Web Based Semantic Query Answering of Yeast Knowledge

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Presentation transcript:

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

yOWL: A semantic web knowledge base for yeast scientists

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 http://ontology.dumontierlab.com/yOWL-primitive

Ontology Initially devised from the data Augmented with expert knowledge

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

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.

http://smart.dumontierlab.com