Ontology meeting 2020-08-24

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Agenda

Relations

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

http://wiki.geneontology.org/index.php/Principles_for_term_obsoletion


AmiGO display of relations

https://github.com/geneontology/amigo/issues/602


Design patterns

Ideas to make ensure design patterns are being used

Other Business

https://github.com/geneontology/go-ontology/projects/1


Minutes should be recorded on individual tickets and in individual projects