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biomedical queries

Theory and Practice of Logic Programming (1)

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Generating explanations for biomedical queries
ESRA ERDEM, UMUT OZTOK
Journal:

Theory and Practice of Logic Programming / Volume 15 / Issue 1 / January 2015

Published online by Cambridge University Press:

17 December 2013, pp. 35-78
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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 PharmGKB, DrugBank, BioGRID, CTD, SIDER, Disease Ontology, and Orphadata.