Ontology meeting 2019-11-18

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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.

Occurs_at -> occurs_adjacent_to?

occurs_adjacent_to: The relationship between a process P1 and a continuant C1 in which (a part of) an entity C2 that is a participant in P1 shares a boundary with C1.

Produced_by: how to handle

Some annotations use the produced_by extension to state which cell produces a CC, for example: Cfl1 (MGI:101757) part_of extracellular space produced_by(CL:0002548 cardiac fibroblast) however this is inconsistent with the definition: a produced_by b iff some process that occurs_in b has_output a. How should this be captured ?

Other Business

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

Minutes should be recorded on individual tickets and in individual projects