Ontology meeting 2021-05-03

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


GOC meeting slides

Ontology updated scheduled for Wed noon EST/6PM Geneva https://docs.google.com/presentation/d/1uid5r-Vq4pkGVF0_KskLGw0r2zAjJkrI6T8HOtc34Qw/edit#slide=id.g9e44e40c5d_0_6

Generate DOS-DP pattern docs

https://github.com/geneontology/go-ontology/pull/21367/commits/80e5b1284d0ae3040a097d754b1c5e8c0dae7394 Jim


RHEA status and future plans

  • Discussion with Paul, Chris, Anne, Harold, Alan, Pascale: now plan to add 'intermediate'/'grouping' classes only - phospholipase example:
    • 'phospholipase activity': children
      • 'phospholipase A2 activity'
      • 'phospholipase C activity'
      • 'phospholipase D activity'

describe the various positions at which the enzyme cleaves, for eg phospholipase A2: Hydrolysis of a glycerophospholipid, removing the fatty acid attached to the sn2-position.

  • RHEA further describes all substrates, however the enzymes are not specific for the R group (as far as we know). So, unless a specific enzyme is characterized, we will stick to the intermediate RHEA class (in this case, RHEA:15801) and will not create the specific forms of the reaction:
    • RHEA:62036: a 1-(9Z-octadecenoyl)-2-acyl-sn-glycero-3-phosphocholine + H2O = a 1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + a fatty acid + H+
    • RHEA:53500 1-hexanoyl-2-acyl-sn-glycero-3-phosphocholine + H2O = 1-hexanoyl-sn-glycero-3-phosphocholine + a fatty acid + H+
    • RHEA:38847 1-(9Z-octadecenoyl)-2-hexadecanoyl-sn-glycero-3-phosphocholine + H2O = a 1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + H+ + hexadecanoate
    • RHEA:38779 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + H2O = (9Z)-octadecenoate + 1-hexadecanoyl-sn-glycero-3-phosphocholine + H+
  • RHEA agrees to create intermediate/grouping classes if the RHEA reactions are too specific compared to the level of granularity GO needs.

See also http://wiki.geneontology.org/index.php/Ontology_meeting_2021-04-19#RHEA_status_and_future_plans Previous action items:

  • AI We need to identify Rhea reactions linked to entries but WITHOUT GO mappings --->>> next ones to map to GO (or create reactions)
  • AI: fix errors reported on Oct 1, 2019

Other items

ACTION ITEM FROM LAST CALL

  • Filter out Rhea xrefs that are not valid (Jim)
  • Should obsolete ECs be removed from obsoleted terms Y/N

Other Business

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

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