kpath: An example of metabolic pathway data integration using Linked Data

Ismael Navas-Delgado1, María Jesús García-Godoy1, Esteban López-Camacho1, Maciej Rybinski1, Armando Reyes-Palomares2,3, Miguel Ángel Medina2,3 and José F. Aldana-Montes1 1 Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga, Andalucía Tech, Ada Byron Research Building, E-29071 Málaga, Spain 2 Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Andalucía Tech, and IBIMA (Biomedical Research Institute of Málaga), E-29071 Málaga, Spain 3 CIBER de Enfermedades Raras (CIBERER) E-29071 Málaga, Spain The main databases related to metabolic pathways, such as Kegg, Brenda, Reactome and Biocyc, provide partially interlinked data on metabolic pathways. This limitation only allows independent searches to retrieve cross-database information on metabolism and restricts the use of more complex searches to discover new knowledge or relationships. Kpath integrates information on metabolic pathways from different sources:  Bio2RDF’s Kegg (core data)  NCBI Taxonomy (organism data)  SwissProt (protein data)  Bio2RDF’s Reactome (related pathway data). Kpath provides a navigational interface to ease the use of the integrated data by end users. It includes three different applications: 1.Pathway Graphical Viewer 2.Pathway Graphical Editor 3.Relationship Search Pathway Graphical Viewer Graphs with the participating biochemical reactions (i.e. metabolites, enzymes and genes) in a given pathway. Components related to other pathways are also shown allowing comparative analyses between pathways. Integrated data available through a public SPARQL (Virtuoso) endpoint: Pathway Graphical Editor Edition functionality, enabling users to customize pathways and save a local copy of their version. The Relationship Search tool enables the graphical browsing of relationships between pathway components (independently of their source). Navas-Delgado, I., García-Godoy, M.J., López-Camacho, E., Rybinski, M., ReyesPalomares, A., Medina, M.A., and Aldana-Montes, J.F. kpath: integration of metabolic pathway linked data. Database 2015 1-11. INTRODUCTION SYSTEM AND METHODS KPATH USER INTERFACE http://sparql.kpath.khaos.uma.es REFERENCE http://browser.kpath.khaos.uma.es ACKNOWLEDGMENTS Ismael Navas-Delgado: [email protected] Maria Jesús García-Godoy: [email protected]s Esteban López-Camacho: est[email protected] Maciej Rybinski,: [email protected] José F. Aldana-Montes: [email protected] CONTACTS