Annotation Conf. Call, May 27, 2014: Difference between revisions

Revision as of 01:53, 27 May 2014

Agenda

Punted from previous call

Alzheimer's Disease Annotation Project (Jane/Paola/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.
- 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

@@ Line 8: / Line 8: @@
 ===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.
+[http://wiki.geneontology.org/images/c/c3/Fixing_extracellular_annotators_meeting.pptx 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.
+** 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
-[http://wiki.geneontology.org/images/c/c3/Fixing_extracellular_annotators_meeting.pptx slides here]
 ===Annotation consistency exercise===
 MF vs BP annotations. Enzyme Regulator activity vs positive regulation of X terms