Annotation Call September 23, 2014

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Agenda

Present: Rama, Rachael, David Hill, Ruth, Becky, Paul, Li, Petra, Paola, Aleks, Kimberly, Edith, Doug, Sabrina (Zfin new curator), Stan, Chris, PaulT (USC), Tanya (late)

Ub/Ub-like functions (David H)

1) We need annotator feedback on the fate of 'ubiquitin thiolesterase activity' (GO:0004221). This term can either be obsoleted or merged into 'ubiquitinyl hydrolase activity' (GO:0036459). There has been an observation that many of the annotations to (GO:0004221) could actually be transferred to 'ubiquitin-specific protease activity' (GO:0004843). Annotators will need to reexamine the annotations to GO:0004221 and reannotate to either GO:0036459 or GO:0004843. See SF items:#11094 and #10519

2) Moving along with the E1,E2, E3 terms, GO:0019787 small conjugating protein ligase activity suffers from the same issues as the original ubiquitin ligase terms. We need to revamp the MF ontology for the other small proteins in the same way that we did for the ubiquitin activating, ligase and conjugating enzymes. Looking at annotations to GO:0019787, it appears that all three types of enzyme activity have been annotated using this term. We need to go back and reexamine those annotations once this part of the ontology has been cleaned up. See SF item #11026

Reminders

GOC agenda items

Add further items here http://wiki.geneontology.org/index.php/2014_Barcelona_GOC_Meeting_Agenda

IPI guidelines

Please take a look at the proposed guidelines sent to the GO email list on 15th September and feed back with suggestions.

Discussion

Ub/Ub-like functions (David H)

  • Action item 1: EC is getting rid of 3.1.2.15 which maps to GO:4221. This term (4221) is going to be merged with GO:36459. Curators are urged to review the annotations to 4221 and decide if the annotations should be moved to 36459 or to an appropriate Ub-specific protease term.
  • Action item 2: Regarding other ontology changes to other small conjugating protein ligase terms. David doesn't want to change the ontology first because if the curators don't review the annotations right away some of hte annotations can be wrong. We want curators to reannotate first. We could use pfam signatures to rehouse the annotations. But the pfam to GO mapping won't change until the ontology changes are in place. David H will send a list of old terms, their fate, new terms etc to Paul T who will then come up with new pfam mappings. These mappings will be used by curators to move the annotations and the ontology changes will be committed after.

Next Annotation Call

  • We will all be at Barcelona on October 14th (next annotation call). We will look into having a call from Barcelona. Otherwise the next Annotation call will be on October 28th. We would like to discuss curation issues at this call. Please post interesting papers (for col-16 or other curation).

Jenkins GAF reports

  • There were a few empty GAF reports in Jenkins. This was fixed by Heiko etal. Please check the report and take care of the flagged annotations.
  • Regarding running the GAF check ourselves, Rama will check with Heiko and write some documentation. This needs setting up OWL tools.