Ontology meeting 2021-08-16: Difference between revisions
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* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul | * '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul | ||
* '''Present: ''' | * '''Present: ''' Paul, Kimberly, Raymond, Chris, Tanya, David, Karen, Pascale, Federica (DisProt/IDPO) | ||
* '''Regrets: ''' | * '''Regrets: ''' Peter, Harold | ||
=Agenda= | =Agenda= | ||
==New GH tokens== | |||
As of last Friday (Aug 13, 2021), GH does not accept password anymore, and we need to switch to tokens. | |||
Documentation is here: | |||
https://docs.google.com/document/d/1BUXPotmW1i3aQeqKv-68TM8nqgSs1VLOCUhOvliuaTk/edit#heading=h.xq7hg7z4k2bo | |||
==IDPO terms== | ==IDPO terms== | ||
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Outstanding: | Outstanding: | ||
* '''self-inhibitor:''' Protein interactions in cis that auto-inhibit the protein function. Source: PMID: 27135163 | * '''self-inhibitor:''' Protein interactions in cis that auto-inhibit the protein function. Source: PMID:27135163 | ||
* '''self-activator:''' Protein interactions in cis that auto-activate the protein function. Source: PMID: 27135163 | * '''self-activator:''' Protein interactions in cis that auto-activate the protein function. Source: PMID:27135163 | ||
** Discussion: this is more mechanistic than what GO aims to represent | |||
** GO describes the function on other proteins, not on itself - for example for a receptor: the ligand activates the receptor, the receptor activates the downstream | |||
** ACTION: bring examples to this call of how these (for eg receptor/self-activation/inhibition/etc) are annotated, and discuss our options | |||
* '''liquid-liquid phase separation:''' Reversible process by which a solution of biopolymers separates into two coexisting phases: a condensate phase with liquid-like properties, and a dilute phase. Source: PMID:29602697 https://europepmc.org/abstract/MED/26455390 | * '''liquid-liquid phase separation:''' Reversible process by which a solution of biopolymers separates into two coexisting phases: a condensate phase with liquid-like properties, and a dilute phase. Source: PMID:29602697 https://europepmc.org/abstract/MED/26455390 | ||
* '''entropic chain:''' Functions directly associated with the disordered state of proteins that stems from their ability to shift between conformational states without becoming structured. Includes entropic bristles, clocks and springs. Source: PMID:24773235 https://europepmc.org/abstract/MED/10585425 | * '''entropic chain:''' Functions directly associated with the disordered state of proteins that stems from their ability to shift between conformational states without becoming structured. Includes entropic bristles, clocks and springs. Source: PMID:24773235 https://europepmc.org/abstract/MED/10585425 | ||
* '''flexible linker/spacer:''' Unstructured region connecting, providing separation and permitting movement between adjacent functional regions, e.g. structured domains or disordered motifs.Source: PMID:24773235 https://europepmc.org/abstract/MED/29739942 | * '''flexible linker/spacer:''' Unstructured region connecting, providing separation and permitting movement between adjacent functional regions, e.g. structured domains or disordered motifs.Source: PMID:24773235 https://europepmc.org/abstract/MED/29739942 | ||
==Ontology editors documentation== | ==Ontology editors documentation== | ||
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* Review cross-reference documentation: [[Guidelines_for_'database_cross_references'_and_'definition_database_cross_references']] | * 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 | * 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 [https://github.com/geneontology/go-ontology/issues/21915 GO:0003845 11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity] - all known enzymes have known specificity, see [https://github.com/geneontology/go-annotation/issues/3869 review ticket] | * NAD/NADP: do we keep a grouping term even if all annotations can be classified to NAD or NADP-dependent? for eg [https://github.com/geneontology/go-ontology/issues/21915 GO:0003845 11-beta-hydroxysteroid dehydrogenase [NAD(P)] activity] - all known enzymes have known specificity, see [https://github.com/geneontology/go-annotation/issues/3869 review ticket] | ||
** added 'do not annotate' | ** added 'do not annotate' | ||
** '''DECISION: This is what we will do''' | |||
==Check for synonym scope== | ==Check for synonym scope== |
Latest revision as of 15:44, 16 August 2021
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Present: Paul, Kimberly, Raymond, Chris, Tanya, David, Karen, Pascale, Federica (DisProt/IDPO)
- Regrets: Peter, Harold
Agenda
New GH tokens
As of last Friday (Aug 13, 2021), GH does not accept password anymore, and we need to switch to tokens. Documentation is here: https://docs.google.com/document/d/1BUXPotmW1i3aQeqKv-68TM8nqgSs1VLOCUhOvliuaTk/edit#heading=h.xq7hg7z4k2bo
IDPO terms
https://docs.google.com/spreadsheets/d/1IKKC9uShylCtf_lcBs6miI8PoqVL3L9S0rR6hz1mXxc/edit#gid=0
Outstanding:
- self-inhibitor: Protein interactions in cis that auto-inhibit the protein function. Source: PMID:27135163
- self-activator: Protein interactions in cis that auto-activate the protein function. Source: PMID:27135163
- Discussion: this is more mechanistic than what GO aims to represent
- GO describes the function on other proteins, not on itself - for example for a receptor: the ligand activates the receptor, the receptor activates the downstream
- ACTION: bring examples to this call of how these (for eg receptor/self-activation/inhibition/etc) are annotated, and discuss our options
- liquid-liquid phase separation: Reversible process by which a solution of biopolymers separates into two coexisting phases: a condensate phase with liquid-like properties, and a dilute phase. Source: PMID:29602697 https://europepmc.org/abstract/MED/26455390
- entropic chain: Functions directly associated with the disordered state of proteins that stems from their ability to shift between conformational states without becoming structured. Includes entropic bristles, clocks and springs. Source: PMID:24773235 https://europepmc.org/abstract/MED/10585425
- flexible linker/spacer: Unstructured region connecting, providing separation and permitting movement between adjacent functional regions, e.g. structured domains or disordered motifs.Source: PMID:24773235 https://europepmc.org/abstract/MED/29739942
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: This is what we will do
Check for synonym scope
https://github.com/geneontology/go-ontology/issues/21610