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Cancer Inform. 2009 May 13;8:65-73. eCollection 2009.

Using semantic web technologies to annotate and align microarray designs.

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Program for Computational Biology and Bioinformatics (CBB), Yale University School of Medicine, New Haven, CT. ; Department of Pathology, Yale University School of Medicine, New Haven, CT.
Department of Pathology, Yale University School of Medicine, New Haven, CT.


In this paper, we annotate and align two different gene expression microarray designs using the Genomic ELement Ontology (GELO). GELO is a new ontology that leverages an existing community resource, Sequence Ontology (SO), to create views of genomically-aligned data in a semantic web environment. We start the process by mapping array probes to genomic coordinates. The coordinates represent an implicit link between the probes and multiple genomic elements, such as genes, transcripts, miRNA, and repetitive elements, which are represented using concepts in SO. We then use the RDF Query Language (SPARQL) to create explicit links between the probes and the elements. We show how the approach allows us to easily determine the element coverage and genomic overlap of the two array designs. We believe that the method will ultimately be useful for integration of cancer data across multiple omic studies. The ontology and other materials described in this paper are available at


annotation; data integration; genomics; ontology; semantic web

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