Ontology meeting 2019-11-18: Difference between revisions
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(Created page with "= Conference Line = See calendar for details On call: = Agenda = ==Discussion topics== ===GOREL relation 'mediated_by'=== Usage is inconsistent: We have cases where some...") |
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* Or replace it ? | * Or replace it ? | ||
===Creating ShEx shapes for specific GO terms=== | |||
*Comparison of relation use in the ontology, dos-dps, and annotation import specs | |||
*[https://docs.google.com/spreadsheets/d/1okodOSG7mWgS8ZE8T95XjPr0-9G1vEIkAy2BkipEfRw Spreadsheet] | |||
==Other Business== | ==Other Business== | ||
Revision as of 15:27, 15 November 2019
Conference Line
See calendar for details
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
Other Business
https://github.com/geneontology/go-ontology/projects/1