Semantic Web-Based Integration of Cancer Pathways and Allele Frequency Data
Autor: | Haseena Rajeevan, Kenneth K. Kidd, Matthew E. Holford, Hongyu Zhao, Kei-Hoi Cheung |
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Rok vydání: | 2009 |
Předmět: |
Cancer Research
Biology lcsh:RC254-282 Oracle 03 medical and health sciences 0302 clinical medicine informatics BioPAX : Biological Pathways Exchange 030212 general & internal medicine data integration Allele frequency Semantic Web Cancer 030304 developmental biology computer.programming_language 0303 health sciences Information retrieval pathway business.industry Methodology Ontology language lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens Data science 3. Good health ComputingMethodologies_PATTERNRECOGNITION Oncology Semantic technology Personalized medicine business computer allele frequency RDF query language |
Zdroj: | Cancer Informatics, Vol 2009, Iss Semantic Technologie, Pp 19-30 (2009) Cancer Informatics, Vol 8, Iss Semantic Technologie, Pp 19-30 (2009) Cancer Informatics Cancer Informatics, Vol 8 (2009) |
ISSN: | 1176-9351 |
DOI: | 10.4137/cin.s1006 |
Popis: | 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. |
Databáze: | OpenAIRE |
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