In order to make the information generated by the Integrated Technology Resource for Biomedical Glycomics accessible to the scientific community, it is necessary to process, interpret, organize, and store data from diverse sources, and to make them available over the Internet in a form that is transparent to clients with expertise in a broad range of disciplines. These challenges are being addressed by the Bioinformatics Research Group (Core 4), which includes members from the Complex Carbohydrates Research Center (CCRC) and the Computer Science Department at the University of Georgia.

The goal for the Bioinformatics Research Group is to develop a bioinformatics resource that includes databases and ontologies along with associated computational tools that facilitate efficient acquisition, description, analysis, sharing and dissemination of the data contained therein. This represents a major challenge, as the potential of this data to explain important biological phenomena will only be fully realized if it is examined in the context of the vast amounts of other data that are becoming available. Therefore, a major emphasis will be placed on data structures and tools that have a high degree of interoperability with the computational infrastructure now being developed for the storage and analysis of genomics and proteomics data. In addition, knowledge in the form of ontologies will be maintained and associated with experimental data.

Provision of this comprehensive bioinformatics data, knowledge and computational resource involves several subprojects:

• Ontologies: This subproject involves the creation several ontologies relevant to the overall project goals. One of the main efforts is to develop a suite of interactive ontologies including the GlycO, ReactO and Enzyo, which focus on the glycoproteomics domain to model glycan structure, the metabolic pathways involved in glycan biosynthesis and function, and the enzymes that catalyze the reactions that comprise these pathways.
• Glyde-II: The purpose of Glyde-II is to provide an XML standard that is suitable for representing large-scale chemical structures, such as glycoproteins. Glyde-II provides a flexible means for defining a chemical structure's partonomy and linkages between the parts.
• GlycoVault: GlycoVault consists of databases, ontologies, and variously formatted data files that are integrated by a sophisticated organizational structure and accessed by a comprehensive, yet easy to use Application Programming Interface (API).
• Visualization: The GlycanBrowser and visualization tool leverages the capabilities of GlycoVault, along with several other technologies to represent structural and pathway information in a way that is intuitive for glycobiologists and to link this information to experimental data (glycomics, proteomics, and transcriptomics analyses).
• Workflows: Efficient collection and processing of biological, glycomics and transcriptomics data by the center will require the development of robust workflows. Several of our workflow implementations enhance and customize a popular Workflow/Web Services engine (jBPM) to more easily and reliably create bioinformatics workflows.
• Data Tools: We have developed several tools to facilitate the interpretation of mass spectral data obtained in glycomics analysis. We are currently developing a graphical user interface for these tools.
• Simulation: The Glycomics Modeling pathway simulation environment (GlyMpse), which is under development will simulate biochemical pathways using Hybrid Petri Nets. Ordinary discrete Petri Nets are useful for Qualitative Modeling, while Petri Nets with continuous places are useful for Quantitative Modeling.