TY - GEN
T1 - Enabling ontology based semantic queries in biomedical database systems
AU - Zheng, Shuai
AU - Wang, Fusheng
AU - Lu, James
AU - Saltz, Joel
PY - 2012
Y1 - 2012
N2 - While current biomedical ontology repositories offer primitive query capabilities, it is difficult or cumbersome to support ontology based semantic queries directly in semantically annotated biomedical databases. The problem may be largely attributed to the mismatch between the models of the ontologies and the databases, and the mismatch between the query interfaces of the two systems. To fully realize semantic query capabilities based on ontologies, we develop a system DBOntoLink to provide unified semantic query interfaces by extending database query languages. With DBOntoLink, semantic queries can be directly and naturally specified as extended functions of the database query languages without any programming needed. DBOntoLink is adaptable to different ontologies through customizations and supports major biomedical ontologies hosted at the NCBO BioPortal. We demonstrate the use of DBOntoLink in a real world biomedical database with semantically annotated medical image annotations.
AB - While current biomedical ontology repositories offer primitive query capabilities, it is difficult or cumbersome to support ontology based semantic queries directly in semantically annotated biomedical databases. The problem may be largely attributed to the mismatch between the models of the ontologies and the databases, and the mismatch between the query interfaces of the two systems. To fully realize semantic query capabilities based on ontologies, we develop a system DBOntoLink to provide unified semantic query interfaces by extending database query languages. With DBOntoLink, semantic queries can be directly and naturally specified as extended functions of the database query languages without any programming needed. DBOntoLink is adaptable to different ontologies through customizations and supports major biomedical ontologies hosted at the NCBO BioPortal. We demonstrate the use of DBOntoLink in a real world biomedical database with semantically annotated medical image annotations.
KW - ontology
KW - query languages
UR - https://www.scopus.com/pages/publications/84871045669
U2 - 10.1145/2396761.2398715
DO - 10.1145/2396761.2398715
M3 - Conference contribution
AN - SCOPUS:84871045669
SN - 9781450311564
T3 - ACM International Conference Proceeding Series
SP - 2651
EP - 2654
BT - CIKM 2012 - Proceedings of the 21st ACM International Conference on Information and Knowledge Management
T2 - 21st ACM International Conference on Information and Knowledge Management, CIKM 2012
Y2 - 29 October 2012 through 2 November 2012
ER -