Semantic Web-Based Integration of Cancer Pathways and Allele Frequency Data

Author:

Holford Matthew E.1,Rajeevan Haseena23,Zhao Hongyu12,Kidd Kenneth K.2,Cheung Kei-Hoi234

Affiliation:

1. Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, U.S.A.

2. Department of Genetics, School of Medicine, Yale University, New Haven, CT, U.S.A.

3. Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT, U.S.A.

4. Department of Computer Science, Yale University, New Haven, CT, U.S.A.

Abstract

We demonstrate the use of Semantic Web technology to integrate the ALFRED allele frequency database and the Starpath pathway resource. The linking of population-specific genotype data with cancer-related pathway data is potentially useful given the growing interest in personalized medicine and the exploitation of pathway knowledge for cancer drug discovery. We model our data using the Web Ontology Language (OWL), drawing upon ideas from existing standard formats BioPAX for pathway data and PML for allele frequency data. We store our data within an Oracle database, using Oracle Semantic Technologies. We then query the data using Oracle's rule-based inference engine and SPARQL-like RDF query language. The ability to perform queries across the domains of population genetics and pathways offers the potential to answer a number of cancer-related research questions. Among the possibilities is the ability to identify genetic variants which are associated with cancer pathways and whose frequency varies significantly between ethnic groups. This sort of information could be useful for designing clinical studies and for providing background data in personalized medicine. It could also assist with the interpretation of genetic analysis results such as those from genome-wide association studies.

Publisher

SAGE Publications

Subject

Cancer Research,Oncology

Cited by 4 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. Uncovering influence links in molecular knowledge networks to streamline personalized medicine;Journal of Biomedical Informatics;2014-12

2. A Semantic-Based Platform for Medical Image Storage and Sharing Using the Grid;Biomedical Engineering Systems and Technologies;2013

3. Knowledge-Based Bioinformatics;Knowledge-Based Bioinformatics;2010-07-07

4. The use of web ontology languages and other semantic web tools in drug discovery;Expert Opinion on Drug Discovery;2010-04-19

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