Abstract
BioPax Level 3 is a novel approach to describe pathways at a semantic level by means of an owl ontology. Data provided as BioPax instances is distributed in several databases, and so it is difficult to find integrated information as instances of this ontology. Biopax is a biology ontology that aims to facilitate the integration and exchanged data maintained in biological pathways data. In this paper we present an approach to integrate pathway information by means of an ontology-based mediator (SB-KOM). This mediator has been enabled to produce instances of BioPax Level 3 from integrated data. Thus, it is possible to obtain information about a specific pathway extracting data from distributed databases.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Baxevanis, A.D., Ouellette, B.F.F.: Bioinformatics: a Practical Guide to the Analysis of Genes and Proteins. John Wiley and Sons, New York (2001)
Krieger, C.J., Zhang, P., Mueller, L.A., Wang, A., Paley, S., Arnaud, M., Pick, J., Rhee, S.Y., Karp, P.D.: Metacyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research 32, 348 (2004)
Alfarano, C., Andrade, C.E., Anthony, K., Bahroos, N., Bayec, M., Bantoft, K., Betel, D., Bobechko, B., Boutilier, K., Burguess, E., et al.: The Biomolecular interaction network database and related tools 2005 update. Nucleic Acids Research 33, 418 (2005)
Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R., Orturk, M.: PATIKA: an Integrated Visual Enviroment for Collaborative construction and analysis of cellular pathaways. Bioinformatics 18, 996 (2002)
Joshi-Tope, G., Gillespie, M., Vastrik, I., D’ Eustachio, P., Schmidt, E., De Bono, B., Jassal, B., Gopinath, G.R., Wu, G.R., Mathews, L., et al.: Reactome: a Knowledge Base of Biological Pathways. Nucleic Acid Research 33, 428 (2005)
Lemer, C., Antezana, E., Couche, F., Fays, F., Santolaria, X., Janky, R., Deville, Y., Richelle, J., Wodak, S.J.: The aMAZE, LightBench: a Web Interface to a Relational Database of Cellular Processes. Nucleic Acid Research 32, 443 (2004)
Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M.: The KEGG Resource for Deciphering the Genome. Nucleic Acid Research 32 (2004)
Alberts, B.: Molecular biology of the cell. Garland Science, New York (2002)
Schaefer, C.F., Anthony, K., Krupa, S., Buchoff, J., Day, M., Hannay, T., Buetow, K.H.: PID.: The Pathway Interaction Database. Nucleic Acids Research 37, 674–679 (2009)
Mi, H., Lazareva-Ulitsky, B., Loo, R., Kejariwal, A., Vandergriff, J., Rabkin, S., Guo, N., Muruganujan, A., Doremieux, O., Campbell, M.J., et al.: The PANTHER database of proteins families, subfamilies, functions and pathway. Nucleics Acid Research 33 (2005)
Navas Delgado, I., Montañez, R., Pino Ángeles, A., Moya García, A., Urdiales, J.L., Sánchez Jiménez, F., Aldana Montes, J.F.: AMMO-Prot: Amine System Project 3D-Model Finder. BMC Bioinformatics 9, S5 (2008)
Navas-Delgado, I., Aldana-Montes, J.F.: Extending SD-Core for Ontology-based Data Integration. J-Jucs 15, 3201–3230 (2009)
Reyes-Palomares, A., Montañez, R., Real-Chicharro, A., Chiniber, O., Kerzazi, A., Navas-Delgado, I., Medina, M.A., Aldana-Montes, J., Sánchez-Jiménez, F.: System Biology Metabolic Assitant: an ontology-based tool for integration of metabolic data in kinetic modeling. Bioinformatics 25, 834–835
Navas-Delgado, I., Montañez, R., Pino-Ángeles, A., Moya-García, A., Urdiales, J.L., Sánchez-Jiménez, F., Aldana-Montes, J.F.: AMMO-Prot: ASP Model Finder. BMC Bioinformatics 9, 1471–2105 (2008)
Chang, A., Scheer, M., Grote, A., Schomburg, I., Schomburg, D.: BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res. 37, 588–592 (2009)
Degtyarenko, K., De Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Darsow, M., Guedj, M., Ashburner, M.: ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, 344–350 (2008)
Bairoch, A., Apweiler, R., Wu, C., Barker, W., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., et al.: The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, 154–159 (2005)
Wittig, U., Golebiewski, M., Kania, R., Krebs, O., Mir, S., Weidemann, A., Anstein, S., Saric, J., Rojas, I.: SABIO-RK: Integration and Curation of Reaction Kinetics Data. In: Leser, U., Naumann, F., Eckman, B. (eds.) DILS 2006. LNCS (LNBI), vol. 4075, pp. 94–103. Springer, Heidelberg (2006)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
García-Godoy, M.J., Navas-Delgado, I., Aldana-Montes, J.F. (2012). SB-KOM: Integration of Pathway Information with BioPax. In: Freitas, A.T., Navarro, A. (eds) Bioinformatics for Personalized Medicine. JBI 2010. Lecture Notes in Computer Science(), vol 6620. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28062-7_6
Download citation
DOI: https://doi.org/10.1007/978-3-642-28062-7_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-28061-0
Online ISBN: 978-3-642-28062-7
eBook Packages: Computer ScienceComputer Science (R0)