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

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  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]
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==Relations==
==Relations==


[[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:acts_on_population_of|acts_on_population_of]]  
 
[[Annotation_Extension_Relation:has_agent|has_agent]] - not in RO: in AE graph the parent for this term is 'has_participant'


[[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:causally_upstream_of|causally_upstream_of]] - align, although in AE graph the parent for this term is 'root node'
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[[Annotation_Extension_Relation:happens_during|happens_during]] - align both have 'root node' as parent
[[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:has_participant|has_participant]] - not for direct annotation; used in the ontology


* [[Annotation_Extension_Relation:has_input|has_input]] - align both have 'has_participant' as parent
*[[Annotation_Extension_Relation:has_input|has_input]]  


:* [[Annotation_Extension_Relation:has_direct_input|has_direct_input]] - align both have 'has_input' as parent
*[[Annotation_Extension_Relation:has_output|has_output]]
 
:* [[Annotation_Extension_Relation:stabilizes|stabilizes]] - not in RO: in AE graph the parent for this term is 'has_input'
 
* [[Annotation_Extension_Relation:has_output|has_output]] - align both have 'has_participant' as parent


:* [[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: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
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[[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: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: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: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:regulates_o_has_input|regulates_o_has_input]] - not in RO: in AE graph the parent for this term is 'has_regulation_target'
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:::* [[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: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_at|occurs_at]] - not in RO: in AE graph the parent for this term is 'root node'


[[Annotation_Extension_Relation:occurs_in|occurs_in]] - Align both have 'root node' as parent
[[Annotation_Extension_Relation:occurs_in|occurs_in]] - Align both have 'root node' as parent
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[[Annotation_Extension_Relation:inhibited_by|inhibited_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'


==Deprecated Relations==
 
* [[Annotation_Extension_Relation requires_localization|(obsolete) requires_localization]]
[[Annotation_Extension_Relation:has_part|has_part]]
* [[Annotation_Extension_Relation requires_modification|(obsolete) requires_modification]]
 
* [[Annotation_Extension_Relation requires_target_sequence_feature|(obsolete) requires_target_sequence_feature]]
[[Annotation_Extension_Relation:during|during]]
* [[Annotation_Extension_Relation requires_regulator|(obsolete) requires_regulator]]
* [[Annotation_Extension_Relation requires_regulation_by|(obsolete) requires_regulation_by]]
* [[Annotation_Extension_Relation requires_direct_regulator|(obsolete) requires_direct_regulator]]
* [[Annotation_Extension_Relation modified_by|modified_by]] **** TO OBSOLETE 0 annotations
* [[Annotation_Extension_Relation not_during|(obsolete) not_during]]
* [[Annotation_Extension_Relation not_exists_during|(obsolete) not_exists_during]]
* [[Annotation_Extension_Relation not_happens_during|(obsolete) not_happens_during]]
* [[Annotation_Extension_Relation not_occurs_at|(obsolete) not_occurs_at]]
* [[Annotation_Extension_Relation not_occurs_in|(obsolete) not_occurs_in]]
* [[Annotation_Extension_Relation has_part|has_part]] **** TO OBSOLETE 4 annotations
* [[Annotation_Extension_Relation during|during]] 0 annotations - parent of other terms
* [[Annotation_Extension_Relation dependent_on|(obsolete) dependent_on]] - old relation no longer listed in AE graph not in RO
* [[Annotation_Extension_Relation localization_dependent_on|(obsolete) localization_dependent_on]] - old relation no longer listed in AE graph not in RO
* [[Annotation_Extension_Relation requires_sequence_feature|(obsolete) requires_sequence_feature]] - old relation no longer listed in AE graph not in RO
* [[Annotation_Extension_Relation requires_substance|(obsolete)  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 **** TO OBSOLETE 14 annotations
* [[Annotation_Extension_Relation in_presence_of|(obsolete) 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


==Relations in Protein2GO graph not in the lists above==
==Relations in Protein2GO graph not in the lists above==


dependent_on
 


produced_by
produced_by
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[[Category:relations]]
[[Category:annotation extension]]
[[Category:annotation extension]]

Revision as of 08:40, 29 June 2022

 UNDER REVIEW

GO relationships OBO file

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 - align both have 'root node' as parent

has_participant - not for direct annotation; used in the ontology

  • 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

regulates_o_has_participant - 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'

process has causal agent

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'


has_part

during

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)
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