Ontology Group Progress Report Q1 2014
Ontology Development Progress Report
Report for Jan-Mar 2014
Prepared and Submitted by Jane Lomax and David Hill
Personnel
- Tanya Berardini (TAIR)
- Heiko Dietze (LBL)
- Harold Drabkin (MGI)
- Becky Foulger (EBI) (left the project Jan 2014)
- David Hill (MGI)
- Jane Lomax (EBI)
- Chris Mungall (LBL)
- David Osumi-Sutherland (EBI)
- Paola Roncaglia (EBI)
Ontology Editing
SourceForge Requests
SF items opened (SF items closed)
Jan 2014 | 39 (26) |
Feb 2014 | 49 (33) |
Mar 2014 | 18 (5) |
Total Q1 2014 | 106 (64) |
Term Statistics
Total number of GO terms added Jan 2014 to Mar 2014: 1826
Total number of GO terms added manually Jan 2014 to Mar 2014: 519 Total number of GO terms added via TermGenie template Jan 2014 to Mar 2014: 1028 Total number of GO terms added via TermGenie freeform Jan 2014 to Mar 2014: 279
Total number of GO terms obsoleted Jan 2014 to Mar 2014:
Major Projects
Transition to OWL
TermGenie templates
Between Jan 2014 and Mar 2014 we have added 4 new templates to our template-based term addition tool, TermGenie. These are:
(CHEBI) Template: biosynthesis_from Description: biosynthetic process of a chemical entity from a chemical entity
(CHEBI) Template: biosynthesis_via Description: biosynthetic process of a chemical entity via an intermediate chemical entity
(CHEBI) Template: catabolism_to Description: degradation of a chemical entity to an other chemical entity
(CHEBI) Template: catabolism_via Description: degradation of a chemical entity via an intermediate chemical entity
Mappings to other ontologies
To take further advantage of the reasoning capabilities of OWL and to integrate the expertise of distributed resources, we have continued to work with developers from other groups to cross-reference GO terms with external ontologies.
Mapping Chemicals in GO to ChEBI
This work continues as needed and is fully described in PMID:23895341
Mapping Reactions in GO to Rhea
Currently we have 2787 of 6372 catalytic activity terms mapped to Rhea reactions.
Improved Biological Representation
Signaling
Apoptosis
Viral work
We are now reaching the end of the ontology changes for the viral processes and cellular components in GO. This work has affected 334 biological process terms and 67 cellular component terms. We are drafting a paper to be submitted to BMC Microbiology.
Metabolic Pathways
- Glycolysis- The model accounting for canonical glycolysis and its variants are in the experimental directory.
- Molybdopterin cofactor biosynthesis- The core pathway and some of its variants are in the live file.