We introduce novel mathematical models and algorithms to generate (shortest or k different) explanations for biomedical queries, using answer set programming. We implement these algorithms and integrate them in BioQuery -ASP. We illustrate the usefulness of these methods with some complex biomedical queries related to drug discovery, over the biomedical knowledge resources Pharm GKB, DrugBank , Bio GRID, CTD, SIDER, Disease Ontology , and Orphadata .
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