Difference between revisions of "Extensions2GO-CAM"

From GO Wiki
Jump to: navigation, search
(has_regulation_target)
(has_regulation_target)
Line 23: Line 23:
 
**No more than one part_of(BP)
 
**No more than one part_of(BP)
 
=has_regulation_target=
 
=has_regulation_target=
 +
NOTE CAN ONLY BE USED ON AN MF ANNOTATION
 
*GP-A [regulation of molecular function Z] has_regulation_target GP-B  
 
*GP-A [regulation of molecular function Z] has_regulation_target GP-B  
 
**can be expressed as [GP-A]<-enabled_by-[ GO:0003674]-regulates->[molecular function Z]-enabled_by->[GP-B]
 
**can be expressed as [GP-A]<-enabled_by-[ GO:0003674]-regulates->[molecular function Z]-enabled_by->[GP-B]

Revision as of 13:30, 23 August 2018

Simple conversions

These are relations that are essentially identical in extensions and GO-CAM

  • 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)
    • No more than one has_input/has_direct_input(geneID or ChEBI)
    • No more than one happens_during(BP)
    • No more than one part_of(BP)
    • No more than one has_regulation_target(geneID)
    • No more than one activated_by(ChEBI)
    • No more than one inhibited_by(ChEBI)
  • If the aspect is C
    • No more than one occurs_in(CC)
    • No more than one occurs_in(CL)
    • No more than one occurs_in(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)
    • 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

  • GP-A [regulation of molecular function Z] has_regulation_target GP-B
    • can be expressed as [GP-A]<-enabled_by-[ GO:0003674]-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”, so you can get the GO ID from that.
  • GP-A [regulation of transcription] has_regulation_target GP-B
    • can be expressed as [GP-A]<-enabled_by-[GO:0003674]-regulates->[transcription]-has_input->[GP-B]
    • These are all children of “regulation of transcription, DNA templated” (GO:0006351). Similarly to above, there are positive/negative variations, and you can get the specific GO ID for [transcription] from the logical definition.
  • Regulation of regulation of protein metabolic process (GO:0051246) and descendants.
    • These can be modeled as GP-A<-enabled_by-[ GO:0003674]-regulates->[protein metabolic process]-has_input->GP-B
  • Regulation of gene expression (GO:0010468) and descendants.
    • These can be modeled like regulation of transcription below (it’s actually a more general case).
  • Regulation of receptor internalization (GO:0002092) and descendants.
    • These can be modeled like protein phosphorylation above.
  • Protein localization (GO:0008104) and descendants.
    • These can be modeled like protein phosphorylation.
  • Protein ubiquitination (GO:0031396) and descendants.
    • These can be modeled like protein phosphorylation.
  • Regulation of protein localization (GO:0032880) and descendants.
    • These should be modeled exactly the same way as protein localization above.