Annotation usage examples for each annotation extension relation: Difference between revisions
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[https://github.com/geneontology/go-ontology/blob/master/src/ontology/extensions/gorel.obo GO relationships OBO file] | |||
Back to [http://wiki.geneontology.org/index.php/Annotation_Extension Annotation Extension] | Back to [http://wiki.geneontology.org/index.php/Annotation_Extension Annotation Extension] | ||
Information on [[Folding and Unfolding]] | Information on [[Folding and Unfolding]] | ||
Annotation extension QuickGO graph [https://www.ebi.ac.uk/QuickGO/annotationExtensionRelations] | |||
In the list below the term available in the Annotation extension QuickGO graph ('AE graph') are compared to the term listed in RO | |||
'Align' means these have the same parents | |||
if the AE graph parent is listed then this means there is a difference between the RO term and the AE graph | |||
==Relations== | ==Relations== | ||
[[Annotation_Extension_Relation:acts_on_population_of|acts_on_population_of]] | [[Annotation_Extension_Relation:acts_on_population_of|acts_on_population_of]] - not in RO: in AE graph the parent for this term is 'has_participant' | ||
[[Annotation_Extension_Relation:has_agent|has_agent]] - not in RO: in AE graph the parent for this term is 'has_participant' | |||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:causally_upstream_of|causally_upstream_of]] - align, although in AE graph the parent for this term is 'root node' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:exists_during|exists_during]] - not in RO: in AE graph the parent for this term is 'root node' | ||
[[Annotation_Extension_Relation:happens_during|happens_during]] - align both have 'root node' as parent | |||
[[Annotation_Extension_Relation:has_participant|has_participant]] - align both have 'root node' as parent | |||
* [[Annotation_Extension_Relation: | * [[Annotation_Extension_Relation:has_input|has_input]] - align both have 'has_participant' as parent | ||
[[Annotation_Extension_Relation: | :* [[Annotation_Extension_Relation:stabilizes|stabilizes]] - not in RO: in AE graph the parent for this term is 'has_input' | ||
[[Annotation_Extension_Relation: | * [[Annotation_Extension_Relation:has_output|has_output]] - align both have 'has_participant' as parent | ||
[[Annotation_Extension_Relation: | :* [[Annotation_Extension_Relation:results_in_formation_of|results_in_formation_of]] - in both RO and AE graph, the parent for this term is 'has_output', although RO has additional parent terms too | ||
* [[Annotation_Extension_Relation: | * [[Annotation_Extension_Relation:results_in_acquisition_of_features_of|results_in_acquisition_of_features_of]] - in both but in AE graph the parent for this term is 'has_participant'; in RO there are other parent terms, although does have 'has participant' as a grandparent | ||
* [[Annotation_Extension_Relation:results_in_development_of|results_in_development_of]] - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent for this term is 'has_participant' | |||
* [[Annotation_Extension_Relation: | * [[Annotation_Extension_Relation:results_in_movement_of|results_in_movement_of]] - in both RO and AE graph, however in RO there one additional parent, although does have 'has participant' as a grandparent, in AE graph the parent for this term is 'has_participant' | ||
* [[Annotation_Extension_Relation: | * [[Annotation_Extension_Relation:results_in_morphogenesis_of|results_in_morphogenesis_of]] - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is 'has_participant' | ||
* [[Annotation_Extension_Relation: | * [[Annotation_Extension_Relation:results_in_maturation_of|results_in_maturation_of]] - in both but in AE graph the parent for this term is 'has_participant'; in RO there are other parent terms, although does have 'has participant' as a grandparent | ||
[[Annotation_Extension_Relation: | * [[Annotation_Extension_Relation:results_in_division_of|results_in_division_of]] - not in RO: in AE graph the parent for this term is 'has_participant' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:regulates_o_has_participant|regulates_o_has_participant]] - not in RO: in AE graph the parent for this term is 'root node' | ||
[[Annotation_Extension_Relation: | * [[Annotation_Extension_Relation:has_regulation_target|has_regulation_target]] - not in RO: in AE graph the parent for this term is 'regulates_o_has_participant' | ||
[[Annotation_Extension_Relation: | :* [[Annotation_Extension_Relation:regulates_o_has_input|regulates_o_has_input]] - not in RO: in AE graph the parent for this term is 'has_regulation_target' | ||
[[Annotation_Extension_Relation: | ::* [[Annotation_Extension_Relation:regulates_expression_of|regulates_expression_of]] - not in RO: in AE graph the parent for this term is 'regulates_o_has_input' | ||
[[Annotation_Extension_Relation: | :::* [[Annotation_Extension_Relation:regulates_transcription_of|regulates_transcription_of]] - not in RO: in AE graph the parent for this term is 'regulates_expression_of' | ||
[[Annotation_Extension_Relation: | :::* [[Annotation_Extension_Relation:regulates_translation_of|regulates_translation_of]] - not in RO: in AE graph the parent for this term is 'regulates_expression_of' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:occurs_at|occurs_at]] - not in RO: in AE graph the parent for this term is 'root node' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:occurs_in|occurs_in]] - Align both have 'root node' as parent | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:part_of|part_of]] - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is the 'root node' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:activated_by|activated_by]] - not in RO: in AE graph the parent for this term is 'root node' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:inhibited_by|inhibited_by]] - not in RO: in AE graph the parent for this term is 'root node' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:results_in_commitment_to|results_in_commitment_to]] - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is the 'root node' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:results_in_determination_of|results_in_determination_of]] - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is the 'root node' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:results_in_specification_of|results_in_specification_of]] - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is the 'root node' | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:has_part|has_part]] | ||
[[Annotation_Extension_Relation: | [[Annotation_Extension_Relation:during|during]] | ||
==Deprecated Relations== | ==Deprecated Relations== | ||
* [[Annotation_Extension_Relation:has_direct_input|has_direct_input]] | |||
* [[Annotation_Extension_Relation:requires_localization|requires_localization]] | * [[Annotation_Extension_Relation:requires_localization|requires_localization]] | ||
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* [[Annotation_Extension_Relation:requires_regulator|requires_regulator]] | * [[Annotation_Extension_Relation:requires_regulator|requires_regulator]] | ||
[[Annotation_Extension_Relation:requires_regulation_by|requires_regulation_by]] | * [[Annotation_Extension_Relation:requires_regulation_by|requires_regulation_by]] | ||
* [[Annotation_Extension_Relation:requires_direct_regulator|requires_direct_regulator]] | * [[Annotation_Extension_Relation:requires_direct_regulator|requires_direct_regulator]] | ||
[[Annotation_Extension_Relation:modified_by|modified_by]] | * [[Annotation_Extension_Relation:modified_by|modified_by]] | ||
[[Annotation_Extension_Relation:not_during|not_during]] | * [[Annotation_Extension_Relation:not_during|not_during]] | ||
* [[Annotation_Extension_Relation:not_exists_during|not_exists_during]] | * [[Annotation_Extension_Relation:not_exists_during|not_exists_during]] | ||
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* [[Annotation_Extension_Relation:not_happens_during|not_happens_during]] | * [[Annotation_Extension_Relation:not_happens_during|not_happens_during]] | ||
[[Annotation_Extension_Relation:not_occurs_at|not_occurs_at]] | * [[Annotation_Extension_Relation:not_occurs_at|not_occurs_at]] | ||
* [[Annotation_Extension_Relation:not_occurs_in|not_occurs_in]] | |||
* [[Annotation_Extension_Relation:dependent_on|dependent_on]] - old relation no longer listed in AE graph, not in RO | |||
* [[Annotation_Extension_Relation:localization_dependent_on|localization_dependent_on]] - old relation no longer listed in AE graph, not in RO | |||
* [[Annotation_Extension_Relation:requires_sequence_feature|requires_sequence_feature]] - old relation no longer listed in AE graph, not in RO | |||
* [[Annotation_Extension_Relation:requires_substance|requires_substance]] - old relation no longer listed in AE graph, not in RO | |||
* [[Annotation_Extension_Relation:in_absence_of|in_absence_of]] - old relation no longer listed in AE graph, not in RO | |||
* [[Annotation_Extension_Relation:in_presence_of|in_presence_of]] - old relation no longer listed in AE graph, not in RO | |||
* [[Annotation_Extension_Relation:independent_of|independent_of]] - old relation no longer listed in AE graph, not in RO | |||
* dependent_on | |||
==Relations in Protein2GO graph not in the lists above== | |||
produced_by | |||
adjacent_to | |||
coincident_with | |||
has_end_location | |||
has_start_location | |||
has_target_end_location | |||
has_target_start_location | |||
regulates | |||
* negatively_regulates | |||
* positively_regulates | |||
* directly_regulates | |||
** directly_negatively_regulates | |||
** directly_positively_regulates | |||
regulates_o_has_input | |||
* regulates_o_results_in_division_of | |||
* regulates_o_results_in_formation_of | |||
* regulates_o_results_in_maturation_of | |||
* regulates_o_results_in_movement_of | |||
* regulates_o_results_in_specification_of | |||
* regulates_o_results_in_acquisition_of_features_of | |||
* regulates_o_results_in_commitment_to | |||
** regulates_o_results_in_morphogenesis_of (parent has_regulation_target) | |||
** regulates_o_has_input (parent has_regulation_target) | |||
*** regulates_transport_of (parent regulates_o_has_input) | |||
[[Category:annotation extension]] | [[Category:annotation extension]] |
Revision as of 16:42, 20 January 2020
Back to Annotation Extension
Information on Folding and Unfolding
Annotation extension QuickGO graph [1]
In the list below the term available in the Annotation extension QuickGO graph ('AE graph') are compared to the term listed in RO
'Align' means these have the same parents
if the AE graph parent is listed then this means there is a difference between the RO term and the AE graph
Relations
acts_on_population_of - not in RO: in AE graph the parent for this term is 'has_participant'
has_agent - not in RO: in AE graph the parent for this term is 'has_participant'
causally_upstream_of - align, although in AE graph the parent for this term is 'root node'
exists_during - not in RO: in AE graph the parent for this term is 'root node'
happens_during - align both have 'root node' as parent
has_participant - align both have 'root node' as parent
- has_input - align both have 'has_participant' as parent
- stabilizes - not in RO: in AE graph the parent for this term is 'has_input'
- has_output - align both have 'has_participant' as parent
- results_in_formation_of - in both RO and AE graph, the parent for this term is 'has_output', although RO has additional parent terms too
- results_in_acquisition_of_features_of - in both but in AE graph the parent for this term is 'has_participant'; in RO there are other parent terms, although does have 'has participant' as a grandparent
- results_in_development_of - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent for this term is 'has_participant'
- results_in_movement_of - in both RO and AE graph, however in RO there one additional parent, although does have 'has participant' as a grandparent, in AE graph the parent for this term is 'has_participant'
- results_in_morphogenesis_of - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is 'has_participant'
- results_in_maturation_of - in both but in AE graph the parent for this term is 'has_participant'; in RO there are other parent terms, although does have 'has participant' as a grandparent
- results_in_division_of - not in RO: in AE graph the parent for this term is 'has_participant'
regulates_o_has_participant - not in RO: in AE graph the parent for this term is 'root node'
- has_regulation_target - not in RO: in AE graph the parent for this term is 'regulates_o_has_participant'
- regulates_o_has_input - not in RO: in AE graph the parent for this term is 'has_regulation_target'
- regulates_expression_of - not in RO: in AE graph the parent for this term is 'regulates_o_has_input'
- regulates_transcription_of - not in RO: in AE graph the parent for this term is 'regulates_expression_of'
- regulates_translation_of - not in RO: in AE graph the parent for this term is 'regulates_expression_of'
occurs_at - not in RO: in AE graph the parent for this term is 'root node'
occurs_in - Align both have 'root node' as parent
part_of - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is the 'root node'
activated_by - not in RO: in AE graph the parent for this term is 'root node'
inhibited_by - not in RO: in AE graph the parent for this term is 'root node'
results_in_commitment_to - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is the 'root node'
results_in_determination_of - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is the 'root node'
results_in_specification_of - in both RO and AE graph, however in RO there are additional parents, in AE graph the parent is the 'root node'
Deprecated Relations
- dependent_on - old relation no longer listed in AE graph, not in RO
- localization_dependent_on - old relation no longer listed in AE graph, not in RO
- requires_sequence_feature - old relation no longer listed in AE graph, not in RO
- requires_substance - old relation no longer listed in AE graph, not in RO
- in_absence_of - old relation no longer listed in AE graph, not in RO
- in_presence_of - old relation no longer listed in AE graph, not in RO
- independent_of - old relation no longer listed in AE graph, not in RO
- dependent_on
Relations in Protein2GO graph not in the lists above
produced_by
adjacent_to
coincident_with
has_end_location
has_start_location
has_target_end_location
has_target_start_location
regulates
- negatively_regulates
- positively_regulates
- directly_regulates
- directly_negatively_regulates
- directly_positively_regulates
regulates_o_has_input
- regulates_o_results_in_division_of
- regulates_o_results_in_formation_of
- regulates_o_results_in_maturation_of
- regulates_o_results_in_movement_of
- regulates_o_results_in_specification_of
- regulates_o_results_in_acquisition_of_features_of
- regulates_o_results_in_commitment_to
- regulates_o_results_in_morphogenesis_of (parent has_regulation_target)
- regulates_o_has_input (parent has_regulation_target)
- regulates_transport_of (parent regulates_o_has_input)