Annotation Conf. Call, March 25, 2014

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Agenda

Present:
SGD: Rama,Paul, Diane, Edith
MGI: David, Judy Li
Dicty: Pascake
WB: Kimberly
Pombase: Midori
UCL: Ruth, Paul, Ana
EBI: Rachael, Jane, Aleks, Susan, Paola
Berkeley: Chris, Suzi
Reactome: Peter
RGD: Stan
TAIR: Tanya (not entire call)

E2/E3 SF ticket

http://sourceforge.net/p/geneontology/ontology-requests/10635/

We will talk about the changes being proposed. Interesting papers:
Overview: http://jcs.biologists.org/content/125/3/531.full
SCF UbLigase RING finger type: http://www.sciencedirect.com/science/article/pii/S0079610799000103?via=ihub

GOC meeting report

Discussion

E2/E3

Mike went through his powerpoint presentation (available on the SF ticket). There are three reactions, but only two terms available with GO:4842 being used for E2 and E3. Also GO:4842 has ATP hydrolysis as part of the definition while ATP is not required. Questions:

  • move E2 and E3 under transferase activity (they are transfering UB and to be a ligase you need ATP hydrolysis)
  • we need separate terms for E2 and E3 when the functions are distinct and one term when the activity is combined
  • we don't have a term for the complex function of E2 and E3 (combined activity). We could create a new term for this complex function and use has_part to relate the E2 function
  • Ruth: Can you create the new terms without obsoleting the old ones so we know how it works? We should let Interpro do the mapping and use that as a guide to remap manual annotations.
  • David will mockup the proposed changes, send it around before he commits it.
  • MikeL has a list of proteins that have this activity. He will send it to us and we can see what they are.

GOC report

  • regarding complex portal, please contact Sandra if you want access to their editor (curator interface) to add complexes.