of) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "This is the combination of the has_output relation with the gene_product_of relation.") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "PR:000000001 SO:0000673") AnnotationAssertion( "This is the combination of the has_output relation with the results_in_specification_of relation.") AnnotationAssertion( "GOREL:0001029") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_output_o_product_of") AnnotationAssertion(rdfs:label "has_output_o_product_of") ObjectPropertyDomain( ) # Object Property: (regulates_o_has_input) AnnotationAssertion(Annotation( "GOC:dph") "This is the combination of the regulates relation with the has_input relation") AnnotationAssertion( "This is the combination of the regulates relation with the has_input relation") AnnotationAssertion( "GOREL:0001030") AnnotationAssertion( "regulates_o_has_input") AnnotationAssertion(rdfs:label "regulates_o_has_input") # Object Property: (obsolete has_intermediate) AnnotationAssertion( ) AnnotationAssertion( "pg") AnnotationAssertion( "2019-11-21T16:32:15Z"^^xsd:dateTime) AnnotationAssertion( "GOREL:0002008") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion(rdfs:label "obsolete has_intermediate"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete results_in_transport_to_from_or_mediated_by) AnnotationAssertion( "pg") AnnotationAssertion( "2019-11-21T18:00:03Z"^^xsd:dateTime) AnnotationAssertion( "GOREL:0002010") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:label "obsolete results_in_transport_to_from_or_mediated_by"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete regulates activity of) AnnotationAssertion( "OBSOLETE. A relation that holds between the regulation of a molecular function and the agent that executes that function.") AnnotationAssertion( "GO:0098772 GO:0065009") AnnotationAssertion( "GO:0032991 SO:0000374 PR:000000001") AnnotationAssertion( "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.") AnnotationAssertion( "regulates_activity_of") AnnotationAssertion(rdfs:comment "This relation has been obsoleted as it is not part of the GO ShEx specifications.") AnnotationAssertion(rdfs:label "obsolete regulates activity of") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete regulates transcription of) AnnotationAssertion( "OBSOLETE. A relationship that holds between a process and a gene whose transcription is regulated by that process.") AnnotationAssertion(Annotation( "GOC:dos") "Relates a regulatory process or function to the gene whose transcription it regulates.") AnnotationAssertion( "regulates_transcription_of") AnnotationAssertion(rdfs:comment "Usage of this relation has been deprecated in favor of 'has direct input'.") AnnotationAssertion(rdfs:label "obsolete regulates transcription of") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete regulates expression of) AnnotationAssertion( "OBSOLETE. A relationship that holds between a process and a gene whose expression is regulated by that process.") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion(Annotation( "GOC:dos") "Relates a regulatory process or function to the gene whose expression it regulates. Expression encompasses transcription, regulation and processing involved in maturation.") AnnotationAssertion( "regulates_expression_of") AnnotationAssertion(rdfs:comment "Usage of this relation has been deprecated in favor of 'has direct input'.") AnnotationAssertion(rdfs:label "obsolete regulates expression of") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (obsolete regulates translation of) AnnotationAssertion( "OBSOLETE. A relationship that holds between a process and a protein coding gene whose translation is regulated by that process.") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "PR:000000001 SO:0000673 SO:0000704") AnnotationAssertion(Annotation( "GOC:dos") "Relates a regulatory process or function to the gene whose translation it regulates.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "regulates_translation_of") AnnotationAssertion(rdfs:comment "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.") AnnotationAssertion(rdfs:comment "Usage of this relation has been deprecated in favor of 'has direct input'.") AnnotationAssertion(rdfs:label "obsolete regulates translation of") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Object Property: (has participant) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CARO:0000000") AnnotationAssertion( "Identifies an entity affected by the gene product's participation in a molecular function or biological process") AnnotationAssertion( "RO:0000057") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_participant") AnnotationAssertion(rdfs:comment "Do not use this relation directly") SubObjectPropertyOf( ) # Object Property: (coincident with) AnnotationAssertion( "GO:0005575") AnnotationAssertion( "CHEBI:24431 SO:0000001 SO:0000704") AnnotationAssertion( "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.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (regulates transport of) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CHEBI:24431 PR:000000001 GO:0005575 SO:0000673 CHEBI:33697") AnnotationAssertion( "Use this relation to link a process that regulates transport to the the entity being transported.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (happens during) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "GO:0008150 WBls:0000075 ZFS:0100000 UBERON:0000105") AnnotationAssertion( "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.") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "during") AnnotationAssertion(Annotation( "GOC:mah") "occurs_during") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "happens_during") AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (gene product of) AnnotationAssertion( "BFO:0000004") AnnotationAssertion( "BFO:0000002") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001028") AnnotationAssertion( "RO:0002204") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "gene_product_of") SubObjectPropertyOf( ) # Object Property: (regulates) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (negatively regulates) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (positively regulates) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (obsolete has active participant) AnnotationAssertion( "GO:0008150") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001007") AnnotationAssertion( "RO:0002218") AnnotationAssertion( "has_agent") AnnotationAssertion(rdfs:comment "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.") # Object Property: (adjacent to) AnnotationAssertion( "GO:0005575") AnnotationAssertion( "GO:0005575 CL:0000000") AnnotationAssertion( "RO:0002220") AnnotationAssertion(Annotation( ) "adjacent to") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "adjacent_to") SubObjectPropertyOf( ) # Object Property: (has start location) AnnotationAssertion( "") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1") AnnotationAssertion( "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.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_start_location") SubObjectPropertyOf( ) # Object Property: (has end location) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766 NCBITaxon:1") AnnotationAssertion( "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'.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_end_location") SubObjectPropertyOf( ) # Object Property: (has input) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697 SO:0000839 SO:0001683 NCBITaxon:1") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0000016") AnnotationAssertion( "GOREL:0000503") AnnotationAssertion( "GOREL:0000753") AnnotationAssertion( "has_target") AnnotationAssertion( "localizes") AnnotationAssertion( "GOREL:0000753") AnnotationAssertion( "RO:0002233") AnnotationAssertion(Annotation( "GOC:ecd") "has_target") AnnotationAssertion(Annotation( "GOC:ecd") "localizes") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_input") AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) # Object Property: (has output) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CHEBI:24431 GO:0032991 MI:0315 PR:000000001 SO:0000673 SO:0000704 CHEBI:33697") AnnotationAssertion( "Identifies an entity that is changed or created after participation in a molecular function or biological process") AnnotationAssertion( "RO:0002234") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_output") AnnotationAssertion(rdfs:comment "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.\" []") SubObjectPropertyOf( ) # Object Property: (results in development of) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001009") AnnotationAssertion( "RO:0002296") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) # Object Property: (results in formation of) AnnotationAssertion(Annotation( "GOC:mtg_berkeley_2013") "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.") AnnotationAssertion( "GO:0008150") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001020") AnnotationAssertion( "RO:0002297") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_formation_of") AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) # Object Property: (results in morphogenesis of) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001015") AnnotationAssertion( "RO:0002298") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) # Object Property: (results in maturation of) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CL:0000000 GO:0005575 PO:0009012 PO:0025131 UBERON:0001062 WBbt:0004017 WBbt:0005766") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001013") AnnotationAssertion( "RO:0002299") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_maturation_of") AnnotationAssertion(rdfs:comment ) AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) # Object Property: (transports or maintains localization of) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CHEBI:24431 PR:000000001 GO:0005575 SO:0000673 CHEBI:33697") AnnotationAssertion( "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.") AnnotationAssertion( "RO:0002313") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "regulates location of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "transports_or_maintains_localization_of") SubObjectPropertyOf( ) # Object Property: (results in acquisition of features of) AnnotationAssertion( "GO:0030154") AnnotationAssertion( "CL:0000000 PO:0009002 WBbt:0004017") AnnotationAssertion( "Use this relation to link a cell differentiation process to the cell type that the process results in the differentiation of.") AnnotationAssertion( "GOREL:0001014") AnnotationAssertion( "RO:0002315") AnnotationAssertion( "results in differentiation of") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) # Object Property: (colocalizes with) SubObjectPropertyOf( ) # Object Property: (contributes to) SubObjectPropertyOf( ) # Object Property: (enables) SubObjectPropertyOf( ) # Object Property: (involved in) SubObjectPropertyOf( ) # Object Property: (regulates levels of) AnnotationAssertion( "GOREL:0000036") AnnotationAssertion( "RO:0002332") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "regulates_level_of") SubObjectPropertyOf( ) # Object Property: (has target start location) AnnotationAssertion( "GO:0005575 CL:0000000 UBERON:0001062") AnnotationAssertion( "Use to relate a transport or localization process to the starting location of the cargo.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (has target end location) AnnotationAssertion( "GO:0005575 CL:0000000 UBERON:0001062") AnnotationAssertion( "Use to relate a transport or localization process to the end location of the transported or localized cargo.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (imports) AnnotationAssertion( "GOREL:0000034") AnnotationAssertion( "RO:0002340") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "imports") SubObjectPropertyOf( ) # Object Property: (exports) AnnotationAssertion( "GOREL:0000035") AnnotationAssertion( "RO:0002345") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "exports") SubObjectPropertyOf( ) # Object Property: (results in commitment to) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CL:0000000 WBbt:0004017") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001017") AnnotationAssertion( "RO:0002348") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_commitment_to") AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) ObjectPropertyRange( ) # Object Property: (results in determination of) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "CL:0000000 WBbt:0004017") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001018") AnnotationAssertion( "RO:0002349") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_determination_of") AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) # Object Property: (results in specification of) AnnotationAssertion( "GO:0008150") AnnotationAssertion( "CL:0000000 WBbt:0004017") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001021") AnnotationAssertion( "RO:0002356") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_specification_of") AnnotationAssertion(rdfs:comment ) AnnotationAssertion(rdfs:comment "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.") SubObjectPropertyOf( ) ObjectPropertyDomain( ) # Object Property: (causally upstream of) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "GO:0008150 GO:0003674") AnnotationAssertion( "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.") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally_upstream_of") SubObjectPropertyOf( ) # Object Property: (parasite of) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (host of) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (has host) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (existence overlaps) AnnotationAssertion( "BFO:0000004") AnnotationAssertion( "GO:0008150 WBls:0000075 ZFS:0100000") AnnotationAssertion( "Identifies a process or life stage during which a cellular component is present") AnnotationAssertion( "RO:0002490") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (existence starts and ends during) AnnotationAssertion( "BFO:0000004") AnnotationAssertion( "GO:0008150 WBls:0000075 ZFS:0100000") AnnotationAssertion( "Identifies a process or life stage during which a cellular component is present") AnnotationAssertion( "RO:0002491") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (pathogen of) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (has pathogen) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (results in movement of) AnnotationAssertion( "GO:0008150") AnnotationAssertion( "CL:0000000 WBbt:0004017") AnnotationAssertion( "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.") AnnotationAssertion( "GOREL:0001001") AnnotationAssertion( "RO:0002565") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_movement_of") AnnotationAssertion(rdfs:comment "For movement of chemicals or cell parts, please use transports_or_maintains_localization_of") SubObjectPropertyOf( ) # Object Property: (directly regulates) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (directly positively regulates) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) # Object Property: (directly negatively regulates) AnnotationAssertion( "BFO:0000015") AnnotationAssertion( "BFO:0000015") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) SubObjectPropertyOf( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) SubObjectPropertyOf(Annotation( "true") ObjectPropertyChain( ) ) AnnotationAssertion( "BFO:0000051") AnnotationAssertion(Annotation( "PomBase:curators") Annotation( ) "has part") AnnotationAssertion( "go/extensions/gorel") AnnotationAssertion( "has_part") AnnotationAssertion( "OBSOLETE. Was not defined before obsoletion.") AnnotationAssertion( "OBSOLETE. Was not defined before obsoletion.") AnnotationAssertion( "OBSOLETE. Was not defined before obsoletion.") AnnotationAssertion( "GO:0003674") AnnotationAssertion( "GO:0003674") AnnotationAssertion( ) AnnotationAssertion( "GO:0003674") AnnotationAssertion( "GO:0003674") AnnotationAssertion( ) AnnotationAssertion( "GO:0005575") AnnotationAssertion( "CL:0000000") AnnotationAssertion( "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.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) )