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


Check for synonym scope

https://github.com/geneontology/go-ontology/issues/21610

Other Business

https://github.com/geneontology/go-ontology/projects/1