Ontology meeting 2021-08-02

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


Agenda

RHEA jamboree summary

https://docs.google.com/document/d/1Ki1xnWU29OkQZSScZ-ge-U_90Ql3-Ni5HbAvFktephs/edit#

  • specificity: The specificity of GO MFs is at the same level of the specificity of enzymes; we do not create terms for each substrate if an enzyme can act on a group of substrates
 Example: GO:0004620 phospholipase activity = RHEA:15801 a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3-phosphocholine + a fatty acid + H+
  RHEA has more 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:40651  1-acyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine + H2O = (5Z,8Z,11Z,14Z)-eicosatetraenoate + a 1-acyl-sn-glycero-3-phosphocholine + H+
   - RHEA:40643  1-acyl-2-(9Z,12Z)-octadecadienoyl-sn-glycero-3-phosphocholine + H2O = (9Z,12Z)-octadecadienoate + a 1-acyl-sn-glycero-3-phosphocholine + 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+
 GO will stick to the more general reaction, since this is the level of specificity of the enzyme
  • impacted terms:
    • GO:0019202 amino acid kinase activity & children (right now, stereospecificity not specified)
    • GO:0006520 cellular amino acid metabolic process & children
    • GO:0015171 amino acid transmembrane transporter activity & children
    • GO:0006865 amino acid transport & children
    • GO:0034219 carbohydrate transmembrane transport
    • GO:0015144 carbohydrate transmembrane transporter activity
    • others?
  • We will only send review notices when there is a change (merge/obsoletion); some terms may just get a change in label


  • NAD/NADP cofactors: we have decided in GO that the reaction represented with NAD(P) indicates that it is not know whether an enzyme uses NAD or NADP (this is different from IUBMB). If the specificity is unknown and there are RHEA IDs for both NAD and NADP, we create a NARROW xref to both reactions. If the specific cofactor is known, we create the one relevant reaction.
    • If an enzyme uses both, then it is annotated to both terms.
    • EC terms will not be linked to the GO terms that contain NAD(P), but to both NAD and NADP, as narrowMatch, and annotations propagated from these.
      • x activity NAD(P)
        • x activity NAD
        • x activity NADP

Peter - examples: Three examples –

  • DUS2:EPRS reduces uridine to dihydrouridine in tRNAs
  • dihydroceramide + NAD(P)H + H+ + O2 => ceramide + NAD(P)+ + H2O
  • And this reaction and its reverse: glutamate + NAD(P)+ => alpha-ketoglutarate + NH4+ + NAD(P)H + H+ [GLUD1]

I think this is all we have (found by searching for uses of NAD(P) in the released content)

  • Enantiomers: create only terms that represent characterized reactions. Do not unnecessary create grouping terms
 Current version of the ontology (August 2, 2021): 
  . GO:0004647 phosphoserine phosphatase activity
  .. [is_a] GO:0036425 D-phosphoserine phosphatase activity
  .. [is_a] GO:0036424 L-phosphoserine phosphatase activity  
 However we only find evidence for a physiological role for L-phosphoserine, not D-phosphoserine. 
 There are 18 annotations to GO:0004647 phosphoserine phosphatase activity, from spot-checking they all represent L-phosphoserine. 
 Therefore we propose to merge GO:0004647 phosphoserine phosphatase activity into its subclass  GO:0036424 L-phosphoserine phosphatase activity and obsolete GO:0036425 D-phosphoserine phosphatase activity

Discussion points

Did we ever make a decision to create/not create these terms? Yes. We have not decided to retire them.

Example http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0001193 epitope specific cytokine production by T cells Equivalents: cytokine production and (process is result of some MHC:epitope complex binding to TCR)

  • Do we use EC/RHEA's/other mf resources as xrefs for CC? See NTR - and existing terms

-> No. ECs are for MFs.

Other Business

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

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