Extensions2GO-CAM: Difference between revisions
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**can be expressed as [GP-A]<-enabled_by-[GO:0003674]-regulates->[transcription]-has_input->[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. | **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 protein phosphorylation (GO:0001932) and descendants. | |||
**These can be modeled as GP-A<-enabled_by-[ GO:0003674]-regulates->[protein phosphorylation]-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 catabolic process (GO:0042176) 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 14:53, 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
- 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 protein phosphorylation (GO:0001932) and descendants.
- These can be modeled as GP-A<-enabled_by-[ GO:0003674]-regulates->[protein phosphorylation]-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 catabolic process (GO:0042176) 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.