Ontology Browser WormBase Workshop International Worm Meeting 2015

1. Ontology Browser
Raymond Lee, Juancarlos Chan,
and the WormBase Consortium
20th IWM WorkShop
June 2015

2. UCLA 2015
WormBase Ontologies and Annotations
• Controlled vocabulary of concepts organized in a hierarchy.
• ** Developed by WormBase
Total Terms (w/ Annotation) Annotations
Anatomy** (AO) 7,223 (33%) 69,778
Gene (GO) 42,338 (9%) 233,727
Human Disease (DO) 8,854 (6%) 2,232
Life Stage** (LSO) 676 (78%) 367,288
Phenotype** (PO) 2,224 (79%) 94,935

3. UCLA 2015
WOBr (/ˈwoʊbɚ/) Design Requirements
● Browse terms and navigate the hierarchy
● Retrieve annotations (apply reasoning)
ASHL->ASH->Sensory neuron->Neuron
● Expandable (more data types and features)
● Integrate into WormBase UI
● Leverage existing technology

4. UCLA 2015
WOBr Implementation
● Backend: OWLTools and Golr (GeneOntology Project)
adapted for WormBase ontologies and annotations.
● Frontend: customized Perl and Java scripts integrated
into WormBase Catalyst framework
● Three viewers: expandable hierarchical, inference tree,
and graph.

5. UCLA 2015
Expandable Hierarchy View

6. UCLA 2015
Expandable Hierarchy View

7. UCLA 2015
Graph View

8. UCLA 2015
Graph View

9. UCLA 2015
Inference Tree View

10. UCLA 2015
Lists of Annotations

11. UCLA 2015
Big Thanks To
● Seth Carbon and Chris Mungall (AmiGO 2, OWLTools)

12. UCLA 2015
AmiGO 2
● Gene Ontology next-generation browser and search
tool.
● Backend - GOlr
○ OWLTools - process ontology and annotation files,
apply reasoning.
○ Apache Solr - document search platform.
● Frontend - Perl, JavaScript API, feature-rich UI.
● Open source, active development, congruent design
requirements, open communication channels.