title: NCBI2RDF: enabling full RDF-based access to NCBI databases.
abstract: RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments.
authors.affiliation: Biomedical Informatics Group, Artificial Intelligence Laboratory, School of Computer Science, Universidad Politécnica de Madrid, Campus de Montegancedo S/N, Boadilla del Monte, 28660 Madrid, Spain. aanguita@infomed.dia.fi.upm.es
authors.forename: Alberto
authors.initials: A
authors.lastname: Anguita
authors.forename: Miguel
authors.initials: M
authors.lastname: García-Remesal
authors.forename: Diana
authors.initials: D
authors.lastname: de la Iglesia
authors.forename: Victor
authors.initials: V
authors.lastname: Maojo
mesh_terms: D022126:Access to Information; D030541:Databases, Genetic; D057386:Search Engine; D012984:Software