Web Based Semantic Query Answering of Yeast Knowledge

Web Based Semantic Query Answering of Yeast Knowledge Michel Dumontier, Alexander De Leon Battista, Natalia Villanueva-Rosales ISMB 2007: HCLS BOF

y. OWL: A semantic web knowledge base for yeast scientists

y. OWL Ontology § YOWL – 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/y. OWL-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: Pathway. Participant is. Participant. In some Pathway Physical. Interaction. Participant is. Participant. In some Physical. Interaction. Experiment

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.

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