Ontology meeting 2021-11-29
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Present:
- Regrets:
Announcements
Agenda
Discussion points
Decision on ChEBI update?
https://github.com/geneontology/go-ontology/pull/22092 Following up
- Action Item Harold
- Create new top level CHEBI ticket to ask why these 3 compounds (succinate, fumarate, tyrosine) are now being classified as lipids - but the 'functional chain' of lipid is very, very short in these case, this is counter-inituitive; can you explain why this is the case?
- Would like clarification on what is a structural derivative
Register GOCHE prefix, or change terms to GO
Let's revisit when the Roles project is done, when we know how many roles are left?
New goslim-generic MF subset
Protein-complex organization/assembly/disassembly
Problem with relations used in logical definition https://github.com/geneontology/go-ontology/issues/22488
Metabolic processes template
Pascale
- I created a template for new term requests in the metabolic triad, see an example here: https://github.com/geneontology/go-ontology/issues/22437
- This lead to some discussion on email among David, Kimberly, Peter and I about the standard definition of 'metabolic process', which is "The chemical reactions and pathways involving substance, [description of substance]." (source: http://wiki.geneontology.org/index.php/Metabolic_process)
A proposal for a new definition by David "The chemical reactions and pathways, including biosynthesis and catabolism, by which living organisms transform chemical substances that are primary inputs or outputs of the process. Primary inputs and outputs of metabolic processes are chemicals for which the goal of the process is to modify, produce, consume or transform the chemical."
- Chris: Use genus + differentia "The biological process that ... "
- wikipedia page may be useful: https://en.wikipedia.org/wiki/Metabolism: The three main purposes of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes.
Set up jamborees for the following?
Rhea boomer project
https://github.com/orgs/geneontology/projects/73 Harold working on this
New taxon constraints project project
https://github.com/orgs/geneontology/projects/71 Harold and Pascale to write to Alan, Anne