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Generating explanations for biomedical queries

Published online by Cambridge University Press:  17 December 2013

ESRA ERDEM  and
UMUT OZTOK
ESRA ERDEM
Affiliation:
Sabancı University, Orhanlı, Tuzla, İstanbul 34956, Turkey (e-mail: esraerdem@sabanciuniv.edu, uoztok@sabanciuniv.edu)
UMUT OZTOK
Affiliation:
Sabancı University, Orhanlı, Tuzla, İstanbul 34956, Turkey (e-mail: esraerdem@sabanciuniv.edu, uoztok@sabanciuniv.edu)
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Abstract

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.

Keywords

answer set programmingexplanation generationquery answeringbiomedical queries
Type
Regular Papers
Information
Theory and Practice of Logic Programming , Volume 15 , Issue 1 , January 2015 , pp. 35 - 78
Copyright
Copyright © Cambridge University Press 2013 

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