Ontology Browser

Raymond Lee, Juancarlos Chan, and the WormBase Consortium

20th IWM WorkShop

June 2015

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

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

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.

UCLA 2015

Expandable Hierarchy View

UCLA 2015

Expandable Hierarchy View

UCLA 2015

Graph View

UCLA 2015

Graph View

UCLA 2015

Inference Tree View

UCLA 2015

Lists of Annotations

UCLA 2015

Big Thanks To

● Seth Carbon and Chris Mungall (AmiGO 2, OWLTools)

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.