Ontology meeting 2021-09-20: Difference between revisions
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=Agenda= | =Agenda= | ||
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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# | ||
==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' | |||
+ 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” | |||
==Protein-containing complex localization & protein localization== | ==Protein-containing complex localization & protein localization== |
Revision as of 09:40, 10 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#
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”
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