Ontology meeting 2019-11-18
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Agenda
Discussion topics
GOREL relation 'mediated_by'
Usage is inconsistent:
We have cases where some process is mediated by a molecule, e.g.: - 'gene silencing' and (mediated_by some 'ribonucleic acid’) - TOR signaling intracellular signal transduction' and (mediated_by some 'TOR complex’)'
Is this different from enabled_by ?
by an organelle:
- vesicle-mediated transport: 'transport and (mediated_by some vesicle)’
by a cell, e.g.
- B cell cytokine production (mediated_by some B cell)
For the B cell cytokine production, should the relation be ‘occurs_in' B cell ?
What do we want to do about this relation:
- We can define it better and clean up its usage in the ontology
- Or replace it ?
Creating ShEx shapes for specific GO terms
- Comparison of relation use in the ontology, dos-dps, and annotation import specs
- Spreadsheet
Other Business
https://github.com/geneontology/go-ontology/projects/1