Annotation Conf. Call, May 27, 2014
Punted from previous call
Alzheimer's Disease Annotation Project (Sejal)
Extracellular branch of GO CC (David OS)
I've done some work on fixing a number of issues with the extracellular branch of GO CC. I'd like to get some feedback from annotators on my proposed changes before committing them. slides here
The changes to the Ub terms have been made. http://sourceforge.net/p/geneontology/ontology-requests/10635/
- GO:0004839 ubiquitin activating enzyme activity
- This term has had definition change.
- Synonym: E1 [currently in place]
- New definition: Catalysis of the reaction: E1 + ubiquitin + ATP --> E1-ubiquitin + AMP + PPi, where the E1-ubiquitin linkage is a thioester bond between the C-terminal glycine of Ub and a sulfhydryl side group of an E1 cysteine residue. This is the first step in a cascade of reactions in which ubiquitin is ultimately added to a protein substrate.
- GO:0004842, ubiquitin-protein transferase activity" will change as follows, allowing for all current annotations to be correct as long as they were for 'E2' or 'E3' activities. Groups can choose to re-annotate as they wish.
- Definition: "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." http://amigo.geneontology.org/amigo/term/GO:0004842#display-lineage-tab
- two new children of GO:0004842, "ubiquitin-protein transferase activity"
- GO:0061631, Ubiquitin conjugating enzyme activity; Synonym E2, Hect E3
- GO:0061630, ubiquitin protein ligase activity; Synonym: E3
Annotation consistency exercise
MF vs BP annotations. Enzyme Regulator activity vs positive regulation of X terms