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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
- 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.
Editor's Notes
- WormBase uses ontologies extensively to organize annotations. Some ontologies are developed in house but we also use and collaboratively develop external ontologies. Most of the ontologies we use share a similar organization and thus are amenable to unified viewing and query tools.
- WOBr - WormBase Ontology Browser
- Front page -> Tools -> Ontology Browser. Use Anatomy Ontology for illustration.
- Click on Organ system, expand to show child terms.
- On specific ontology term pages, graph view of all paths (including all relationship types) from focus term to root.
- Inset shows all parent branches. Expedite discovery of sibling terms.
- Shows inferable relationship from the focus term to the root. For the focus term and child terms, there are numbers of annotations. The first number indicates the total, combining direct and inferred, annotations.