Ontology Development Progress Report December 2014

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Ontology Development Progress Report

GOC Meeting Dec 2014

Prepared and Submitted by Jane Lomax and David Hill


  • 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.

Mappings to other ontologies

GO relations


Improved Biological Representation


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.

Membrane proteins

We developed design patterns for classes used to record the relationship of proteins and protein complexes to membranes (integral, anchored, peripheral etc).

Cell cycle

(Jane or Val)


(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)


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.