Ontology Group Progress Report Q1 2014

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Ontology Development Progress Report

Report for Jan-Mar 2014

Prepared and Submitted by Jane Lomax and David Hill


  • 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:  318
 Total number of GO terms added manually Jan 2014 to Mar 2014:  124
 Total number of GO terms added via TermGenie template Jan 2014 to Mar 2014:  153  
 Total number of GO terms added via TermGenie freeform Jan 2014 to Mar 2014:  41
Total number of GO terms obsoleted Jan 2014 to Mar 2014:  7

Major Projects

Transition to OWL

Lots of work consolidating the ontology files in order to simplify OBO-OWL roundtrip. ~/go-trunk/ontology/editors/gene_ontology_write_xp.obo is now part of ~/go-trunk/ontology/editors/gene_ontology_write.obo which imports subsets of all external ontologies referenced.

Work on the reasoner assertion pipeline.

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


Rebecca Foulger left the GO project in Jan, her work on signaling to date is summarized on the signaling wiki page.


We've performed further quality checks on apoptosis ontology and annotations focusing mainly on the execution phase of apoptosis. This resulted in rehousing a number of annotations, and in the addition of annotation examples and annotation guidance both directly in the ontology and in the apoptosis curation manual (http://wiki.geneontology.org/index.php/Apoptosis_Curation_Manual). We've also rehoused some existing annotations to GO:0070265 'necrotic cell death' and its regulation terms to take advantage of the revised and enriched ontology for necroptosis terms.


In collaboration with Scott Dawson's lab at UC Davis, we're working on adding GO Cellular Component terms to annotate gene products that localize to specific locations in Giardia species. So far, we've added 27 new terms. On-going work includes addition of taxon restrictions to Giardia-specific terms where needed.

Cilial Project

Project in conjuction with the Syscillia Consortium. A number of new GO cc terms have been added, and annotation by the Syscillia Consortium has begun. Biological process terms to follow.

Viral work

We have now finished 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. The SIB paper that describes the mapping element of this project has been submitted to PloS One.

Metabolic Pathways

  1. Glycolysis- The model accounting for canonical glycolysis and its variants are in the experimental directory.
  2. Molybdopterin cofactor biosynthesis- The core pathway and some of its variants are in the live file.

Alzheimer's Project

Sejal Patel has joined the GO team at EBI for 3 months to annotate and improve the ontological representation of normal processes affected by Alzheimer's disease, see project page.