Ontology Development Progress Report December 2014
Ontology Development Progress Report
GOC Meeting Dec 2014
Prepared and Submitted by Jane Lomax and David Hill
Personnel
- David Hill (MGI)
- Tanya Berardini (TAIR)
- Heiko Dietze (LBL)
- Harold Drabkin (MGI)
- Becky Foulger (EBI) (left Jan 2014)
- Jane Lomax (EBI)
- Chris Mungall (LBL)
- David Osumi-Sutherland (EBI)
- Paola Roncaglia (EBI)
Ontology Editing
SourceForge Requests
SF items opened (SF items closed)
Mar 2014 | [data lost in tracker transition] |
Apr 2014 | () |
May 2014 | () |
Jun 2014 | () |
Jul 2014 | () |
Aug 2014 | () |
Sept 2014 | () |
Oct 2014 | () |
Nov 2014 | () |
Dec 2014 | () |
Total 2014 | () |
Term Statistics
Total number of GO terms added Jan 2014 to Dec 2014:
Total number of GO terms added manually Jan 2014 to Dec 2014: Total number of GO terms added via TermGenie template Jan 2014 to Dec 2014: Total number of GO terms added via TermGenie freeform Jan 2014 to Dec 2014:
Total number of GO terms obsoleted Jan 2014 to Dec 2014:
Major Projects
Transition to OWL
Ontology editors are routinely using the OWL version of GO to check for logical consistency in the ontology and to create terms with logical definitions. OWL is also used as the underlying format for creating new terms via the termgenie tool.
TermGenie templates
Since Jan 2014 we have added ? new templates to our template-based term addition tool, TermGenie. These are:
These templates utilise both classes within GO and classes from external ontologies, shown in parentheses. PO = plant ontology, CL = cell ontology, CHEBI = chemicals of biological interest ontology.
Mappings to other ontologies
Mapping Reactions in GO to Rhea
Improved Biological Representation
Apoptosis
Viral work
Metabolic Pathways (Glycolysis)
The representation of glycolytic pathways is now complete in the ontology and we have begun working on the representation of glycolytic fermentation using the existing glycolysis framework.
Ubiquitin and other small conjugating proteins
As a result of a request from the BioGrid group, we have refactored the molecular function terms that represent the E1, E2 and E3 enzymatic activities for the enzymes that attach ubiquitin to proteins. This work was recently extended to include all other small conjugated proteins.