Ontology Group Progress Report Q1 2014: Difference between revisions

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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.
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)=====
=====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.


[[Category:Reports]]
[[Category:Reports]]
[[Category:Ontology]]
[[Category:Ontology]]

Revision as of 15:13, 11 March 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
Feb 2014 ()
Mar 2014 ()
Total Q1 2014 ()

Term Statistics

Total number of GO terms added Jan 2014 to Mar 2014: 
 Total number of GO terms added manually Jan 2014 to Mar 2014:         
 Total number of GO terms added via TermGenie template Jan 2014 to Mar 2014: 
 Total number of GO terms added via TermGenie freeform Jan 2014 to Mar 2014: 
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 x new templates to our template-based term addition tool, TermGenie. These are:

These templates utilise both classes within GO and classes from external ontologies, shown in parentheses. PO = plant ontology, CL = cell ontology, CHEBI = chemicals of biological interest ontology.

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 is fully described in PMID:23895341

Mapping Reactions in GO to Rhea

Currently we have 2787 of ### 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
  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.