Ontology Development Progress Report December 2013
Ontology Development Progress Report
GOC Meeting Dec 2013
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)
- Jane Lomax (EBI)
- Chris Mungall (LBL)
- David Osumi-Sutherland (EBI)
- Paola Roncaglia (EBI)
Ontology Editing
SourceForge Requests
SF items opened (SF items closed)
Term Statistics
Total number of GO terms added Jan 2013 to Dec 2013: 1365
Total number of GO terms added manually Jan 2013 to Dec 2013: 344 Total number of GO terms added via TermGenie template Jan 2013 to Dec 2013: 803 Total number of GO terms added via TermGenie freeform Jan 2013 to Dec 2013: 218
Total number of GO terms obsoleted Jan 2013 to Dec 2013: 67
TermGenie Terms
Major Projects
Transition to OWL
We have now completed a shift in which all ontology reasoning is performed using OWL-based reasoners run during automated jobs or manually by ontology editors. Ontology editors were trained on the use of the Protege editor during several focus group meetings to prepare for the OBO-OWL shift. Most ontology editing on a day-to-day basis is still performed using obo-edit and the ontologies are committed in obo format. Once a commit is requested the GO is automatically transferred to an OWL format and the main obo file, auxiliary cross-product files and external ontologies are checked for logical errors in the Jenkins environment. If errors are found, an automated e-mail is sent to ontology editors indicating that the ontology build has failed the checks and a report is included that indicates where the problem was encountered. Ontology editors can then fix the problem before the 'public' version of the ontology is released. In addition, ontology editors use the OWL version directly in the Protege editor to test new ideas and to further troubleshoot build failures.
As a result of this work, many of the relationships in the ontology are now automatically inferred rather than manually asserted by ontology editors. A report report listing added and deleted relationships is delivered each week to the ontology editing group as a 'sanity' check.
Internal logical definitions
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
We have completed the first phase of our integration with The Chemicals of Biological Interest (ChEBI) resource. All terms that follow standard patterns and are differentiated by chemical structure are defined using references to the ChEBI resource. GO ontology editors work together with ChEBI editors to address queries about ontology alignment and to make additions to ChEBI when necessary. This work is fully described in PMID:23895341
Mapping Reactions in GO to Rhea
Mapping cellular Components in GO to SAO
PMID:24093723
Improved Biological Representation
Signaling
Apoptosis
Viral work
Metabolic Pathways (Glycolysis)
We have begun work on better modeling metabolic pathways by choosing a universal pathway that although straightforward still presents challenges for GO representation, glycolysis. Taking advantage of the knowledge in the Reactome resource, we have been working with an expert from reactome to represent the pathway in the GO framework. As a test-case for the representation of other metabolic pathways in GO, we have begun creating has_part links between the biological process and the molecular functions that are always a part of a process. We are exploring the use of these representations to create individual views that can be used in a modular annotation framework.