Ontology meeting 2020-08-24
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has agent (Kimberly and David)
- Curators used this relation in annotation extensions to capture an entity (often a cell type) that participated in a process; many of the terms they used with this extension relation do not have a logical definition that captures this type of information
- Proposal: review existing annotations (see below), where desired, replace 'has agent' (now obsolete in gorel) with 'process has causal agent' (RO:0002608), the inverse of 'causal agent in process' (RO:0002500), defined as:
A relationship between a material entity and a process where the material entity has some causal role that influences the process.
- Should we then use 'process has causal agent' in logical definitions?
- Terms like cell-cell adhesion do not have logical definitions.
- Unique terms that use(d) 'has agent' in annotation extensions. Likely that not all of these annotations should use 'process has causal agent' in an extension, but review will be needed to see if there's a better way (and a GO-CAM) to express the biology curators were trying to capture.
activation of protein kinase activity has_agent(membrane raft (GO:0045121)),has_regulation_target(UniProtKB:P06241) amyloid-beta clearance cell surface receptor signaling pathway involved in cell-cell signaling cell-cell adhesion has_agent(peritoneal macrophage (CL:0000581))|occurs_in(spleen(UBERON:0002106)) cell-cell adhesion in response to extracellular stimulus cell-cell adhesion mediated by integrin cell-cell signaling chemoattractant activity has_agent(neuron of cerebral cortex (CL:0002609)),occurs_in(extracellular region (GO:0005576)),part_of(cellular response to stress (GO:0033554)),results_in_movement_of(microglial cell (CL:0000129)) complement-mediated synapse pruning endosome to lysosome transport heterotypic cell-cell adhesion inflammatory response microglia development monocyte extravasation negative regulation of amyloid-beta clearance negative regulation of canonical Wnt signaling pathway 'has agent' (very-low-density lipoprotein particle (GO:0034361)) negative regulation of cytolysis negative regulation of gene expression negative regulation of heterotypic cell-cell adhesion negative regulation of leukocyte adhesion to vascular endothelial cell negative regulation of neurogenesis negative regulation of oxidative stress-induced neuron death negative regulation of protein catabolic process negative regulation of protein secretion neuron remodeling positive regulation of amyloid-beta clearance positive regulation of blood microparticle formation positive regulation of defense response to bacterium positive regulation of gliogenesis positive regulation of glutamate secretion positive regulation of heterotypic cell-cell adhesion positive regulation of leukocyte adhesion to vascular endothelial cell positive regulation of phagocytosis positive regulation of protein catabolic process positive regulation of protein localization to plasma membrane protein binding involved in heterotypic cell-cell adhesion protein catabolic process response to axon injury synapse pruning tube formation tumor necrosis factor production has_agent(bone marrow cell (CL:0002092)),occurs_in(hippocampal formation (EMAPA:35405)) vertebrate eye-specific patterning
Review obsoletion policy
AmiGO display of relations
Ideas to make ensure design patterns are being used