1. Web Based Semantic Query Answering of Yeast Knowledge
Michel Dumontier, Alexander De Leon Battista, Natalia Villanueva-Rosales
ISMB2007: HCLS BOF

2. yOWL: A semantic web knowledge base for yeast scientists

3. yOWL Ontology YOWL Coverage
244 classes
38 defined
57 object properties
11 data properties
22 annotation
Coverage
structural and functional chromosome features
database cross references GO
molecular function
cellular component
biological process
interactions
pathways
phenotypes
literature

4. Ontology Initially devised from the data
Augmented with expert knowledge

5. Semantic Query Answering: DL Query
Find pathway participants that are also physical interaction participants.
Defined Classes:
PathwayParticipant
isParticipantIn some Pathway
PhysicalInteractionParticipant
isParticipantIn some PhysicalInteractionExperiment

6. Semantic Query Answering: Broad Query
Conjunctive query
Variable Binding
Ontology Integration
Find genes/proteins with transferase activity that are part of a complex, have rescued a non-viable phenotype by overexpression and have a known role in some pathway. Retrieve the genes, sources, pathways, experiments, chromosome and complex that satisfy these requirements.