Ontology Browser WormBase Workshop International Worm Meeting 2015
-
Upload
raymond91105 -
Category
Science
-
view
98 -
download
3
Transcript of Ontology Browser WormBase Workshop International Worm Meeting 2015
![Page 1: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/1.jpg)
Ontology Browser
Raymond Lee, Juancarlos Chan, and the WormBase Consortium
20th IWM WorkShop
June 2015
![Page 2: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/2.jpg)
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
![Page 3: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/3.jpg)
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
![Page 4: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/4.jpg)
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.
![Page 5: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/5.jpg)
UCLA 2015
Expandable Hierarchy View
![Page 6: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/6.jpg)
UCLA 2015
Expandable Hierarchy View
![Page 7: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/7.jpg)
UCLA 2015
Graph View
![Page 8: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/8.jpg)
UCLA 2015
Graph View
![Page 9: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/9.jpg)
UCLA 2015
Inference Tree View
![Page 10: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/10.jpg)
UCLA 2015
Lists of Annotations
![Page 11: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/11.jpg)
UCLA 2015
Big Thanks To
● Seth Carbon and Chris Mungall (AmiGO 2, OWLTools)
![Page 12: Ontology Browser WormBase Workshop International Worm Meeting 2015](https://reader034.fdocuments.us/reader034/viewer/2022052602/55ce146dbb61ebd9488b47dd/html5/thumbnails/12.jpg)
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.