Ontology meeting 2021-08-16

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  • 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