Extensions2GO-CAM

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Simple conversions

These are relations that are essentially identical in extensions and GO-CAM, and can be combined together into a "standard" GO-CAM activity.

  • If the aspect is F (column A)
    • No more than one occurs_in(CC)
    • No more than one occurs_in(CL)
    • No more than one occurs_in(UBERON or EMAPA or WBbt)
    • No more than one has_input/has_direct_input(geneID or ChEBI)
      • EXCEPTION: if term is "molecular function regulator activity" or descendant, can also add -directly-regulates->[MF of GP-B]
    • No more than one happens_during(BP)
    • No more than one part_of(BP)
    • No more than one activated_by(ChEBI)
    • No more than one inhibited_by(ChEBI)
  • If the aspect is C
    • No more than one part_of(CC)
    • No more than one part_of(CL)
    • No more than one part_of(UBERON or EMAPA)
  • If the aspect is P
    • No more than one occurs_in(CC)
    • No more than one occurs_in(CL)
    • No more than one occurs_in(UBERON or EMAPA or WBbt)
    • No more than one has_input/has_direct_input(geneID or ChEBI)
    • No more than one part_of(BP)

has_regulation_target

NOTE CAN ONLY BE USED ON AN MF ANNOTATION; CARDINALITY MUST BE 0 OR 1

  • GP-A [regulation of molecular function Z] has_regulation_target GP-B
    • term is GO:0065009 and descendants
    • can be expressed as [GP-A]<-enabled_by-[root MF]-regulates->[molecular function Z]-enabled_by->[GP-B]
    • The variations on this are all children of the term “regulation of molecular function” (GO:0065009). Variations are “positive regulation of MF Z”, which would be expressed with the positively_regulates relation instead; “negative regulation of MF Z”. **Note that MF Z should appear in the logical definition of the term “regulation of MF Z”, or in a triple with the regulates relation, so we can get the GO ID from that.
  • GP-A [regulation of gene expression OR regulation of protein biosynthetic process Z] has_regulation_target GP-B
    • These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-regulates->[root MF]-enabled_by->GP-B
    • Will be positively or negatively regulates instead, if in the original term.
  • GP-A [Regulation of receptor internalization (GO:0002092) OR regulation of protein catabolic process Z] has_regulation_target GP-B
    • These are GO:0002092 and descendants, or GO:0042176 and descendants
    • These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-regulates->[root MF]-enabled_by->GP-B
    • If term is positive regulation, relation will be negatively-regulates; if negative reg, relation will be positively-regulates
  • GP-A [regulation of protein metabolic process Z, not including cases above, or regulation of protein localization] has_regulation_target GP-B
  • These are GO:0019538 and the descendants that are not also descendants of terms listed above, or GO:0032880 and descendants
    • These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B

extensions that need to be handled

MGI

P has_participant(EMAPA) P results_in_development_of(EMAPA) P regulates_o_occurs_in(EMAPA) P has_regulation_target(geneID) P regulates_o_occurs_in(CL) P regulates_o_occurs_in(CL),regulates_o_occurs_in(EMAPA) P has_participant(CL) P occurs_in(EMAPA),results_in_acquisition_of_features_of(CL) P has_output_o_axis_of(EMAPA) P has_participant(CL),occurs_in(EMAPA) P has_participant(CL),has_participant(EMAPA) P regulates_o_acts_on_population_of(CL) F has_participant(geneID) P regulates_o_acts_on_population_of(CL),regulates_o_occurs_in(EMAPA) C part_of(CL),part_of(EMAPA),part_of(EMAPA) P regulates_o_results_in_acquisition_of_features_of(CL) P has_participant(CL),results_in_development_of(EMAPA) P results_in_acquisition_of_features_of(CL) P regulates_o_has_participant(EMAPA) P regulates_o_has_agent(CL) P occurs_in(EMAPA),regulates_o_results_in_acquisition_of_features_of(CL) P results_in_formation_of(EMAPA) P occurs_in(EMAPA),results_in_movement_of(CL) P occurs_in(EMAPA),regulates_o_occurs_in(CL) P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA) P acts_on_population_of(CL) P acts_on_population_of(CL),occurs_in(EMAPA) P occurs_in(EMAPA),results_in_development_of(CL) C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) P occurs_in(EMAPA),regulates_o_acts_on_population_of(CL) P regulates_o_has_participant(CL) P has_participant(geneID) P regulates_o_has_participant(geneID) P occurs_in(CL),regulates_o_occurs_in(CL) P occurs_in(EMAPA),results_in_acquisition_of_features_of(CL),results_in_acquisition_of_features_of(CL) P regulates_o_has_participant(CL),regulates_o_occurs_in(EMAPA) P has_participant(CL),occurs_in(EMAPA),occurs_in(EMAPA) P has_participant(CL),has_participant(EMAPA),has_participant(EMAPA) P has_regulation_target(geneID),regulates_o_occurs_in(CL) P regulates_o_has_participant(CL),regulates_o_has_participant(EMAPA) P has_participant(CL),results_in_development_of(EMAPA),results_in_development_of(EMAPA) P results_in_movement_of(CL) P transports_or_maintains_localization_of(geneID) P results_in_development_of(CL) C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) P has_regulation_target(geneID),regulates_o_occurs_in(EMAPA) P regulates_o_occurs_in(EMAPA),regulates_o_results_in_acquisition_of_features_of(CL) P regulates_o_acts_on_population_of(CL),regulates_o_occurs_in(EMAPA),regulates_o_occurs_in(EMAPA) P regulates_o_occurs_in(CL),regulates_o_occurs_in(EMAPA),regulates_o_occurs_in(EMAPA) P regulates_o_results_in_movement_of(CL) P results_in_morphogenesis_of(EMAPA) P occurs_in(EMAPA),regulates_o_occurs_in(EMAPA) P has_regulation_target(geneID),regulates_o_occurs_in(CL),regulates_o_occurs_in(EMAPA) P has_regulation_target(geneID),occurs_in(CL) P regulates_o_occurs_in(EMAPA),regulates_o_results_in_movement_of(CL) P occurs_in(EMAPA),results_in_commitment_to(CL) P occurs_in(EMAPA),occurs_in(EMAPA) P occurs_in(EMAPA),results_in_movement_of(CL),results_in_movement_of(CL) P occurs_in(EMAPA),results_in_maturation_of(CL) P has_regulation_target(geneID),occurs_in(EMAPA) P occurs_in(CL),transports_or_maintains_localization_of(geneID) C part_of(EMAPA),part_of(EMAPA) P occurs_in(EMAPA),regulates_o_results_in_acquisition_of_features_of(CL),regulates_o_results_in_acquisition_of_features_of(CL) P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) P occurs_in(EMAPA),regulates_o_acts_on_population_of(CL),regulates_o_acts_on_population_of(CL) P regulates_o_has_participant(geneID),regulates_o_occurs_in(CL) P has_participant(EMAPA),results_in_commitment_to(CL) P occurs_in(CL),occurs_in(EMAPA),transports_or_maintains_localization_of(geneID) P regulates_o_results_in_development_of(EMAPA) P acts_on_population_of(CL),occurs_in(EMAPA),occurs_in(EMAPA) P occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) P regulates_o_has_participant(geneID),regulates_o_occurs_in(EMAPA) C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) P has_regulation_target(geneID),occurs_in(CL),regulates_o_occurs_in(CL) C adjacent_to(CL) P regulates_o_has_output(geneID) P has_input(PR),has_output(PR) P has_input(geneID),negatively_regulates(GO:P),positively_regulates(GO:F) P has_regulation_target(geneID),occurs_in(CL),occurs_in(EMAPA) P has_participant(geneID),occurs_in(CL) P regulates_o_results_in_formation_of(EMAPA) P occurs_in(EMAPA),results_in_morphogenesis_of(CL) P results_in_commitment_to(CL) P regulates_o_has_agent(CL),regulates_o_occurs_in(EMAPA) C part_of(GO:C) P results_in_morphogenesis_of(CL) P results_in_maturation_of(CL) P part_of(EMAPA) F occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA) P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA),transports_or_maintains_localization_of(geneID),transports_or_maintains_localization_of(geneID) P occurs_in(EMAPA),regulates_o_occurs_in(CL),regulates_o_occurs_in(CL) P has_participant(geneID),occurs_in(CL),occurs_in(EMAPA) C part_of(CL),part_of(CL) P has_participant(geneID),occurs_in(EMAPA) P occurs_in(EMAPA),results_in_maturation_of(CL),results_in_maturation_of(CL) P regulates_o_has_input(geneID) C part_of(CL),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA),part_of(EMAPA) P has_participant(CL),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) P acts_on_population_of(CL),regulates_o_occurs_in(EMAPA) P has_agent(CL) P occurs_in(CL),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA),occurs_in(EMAPA) P has_direct_input(PR) P occurs_in(EMAPA),transports_or_maintains_localization_of(geneID)

PomBase

C exists_during(GO:P) P happens_during(GO:P) C coincident_with(SO) F occurs_at(SO)

UCL

P regulates_expression_of(geneID) P happens_during(GO:P),results_in_movement_of(geneID)

IntAct

F occurs_in()

SGD

P regulates_transcription_of(geneID)