GlycoBrowser: A Tool for Contextual Visualization of Biological Data and Pathways Using Ontologies

This paper introduces GlycoBrowser, a dynamic biological pathwayexploration and visualization tool. Its capabilities include incremental navigationof pathways, as well as overlaying relevant experimental data about glycans andreactions within a pathway. The use of ontologies not only allows dynamic constructionof pathways, but also facilitates more accurate validation of the informationretrieved. Pathway exploration is initiated by means of an ontologicallydriven glycan structure building tool, which facilitates glycan structure constructionand searching with minimal user error. Because of the complex nature ofglycan structures and the difficulty involved in interpreting the associated data,GlycoBrowser is tailored especially to suit the needs of glycobiologists.

[1]  Frank van Harmelen,et al.  Web Ontology Language: OWL , 2004, Handbook on Ontologies.

[2]  Krys J. Kochut,et al.  SPARQLeR: Extended Sparql for Semantic Association Discovery , 2007, ESWC.

[3]  Sergei Egorov,et al.  Pathway studio - the analysis and navigation of molecular networks , 2003, Bioinform..

[4]  James Paulson,et al.  Automatic annotation of matrix‐assisted laser desorption/ionization N‐glycan spectra , 2005, Proteomics.

[5]  Enrico Motta,et al.  The Semantic Web - ISWC 2005, 4th International Semantic Web Conference, ISWC 2005, Galway, Ireland, November 6-10, 2005, Proceedings , 2005, SEMWEB.

[6]  Amit P. Sheth,et al.  Modular Ontology Design Using Canonical Building Blocks in the Biochemistry Domain , 2006, FOIS.

[7]  J. Carroll,et al.  Jena: implementing the semantic web recommendations , 2004, WWW Alt. '04.

[8]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[9]  Gene Ontology Consortium,et al.  The Gene Ontology (GO) project in 2006 , 2005, Nucleic Acids Res..

[10]  Emden R. Gansner,et al.  Graphviz - Open Source Graph Drawing Tools , 2001, GD.

[11]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[12]  Krys J. Kochut,et al.  BRAHMS: A WorkBench RDF Store and High Performance Memory System for Semantic Association Discovery , 2005, SEMWEB.

[13]  John A. Miller,et al.  GlycoVault: A Bioinformatics Infrastructure for Glycan Pathway Visualization, Analysis and Modeling , 2008, Fifth International Conference on Information Technology: New Generations (itng 2008).

[14]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[15]  Chris North,et al.  Visualizing Biological Pathways: Requirements Analysis, Systems Evaluation and Research Agenda , 2005, Inf. Vis..

[16]  Peter D. Karp,et al.  The MetaCyc Database , 2002, Nucleic Acids Res..

[17]  Philippa Rhodes,et al.  ApiDB: integrated resources for the apicomplexan bioinformatics resource center , 2006, Nucleic Acids Res..

[18]  Amit P. Sheth,et al.  Knowledge modeling and its application in life sciences: a tale of two ontologies , 2006, WWW '06.

[19]  Steven C. Lawlor,et al.  GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways , 2002, Nature Genetics.

[20]  Lora Aroyo,et al.  The Semantic Web: Research and Applications , 2009, Lecture Notes in Computer Science.

[21]  Nigel Shadbolt,et al.  Resource Description Framework (RDF) , 2009 .

[22]  Alexander R. Pico,et al.  WikiPathways: Pathway Editing for the People , 2008, PLoS biology.

[23]  Alessio Ceroni,et al.  The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures , 2007, Source Code for Biology and Medicine.

[24]  Joe Lennon,et al.  Introduction to JSON , 2009 .