Annotation Conf. Call, May 27, 2014

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Agenda

Punted from previous call

Alzheimer's Disease Annotation Project (Sejal)

http://wiki.geneontology.org/index.php/Alzheimer%27s_Disease_Annotation_Project

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

E2/E3 terms

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.
  • 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