Remove GOREL relation 'results_in'?

pgaudet commented 4 years ago

Hello,

The GOREL relation is used 10 times in the ontology, and I think in all cases it can be replaced by 'part of'. I also propose we merge one term and obsolete two terms using this relation:

[ ] id: GO:0010609 name: mRNA localization resulting in posttranscriptional regulation of gene expression is_a: GO:0010608 ! posttranscriptional regulation of gene expression intersection_of: GO:0008298 ! intracellular mRNA localization intersection_of: results_in GO:0010608 ! posttranscriptional regulation of gene expression -> 6 EXP annotations PROPOSAL: Change term to use 'involved in' and LD to use to 'part of' ? => 'mRNA localization (resulting) INVOLVED in posttranscriptional regulation of gene expression' Proposed LD: intersection_of: GO:0008298 ! intracellular mRNA localization intersection_of: (results_in) PART_OF GO:0010608 ! posttranscriptional regulation of gene expression
[ ] id: GO:0022002 name: negative regulation of anterior neural cell fate commitment of the neural plate by Wnt signaling pathway intersection_of: GO:0016055 ! Wnt signaling pathway intersection_of: results_in GO:0022001 ! negative regulation of anterior neural cell fate commitment of the neural plate -> 1 annotation

PROPOSAL: Change LD to use to 'part of' => intersection_of: GO:0016055 ! Wnt signaling pathway intersection_of: (results_in) PART_OF GO:0022001 ! negative regulation of anterior neural cell fate commitment of the neural plate

[ ] id: GO:0035818 name: positive regulation of urine volume by pressure natriuresis is_a: GO:0035810 ! positive regulation of urine volume intersection_of: GO:0003095 ! pressure natriuresis intersection_of: results_in GO:0035810 ! positive regulation of urine volume -> 0 annotations PROPOSAL: Change LD to use to 'part of' => intersection_of: GO:0003095 ! pressure natriuresis intersection_of: (results_in) PART_OF GO:0035810 ! positive regulation of urine volume
[ ] id: GO:0038108 name: negative regulation of appetite by leptin-mediated signaling pathway is_a: GO:0032099 ! negative regulation of appetite intersection_of: GO:0033210 ! leptin-mediated signaling pathway intersection_of: results_in GO:0032099 ! negative regulation of appetite -> 8 EXP annotations PROPOSAL: Change LD to use to 'part of' => intersection_of: GO:0033210 ! leptin-mediated signaling pathway intersection_of: (results_in) PART_OF GO:0032099 ! negative regulation of appetite
[ ] id: GO:1900383 name: regulation of synaptic plasticity by receptor localization to synapse intersection_of: GO:0097120 ! receptor localization to synapse intersection_of: results_in GO:0048167 ! regulation of synaptic plasticity -> 1 EXP annotation PROPOSAL: Change LD to use to 'part of' => intersection_of: GO:0097120 ! receptor localization to synapse intersection_of: (results_in) PART OF GO:0048167 ! regulation of synaptic plasticity
[ ] id: GO:0086091 name: regulation of heart rate by cardiac conduction is_a: GO:0002027 ! regulation of heart rate intersection_of: GO:0061337 ! cardiac conduction intersection_of: results_in GO:0002027 ! regulation of heart rate -> 8 EXP annotations PROPOSAL: Change LD to use to 'part of' => intersection_of: GO:0061337 ! cardiac conduction intersection_of: (results_in) PART OF GO:0002027 ! regulation of heart rate
[ ] id: GO:0086092 name: regulation of the force of heart contraction by cardiac conduction is_a: GO:0002026 ! regulation of the force of heart contraction intersection_of: GO:0061337 ! cardiac conduction intersection_of: results_in GO:0002026 ! regulation of the force of heart contraction PROPOSAL: Change LD to use to 'part of' => intersection_of: GO:0061337 ! cardiac conduction intersection_of: (results_in) PART OF GO:0002026 ! regulation of the force of heart contraction

=== MERGE

[x] #18245 id: GO:0006985 name: positive regulation of NF-kappaB transcription factor activity by ER overload response is_a: GO:0051092 ! positive regulation of NF-kappaB transcription factor activity intersection_of: GO:0006983 ! ER overload response intersection_of: results_in GO:0051092 ! positive regulation of NF-kappaB transcription factor activity -> 0 annotations -> Merge into ER overload response, since this in included in the def: "The series of molecular signals generated by the accumulation of normal or misfolded proteins in the endoplasmic reticulum and leading to activation of transcription by NF-kappaB."

=== OBSOLETE

[ ] id: GO:0086094 name: positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction is_a: GO:0086023 ! adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process intersection_of: GO:0071875 ! adrenergic receptor signaling pathway intersection_of: part_of GO:0060452 ! positive regulation of cardiac muscle contraction intersection_of: results_in GO:0060316 ! positive regulation of ryanodine-sensitive calcium-release channel activity relationship: part_of GO:0003062 ! regulation of heart rate by chemical signal relationship: part_of GO:0060452 ! positive regulation of cardiac muscle contraction -> 1 annotation PROPOSAL: Obsolete and suggest to annotate as GO-CAM ?
[ ] id: GO:0022003 name: negative regulation of anterior neural cell fate commitment of the neural plate by fibroblast growth factor receptor signaling pathway intersection_of: GO:0008543 ! fibroblast growth factor receptor signaling pathway intersection_of: results_in GO:0022001 ! negative regulation of anterior neural cell fate commitment of the neural plate -> 0 annotations PROPOSAL: Obsolete and suggest to annotate as GO-CAM if needed ?

What do you think @ukemi @vanaukenk ?

Thanks, Pascale

pgaudet commented 4 years ago

@ukemi @vanaukenk Did you have a chance to look at this ?

pgaudet commented 4 years ago

Similar issue with the use of the relation 'causally_upstream_of' in the ontology: There are 3 instances:

[x] id: GO:0042297 name: vocal learning relationship: causally_upstream_of GO:0098583 ! learned vocalization behavior

[x] id: GO:0097401 name: synaptic vesicle lumen acidification relationship: causally_upstream_of GO:0098700 ! neurotransmitter loading into synaptic vesicle

[x] id: GO:0098778 name: curli subunit secretion coupled to curli assembly relationship: causally_upstream_of GO:0098775 ! curli assembly 0 annotations

Are these relevant in the ontology ?

Thanks, Pascale

pgaudet commented 3 years ago

Removed 'causally_upstream_of' relations from these terms:

[x] id: GO:0042297 name: vocal learning relationship: causally_upstream_of GO:0098583 ! learned vocalization behavior

[x] id: GO:0097401 name: synaptic vesicle lumen acidification relationship: causally_upstream_of GO:0098700 ! neurotransmitter loading into synaptic vesicle

[x] id: GO:0098778 name: curli subunit secretion coupled to curli assembly relationship: causally_upstream_of GO:0098775 ! curli assembly 0 annotations

geneontology / go-ontology

Remove GOREL relation 'results_in'? #18244