Difference between revisions of "Extensions2GO-CAM"

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(has_regulation_target)
(has_regulation_target)
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**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]
 
**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.
 
**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 transcription] has_regulation_target GP-B  
+
*GP-A [regulation of gene expression OR regulation of protein biosynthetic process Z] has_regulation_target GP-B  
**can be expressed as [GP-A]<-enabled_by-[GO:0003674]-regulates->[transcription]-has_input->[GP-B]
+
**These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-positively-regulates->[root MF]-enabled_by->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.
+
*GP-A [Regulation of receptor internalization (GO:0002092) OR regulation of protein catabolic process Z] has_regulation_target GP-B  
*Regulation of regulation of protein metabolic process (GO:0051246) and descendants.  
+
**These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-negatively-regulates->[root MF]-enabled_by->GP-B
**These can be modeled as GP-A<-enabled_by-[ GO:0003674]-regulates->[protein metabolic process]-has_input->GP-B
+
* GP-A [regulation of protein metabolic process Z, not including cases above, or regulation of protein localization] has_regulation_target GP-B
*Regulation of gene expression (GO:0010468) and descendants. 
+
**These can be modeled as GP-A<-enabled_by-[root MF]-part_of->[regulation of Z]-has_input->GP-B,-negatively-regulates->[root MF]-enabled_by->GP-B
**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.
 

Revision as of 10:26, 28 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 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; CARDINALITY MUST BE 0 OR 1

  • GP-A [regulation of molecular function Z] has_regulation_target GP-B
    • term is GO:0065009 or descendant
    • 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”, 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,-positively-regulates->[root MF]-enabled_by->GP-B
  • GP-A [Regulation of receptor internalization (GO:0002092) OR regulation of protein catabolic 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,-negatively-regulates->[root MF]-enabled_by->GP-B
  • GP-A [regulation of protein metabolic process Z, not including cases above, or regulation of protein localization] 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,-negatively-regulates->[root MF]-enabled_by->GP-B