Annotation usage examples for each annotation extension relation: Difference between revisions

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   UNDER REVIEW
   UNDER REVIEW


[https://github.com/geneontology/go-ontology/blob/master/src/ontology/extensions/gorel.obo GO relationships OBO file]
[https://github.com/geneontology/go-ontology/blob/master/src/ontology/extensions/gorel.obo GO relationships OBO file] (GOREL)


Back to [http://wiki.geneontology.org/index.php/Annotation_Extension Annotation Extension]
Back to [http://wiki.geneontology.org/index.php/Annotation_Extension Annotation Extension]
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==Relations==
==Relations==


[[Annotation_Extension_Relation:acts_on_population_of|acts_on_population_of]]  
[[acts on population of]]  


[[Annotation_Extension_Relation:causally_upstream_of|causally_upstream_of]] - align, although in AE graph the parent for this term is 'root node'
[[causally upstream of]] - align, although in AE graph the parent for this term is 'root node'


[[Annotation_Extension_Relation:exists_during|exists_during]] - not in RO: 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'


[[Annotation_Extension_Relation:happens_during|happens_during]] - align both have 'root node' as parent
[[happens during]]


[[Annotation_Extension_Relation:has_participant|has_participant]] - not for direct annotation; used in the ontology
*[[has_input]]  


*[[Annotation_Extension_Relation:has_input|has_input]]  
*[[has_output]]


*[[Annotation_Extension_Relation:has_output|has_output]]
[[Annotation_Extension_Relation:occurs_in|occurs_in]]  


:* [[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:part_of|part_of]]  


* [[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
[[has small molecular inhibitor]]  


* [[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'
[[has small molecular activator]]


* [[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'
[[results in formation_of]]


* [[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: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_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: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: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: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: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: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: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: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: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:regulates_transcription_of|regulates_transcription_of]] - not in RO: in AE graph the parent for this term is 'regulates_expression_of'
 
:::* [[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:occurs_in|occurs_in]] - Align both have 'root node' as parent
 
[[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:activated_by|activated_by]] - not in RO: in AE graph the parent for this term is 'root node'
 
[[Annotation_Extension_Relation:inhibited_by|inhibited_by]] - not in RO: in AE graph the parent for this term is 'root node'
 
process has causal agent


[[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: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'
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[[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: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: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:has_part|has_part]]
 
[[Annotation_Extension_Relation:during|during]]
 
==Deprecated Relations==
 
These relations are not supported in the ontology, in GO-CAM or in Protein2GO anymore:
 
*[[Annotation_Extension_Relation:occurs_at|occurs_at]] - not in RO: in AE graph the parent for this term is 'root node'
* dependent_on
*[[Annotation_Extension_Relation:has_agent|has_agent]] - not in RO: in AE graph the parent for this term is 'has_participant'
* has_direct_input
* in_absence_of
* in_presence_of
* independent_of
* localization_dependent_on
* modified_by
* not_during
* not_exists_during
* not_happens_during
* not_occurs_at
* not_occurs_in
* requires_direct_regulator
* requires_localization
* requires_modification
* requires_regulation_by
* requires_regulator
* requires_sequence_feature
* requires_substance
* requires_target_sequence_feature


==Relations in Protein2GO graph not in the lists above==
==Relations in Protein2GO graph not in the lists above==
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coincident_with
coincident_with
has_end_location
has_start_location


has_target_end_location
has_target_end_location
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** directly_negatively_regulates
** directly_negatively_regulates
** directly_positively_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]]

Latest revision as of 10:45, 13 February 2024

 UNDER REVIEW

GO relationships OBO file (GOREL)

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

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

occurs_in

part_of

has small molecular inhibitor

has small molecular activator

results in formation_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

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_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'

results_in_division_of - not in RO: in AE graph the parent for this term is 'has_participant'

Relations in Protein2GO graph not in the lists above

produced_by

adjacent_to

coincident_with

has_target_end_location

has_target_start_location

regulates

  • negatively_regulates
  • positively_regulates
  • directly_regulates
    • directly_negatively_regulates
    • directly_positively_regulates
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