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)
Jan 2014 | 39 (44) |
Feb 2014 | 50 (81) |
Mar 2014 | 59 (41) |
Apr 2014 | 74 (52) |
May 2014 | 71 (75) |
Jun 2014 | 79 (70) |
Jul 2014 | 66 (58) |
Aug 2014 | 76 (115) |
Sept 2014 | 110 (52) |
Oct 2014 | 52 (73) |
Nov 2014 | 83 (69) |
Dec 2014 | 26 (5) |
Total 2014 | 746 (691) |
Term Statistics
Total number of GO terms added Jan 2014 to Dec 2,2014: 1868
Total number of GO terms added manually Jan 2014 to Dec. 2,2014: 549 Total number of GO terms added via TermGenie template Jan 2014 to Dec 2,2014: 1046 Total number of GO terms added via TermGenie freeform Jan 2014 to Dec 2,2014: 273
Total number of GO terms obsoleted Jan 2014 to Dec 2,2014: obsolete 57, merged 34
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 6 new templates to our template-based term addition tool, TermGenie. These are:
new templates:
- cell_migration (CL)
- biosynthesis_from (CHEBI)
- biosynthesis_via (CHEBI)
- catabolism_to (CHEBI)
- catabolism_via (CHEBI)
- metazoan_development (UBER)
templates with additional functionality:
- add plant cells for cell_differentiation (PO)
- add option to also create transmembrane transport for chemical
transport from to (CHEBI)
These templates utilize both classes within GO and classes from external ontologies, shown in parentheses. PO = plant ontology, CL = cell ontology, CHEBI = chemicals of biological interest ontology, UBER= Uberon.
GO relations
TODO
Improved Biological Representation
Transport
We developed design patterns for transport processes with specification of start and end location and barriers transported across as well as the nature of the entity transported. Newly added OWL axioms allow inference of start and end location over part relations in the GO. 11 different TermGenie templates for transport processes are now available to users.
Membrane proteins
We developed design patterns for classes used to record the relationship of proteins and protein complexes to membranes (integral, anchored, peripheral etc).
Apoptosis
(Paola - will send w/c 8 Dec)
Cilia/Guardia components
(Paola - will send w/c 8 Dec)
Extracellular vesicles
(Paola - will send w/c 8 Dec)
Viruses
The ontology work on this project has reached completion. There are now total of 344 classes under ‘viral process’ (GO:0016032) and 65 classes of ‘virion part’ (GO:0044423). A viral GO slim was also created. A paper 'Representing microbe-host interactions in the Gene Ontology' Foulger & Lomax et. al. has been submitted to BMC Microbiology.
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.