Ontology meeting 2022-11-21

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  • Group members: Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul
  • Present: Pascale, Raymond, Val, Jim, Tanya, Karen, Kimberly, David, Chris, Paul
  • Regrets: Harold, Peter, Edith


Editors discussion items

Design patterns doc

https://docs.google.com/document/d/1cmcMbXmEY3Ko1emGZX3Gd6ttDi9_iQB2fLAprLD3aGI/edit#

Differentiation:


BP refactoring

Homeostasis

  1. Obsolete GO:0055079 aluminum ion homeostasis and GO:0010217 cellular aluminum ion homeostasis + replace by NTR cellular detoxification of aluminum ion
    • Create parent class: cellular detoxification of heavy metal ion
  2. obsolete GO:0035784 nickel cation homeostasis
    • Single annotation EcoCyc - obsolete + replace by GO:0035785 cellular nickel ion homeostasis
  3. obsolete GO:0055069 zinc ion homeostasis
    • -> review done
    • keep cellular zinc homeostasis
  4. obsolete GO:0055073 cadmium ion homeostasis
  5.  GO:0055068 cobalt ion homeostasis -> 1 TAIR annotation seems to be NOT cellular: controls Co levels from root to shoot -> ask Tanya + multicellular OR circulating ??
    • PMID:9115231 SGD: incorrect annotation of KO: Instead, this cobalt accumulation was found to be specifically mediated through the SMF1 homologue, SMF2. Hence, BSD2 prevents metal hyperaccumulation by exerting negative control over the SMF1 and SMF2 metal transport systems
    • GO:0006877 cellular cobalt ion homeostasis OK
  6. GO:0055070 copper ion homeostasis
    • GO:0006878 cellular copper ion homeostasis
    • to check ~10 annotations
  7. GO:0055072 iron ion homeostasis -> 112 annotations: https://docs.google.com/spreadsheets/d/13Cz2hzXhcC3bqhJir9XNAO9PYWklLOiARWrzUo6B3Rc/edit#gid=0
    • GO:0006879 cellular iron ion homeostasis
    • GO:0060586 multicellular organismal iron ion homeostasis
  8. GO:0055071 manganese ion homeostasis
  9. GO:0055074 calcium ion homeostasis
    • GO:0006874 cellular calcium ion homeostasis
    • 130 EXP annotations to calcium ion homeostasis
  10. GO:0010960 magnesium ion homeostasis
    • GO:0010961 cellular magnesium ion homeostasis
    • 57 EXP annotations to magnesium ion homeostasis
  11. GO:0055075 potassium ion homeostasis
    • GO:0030007 cellular potassium ion homeostasis
    • 39 EXP annotations to potassium ion homeostasis
  12. GO:0055078 sodium ion homeostasis
    • GO:0006883 cellular sodium ion homeostasis
    • 68 EXP annotations to sodium ion homeostasis
      • GO:0055078 sodium ion homeostasis
      • GO:0055062 phosphate ion homeostasis
      • 65 EXP to phosphate ion homeostasis

Tickets by ontology editors