Difference between revisions of "Annotation Conf. Call 2021-08-03"

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= Attendance =
= Attendance =
* On call:  
* On call: DavidH, Suzi, Pascale, Harold, Cailey, Peter, Dmitry, Dustin, Edith, Guilia, Karen, Li, Midori, Patrick, Raymond, Rob, Seth, Debbie, Sridhar, Stan, Tanya
[[Category:Annotation Working Group]]
[[Category:Annotation Working Group]]

Revision as of 08:10, 3 August 2021

Agenda and Minutes

Meetings and Announcements

October Consortium Meeting

  • Wednesday, October 13th - Friday, October 15th
  • Hosted by:
    • University of Maryland Medical School, Baltimore MD
    • Michelle Gwinn-Giglio
  • Agenda

Noctua Outage in August

The Berkeley site will have a planned downtime mid-August as part of Lawrence Berkeley Lab's continuing operations to better secure the Lab's electrical systems against seasonal wildfires. This is the newly rescheduled date from the previously planned July date. The downtime is currently planned to be:

  • Friday, August 13th, from 11am-5pm PT

These times are approximate.

While most services will continue during this downtime, the following will be unavailable:

  • Noctua (production and development)
  • GO-CAM site (latest models component)
  • RDF endpoint

Noctua curators will need to save any work they wish to be preserved before the scheduled downtime.

GO-CAM Office Hours

  • Tuesday, August 24th at 8am PDT
  • Please add agenda items if you have models you'd like to share and discuss

Annotation Issues

Annotation documentation

New table of contents view that lists when a document was updated. http://wiki.geneontology.org/index.php/Annotation

RHEA Ontology Jamboree

  • Last week the ontology editors had a jamboree that addressed MF cross-references for enzymatic reactions. The jamboree resulted in a number of annotation guidelines.
  • Pascale will summarize.

  • 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
For amino acids, in which the biologically active enantiomer is the L form, and sugars, where it's the D form, even when the specific enantionmer is not mentioned, the annotation can be put on the more specific form; any activity on the uncommon forms would be explicitly mentioned in papers. 
  • 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

  • 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]


  • On call: DavidH, Suzi, Pascale, Harold, Cailey, Peter, Dmitry, Dustin, Edith, Guilia, Karen, Li, Midori, Patrick, Raymond, Rob, Seth, Debbie, Sridhar, Stan, Tanya