Ontology meeting 2021-09-20: Difference between revisions
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Suggestions | Suggestions | ||
https://docs.google.com/document/d/15_TIWfnu2X_3CVzdcou14PyV4Ff8F9Hz8WSASi1bsaE/edit# | https://docs.google.com/document/d/15_TIWfnu2X_3CVzdcou14PyV4Ff8F9Hz8WSASi1bsaE/edit# | ||
==New Taxon constraints== | |||
https://github.com/geneontology/go-ontology/issues/16298 | |||
==Multiorganism processes== | ==Multiorganism processes== |
Revision as of 02:33, 20 September 2021
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Present:
- Regrets:
Announcements
Agenda
Aims for GOC meeting - Oct 12-14
Suggestions https://docs.google.com/document/d/15_TIWfnu2X_3CVzdcou14PyV4Ff8F9Hz8WSASi1bsaE/edit#
New Taxon constraints
https://github.com/geneontology/go-ontology/issues/16298
Multiorganism processes
Current pattern is
- 'modulation of process of other organism'
- 'modulation of process of other organism involved in symbiotic interaction'
- 'modulation by symbiont of host process'
- 'modulation by host of symbiont process'
- 'modulation of process of other organism involved in symbiotic interaction'
+ suppression/induction children
Issues are : - structure is complex - forces to create 2 independent branches for (intra-organism) symbionts and others (snakes, frogs, etc) - not always very relevant, usually by knowing the pair of organisms you know the relationship - there is probably a better way to capture this information, using context (extensions) that would represent inter-organism relation(host/symbiont, prey/predator, etc) - proposal would be to collapse all terms to “modulation/suppression/induction of x in another organism”
MF regulator activity
As we (try to) remove BPs of type 'regulation of MF', people are asking for 'x regulator activity', but in many cases it is not clear whether it is true regulation, or just that the protein is 'required for' the activity (whatever that might mean) see NTR: tRNA ligase activator activity, citing PMID:30943413
Protein-containing complex localization & protein localization
Inconsistent 'design patterns'
Amino acid conjugates
https://github.com/geneontology/go-ontology/issues/22096
Ontology editors documentation
- Review new term creation documentation: Guidelines_for_new_Molecular_Functions and Principles_for_creating_a_GO_term
- Review cross-reference documentation: Guidelines_for_'database_cross_references'_and_'definition_database_cross_references'
- Review protein binding term documentation http://wiki.geneontology.org/index.php/Guidelines_for_new_Binding_terms
- Optional: Review Chris's slides on aligning editor/contributor docs across all of OBO: https://docs.google.com/presentation/d/1YyWYSetDML3nhNgMUmcrsw80Xx1Uf1n1dWI-A20PMa8/edit#slide=id.p
- NAD/NADP: do we keep a grouping term even if all annotations can be classified to NAD or NADP-dependent? for eg GO:0003845 11-beta-hydroxysteroid dehydrogenase [NAD(P) activity] - all known enzymes have known specificity, see review ticket
- added 'do not annotate'
- DECISION (last call): This is what we will do
- Need to add to documentation