Ontology meeting 2023-11-27
- Group members: Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, David, Chris, Paul
- Present: Pascale, Raymond,Jim, Tanya, Kimberly, Peter, David
- Regrets: Edith, Val, Chris, Paul
Discussion points
- MetaCyc now requires a subscription; what is the GO policy WRT links?
- Pascale - I dont have access to the site anymore, so I cannot verify the reactions.
- One suggestion would be to limit to using RHEA mappings : https://ftp.expasy.org/databases/rhea/tsv/rhea2metacyc.tsv
and any mapping not there would be removed
- We could use this file to automatically maintain the mappings
Ontology tickets
Questions/follow up on ongoing tickets
Interspecies interactions
- We propose to obsolete all terms of the patterns ‘modification/perturbation of host x process by symbiont’ and ‘modification/perturbation of host x process by virus’, to be replaced by the corresponding term ‘modification/perturbation of x process in another organism’. This also includes ‘evenomation’
- Background: The ‘multispecies’ working group had been struggling to decide at which level symbiont-host interactions need to be captured. Right now we have three general patterns:
modification/perturbation of x process in another organism modification/perturbation of host x process by symbiont modification/perturbation of host x process by virus
- Problems:
the ontology is not consistent, some processes that viruses can affect in the host are also targeted by other symbionts or free-living organisms this organization does not cover fungus, protozoa, and may other taxonomic groups that can interact with other species
- The ‘multispecies’ working group has explored the idea of only having one term (“in another organism”) instead of the current triad. I have now also discussed this with all the Swiss-Prot curators working in these areas: venoms, fungi, bacteria, plants, as well as with Gene Godbold from Signature Science/PathGO.
The consensus was that we should go ahead with the plan to only keep ‘in another organism’. All obsoleted terms will be ‘replaced_by’ by the corresponding ‘in another organism’ term, so there should not be any review needed.
Older 'editors discuss' tickets
Regulation of biological quality
Problematic DP: https://github.com/geneontology/go-ontology/issues/24125
zinc ion import into secretory vesicle
What is the scope of GO WRT transport of specific molecules? https://github.com/geneontology/go-ontology/issues/23879