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Comput Methods Programs Biomed. 2013 Jul;111(1):220-7. doi: 10.1016/j.cmpb.2013.04.009. Epub 2013 May 11.

RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.

Author information

1
Biomedical Informatics Group, Artificial Intelligence Laboratory, School of Computer Science, Universidad Polit├ęcnica de Madrid, Campus de Montegancedo S/N, 28660 Boadilla del Monte, Madrid, Spain. aanguita@infomed.dia.fi.upm.es

Abstract

This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to execute SPARQL queries for retrieving microarray data, either from specific experiments or from more than one experiment at a time. Our system optimizes response times by caching and reusing information from previous queries. In this paper, we describe our methods for achieving this transformation. We show that our approach is complementary to other existing initiatives, such as Bio2RDF, for accessing and retrieving data from the ArrayExpress database.

PMID:
23669178
DOI:
10.1016/j.cmpb.2013.04.009
[Indexed for MEDLINE]

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