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

miRNA update (Ruth): http://gocwiki.geneontology.org/index.php/2014_College_Station_GOC_Meeting_Agenda
Orion: new tool to build LEGO models (URL: http://go-genkisugi.rhcloud.com/seed/model/gomodel:goa_human-5323da180000002)
integrating CANTO (community annotation tool developed by Pombase) into the CAF framework to receive annotations from the community
tool registry- we are not going to maintain a tool registry. We will provide relevant tools ourselves.
protein2GO
- is showing ECO terms that map to the GO 3-letter evidence starting this week (they have plans to allow ECO terms by the end of the year)
- are working on integrating RNA central and Complex IDs for curation with protein2GO
GOC new website to be rolled out in April (date TBA). Everybody can get an account in the new Drupal system and make edits to pages (no more SVN co/ci etc)
jsPAINT prototype -http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo/phylo_graph
AmiGO2 has been live for more than a week now. Please check your linkouts.

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.