Ontology meeting 2019-11-18

Conference Line

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On call:

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

GOREL & RO

(Pascale):

• I have removed the relation 'has_direct_input' from GOREL, but it's still in RO (and therefore still in GOREL). Should we ask to remove it ? (Is all of RO loaded in GOREL?)

• Do we want to keep the relation 'has regulatory target' for targets that are not directly bound - for example to express the relationship between a transcription factor and the gene its regulates ? At the GOC meeting it seemed like we wanted to keep that notion.

Other Business

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