Abstract
This paper introduces GlycoBrowser, a dynamic biological pathway exploration and visualization tool. Its capabilities include incremental navigation of pathways, as well as overlaying relevant experimental data about glycans and reactions within a pathway. The use of ontologies not only allows dynamic construction of pathways, but also facilitates more accurate validation of the information retrieved. Pathway exploration is initiated by means of an ontologically driven glycan structure building tool, which facilitates glycan structure construction and searching with minimal user error. Because of the complex nature of glycan structures and the difficulty involved in interpreting the associated data, GlycoBrowser is tailored especially to suit the needs of glycobiologists.
GlycoBrowser was developed as part of the Integrated Technology Resource for Biomedical Glycomics (P41 RR18502-02), funded by the National Institutes of Health - National Center for Research Resources.
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
Joseki, http://www.joseki.org
Open Biomedical Ontology
Aurrecoechea, C., Heiges, M., Wang, H., Wang, Z., Fischer, S., Rhodes, P., Miller, J., Kraemer, E., Stoeckert, C.J., Roos, D.S., Kissinger, J.C.: ApiDB: Integrated resources for the apicomplexan bioinformatics resource center. Nucleic Acids Research 35, D427–D430 (2007)
Brown, M.R.: FastCGI: A High-Performance Gateway Interface. In: Programming the Web - a search for APIs workshop. 5th Int. World Wide Web Conference, Paris, France (1996)
Carroll, J.J., Dickinson, I., Dollin, C., Reynolds, D., Seaborne, A., Wilkinson, K.: Jena: Implementing the Semantic Web Recommendations. In: Proc. of the 13th Int. World Wide Web Conference (WWW), pp. 74–83 (May 2004)
Ceroni, A., Dell, A., Haslam, S.M.: The GlycanBuilder: A fast, intuitive and flexible software tool for building and displaying glycan structures. Source Code for Biology and Medicine 2(3) (2007)
Dahlquist, K.D., Salomonis, N., Vranizan, K., Lawlor, S.C., Conklin, B.R.: GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genetics 31, 19–20 (2002)
Ellson, J., Gansner, E., Koutsofios, L., North, S.: GordonWoodhull: Graphviz - Open Source Graph Drawing Tools. Lucent Technologies/AT&T Labs Research Tech. Report (2000)
Goldberg, D., Sutton-Smith, M., Paulson, J., Dell, A.: Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra. PROTEOMICS 5, 865–875 (2005)
Harris, M.A., Clark, J.I., Ireland, A.: The Gene Ontology (GO) project in 2006. Nucleic Acids Research 34, D322–D326 (2006)
Janik, M., Kochut, K.: BRAHMS: A WorkBench RDF Store And High Performance Memory System for Semantic Association Discovery. In: Gil, Y., Motta, E., Benjamins, V.R., Musen, M.A. (eds.) ISWC 2005. LNCS, vol. 3729, Springer, Heidelberg (2005)
Karp, P.D., Riley, M., Paley, S., Pellegrini-Toole, A.: The MetaCyc Database. Nucleic Acids Research 30, 59–61 (2002)
Kelder, T., Pico, A.R., Iersel, M.v., Conklin, B., Evelo, C.: WikiPathways: Pathway Editing for the People. In: 11Th Annual International Conference on Research in Computational Biology, SanFrancisco (April 2007)
Klyne, G., Carroll, J.: Resource Description Framework (RDF). W3C recommendation (February 2004)
Kochut, K., Janik, M.: SPARQLeR: Extended SPARQL for Semantic Association Discovery. In: Franconi, E., Kifer, M., May, W. (eds.) ESWC 2007. LNCS, vol. 4519, pp. 145–159. Springer, Heidelberg (2007)
McGuinness, D.L., Frank van Harmelen, e.: Web Ontology Language (OWL). W3C recommendation (February 2004)
Nikitin, A., Egorov, S., Daraselia, N., Mazo, I.: Pathway studio—the analysis and navigation of molecular networks. Bioinformatics 19, 2155–2157 (2003)
Nimmagadda, S., Basu, A., Eavenson, M., Han, J., Janik, M., Narra, R., Nimmagadda, K., Sharma, A., Kochut, K.J., Miller, J.A., York, W.S.: GlycoVault: A Bioinformatics Infrastructure for Glycan Pathway Visualization, Analysis and Modeling. In: Proceedings of the 5th International Conference on Information Technology: New Generations (ITNG 2008), Las Vegas, Nevada (April 2008)
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., Kanehisa, M.: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 27, 29–34 (1999)
Prud’hommeaux, E., Seaborne, A.: SPARQL: A Query Language for RDF. W3C recommendation (June 2007)
Rubio, D.: An Introduction to JSON (2007), http://dev2dev.bea.com/pub/a/2007/02/introduction-json.html
Sahoo, S.S., Thomas, C., Sheth, A., York, W.S., Tartir, S.: Knowledge Modeling and its Application in Life Sciences: A Tale of two Ontologies. In: World Wide Web Conference [WWW 2006], Edinburgh, Scotland (2006)
Saraiya, P., North, C., Duca, K.: Visualizing biological pathways: Requirements analysis, systems evaluation and research agenda. Information Visualization, 1–15 (2005)
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T.: Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003)
Thomas, C., Sheth, A.P., York, W.S.: Modular Ontology Design Using Canonical Building Blocks in the Biochemistry Domain. In: Proc. of the 4th Int. Conference on Formal Ontology in Information Systems (FOIS), Baltimore (November 2006)
York, W.S., Kochut, K.J., Miller, J.A., Sahoo, S., Thomas, C., Henson, C.: GLYDE- II – GLYcan structural Data Exchange using Connection Tables. University of Georgia Technical Report (2007)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Eavenson, M., Janik, M., Nimmagadda, S., Miller, J.A., Kochut, K.J., York, W.S. (2008). GlycoBrowser: A Tool for Contextual Visualization of Biological Data and Pathways Using Ontologies. In: Măndoiu, I., Sunderraman, R., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2008. Lecture Notes in Computer Science(), vol 4983. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-79450-9_29
Download citation
DOI: https://doi.org/10.1007/978-3-540-79450-9_29
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-79449-3
Online ISBN: 978-3-540-79450-9
eBook Packages: Computer ScienceComputer Science (R0)