Annotation Conf. Call, March 25, 2014: Difference between revisions
(→E2/E3) |
|||
| Line 37: | Line 37: | ||
==Discussion== | ==Discussion== | ||
===E2/E3=== | ===E2/E3=== | ||
Mike went through his powerpoint presentation (available on the SF ticket). | 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: <br> | Questions: <br> | ||
* move E2 and E3 under transferase activity (they are transfering UB and to be a ligase you need ATP hydrolysis) | * move E2 and E3 under transferase activity (they are transfering UB and to be a ligase you need ATP hydrolysis) | ||
Revision as of 17:13, 25 March 2014
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
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
- 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.
GOC report
- regarding complex portal, please contact Sandra if you want access to their editor (curator interface) to add complexes.