Bioinformatics Support for Glycomics Research

XML Interchange Language for Glycan Structures

The purpose of Glyde-II is to provide an XML markup language that is more suitable for representing larger scale chemical structure than the commonly used Chemical Markup Language (CML). CML provides a two level view (atoms and molecules), while Glyde-II provides a four level view (atoms, residues, moieties and molecules). Glyde-II provides a flexible means for defining a chemical structure's partonomy and linkages between the parts in the partonomy.

• Literature on Bioinformatics Markup Languages
• Glyde-II DTD
• Glyde-II Sample XML Files
• Glyde-II Object Model
• Glyde-II Paper

Ontology for Glycomics

The Glycomics Ontology (GlycO) focuses on the glycoproteomics domain to model the structure and functions of glycans and glycoconjugates, the enzymes involved in their biosynthesis and modification, and the metabolic pathways in which they participate. GlycO is intended to provide both a schema and a sufficiently large knowledge base, which will allow classification of concepts commonly encountered in the field of glycobiology in order to facilitate automated reasoning and information analysis in this domain. It serves as a standalone ontology, as well as a centerpiece in GlycoVault (see below).

• Literature on Bioinformatics Ontologies
• GlycO Ontology
• GlycO Paper
• Ontology Checking Tool (oct.zip)

Bioinformatics Infrastructure to Support Glycomics Research

GlycoVault provides a means of storing and retrieving data to support glycomics research at the Complex Carbohydrates Research Center (CCRC) at the University of Georgia. These data include quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) data as well as basic glycomics data. Biologically relevant parameters (such as flow cytometry profiles) and various types of data collected by the analytical services component of the Center, along with the explicit and implicit knowledge required to analyze and interpret these data. 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). The API facilitates the development of methods for querying the knowledge and exporting the results in formats (such as XML) that can be readily digested by external applications. Thus, GlycoVault not only provides scientists within the Center with a robust means of retrieving and analyzing their results, it provides an Internet gateway for publication of the knowledge and data collected by the Center, including results obtained for diverse samples provided by scientists who use the analytical services. GlycoVault provides access to data and knowledge stored as XML, RDF, OWL, Relational Tables, Object Model and Spreadsheets. The following query languages are also available: XPath, XQuery, SPARQL, SQL and JPQL.

• Literature on Bioinformatics Infrastructure
• GlycoVault Software
• GlycoVault Paper   ( GlycoVault.ps )   ( GlycoVault.tex )

Workflow and Web Services

Efficient collection and processing of biological, glycomics and transcriptomics data by the center will require the development of robust workflows. GlycoFlow enhances and customizes a popular Workflow/Web Services engine (jBPM) to more easily and reliably create bioinformatics workflows. The deployed workflows will be integrated with GlycoVault, which will provide the storage for the final experimental results, as well as important intermediate values. During the initial design stage, glycobiologists will be able to indicate what part of the results and at what point during the workflow execution must be stored in GlycoVault, or which previously stored results to bring back for post-analysis tasks.

• Literature on Bioinformatics Workflow
• GlycoFlow Software
• GeneFlow Software
• GlycoFlow Paper
• GeneFlow Paper1 , GeneFlow Paper2

Visualization and Analysis of Biochemical Pathways

The Glycan Browser (GlyB) and visualization tool leverages the capabilities of GlycoVault, along with several other technologies (including RDF, OWL, AJAX, JavaScript, BRAHMS and GraphViz) to represent structural information in a way that is intuitive for glycobiologists and to link this information to experimental data (glycomics, proteomics, and transcriptomics analyses). GlyB provides a graphical display of glycan biosynthetic pathways and associated experimental data. Glycans are rendered "on the fly" using the standard representation endorsed by the Consortium for Functional Glycomics (CFG), extended to include partonomy relationships (e.g., a carbohydrate residue is drawn in a larger box that represents a glycan moiety). Relevant experimental data (such as the abundance of the Man9GlcNAc2 glycan) can be shown in a separate panel. This is a prototype application that is being extended to include a more powerful graphical interface that can be used for knowledge curation as well as knowledge browsing.

• Literature on Visualizing Biochemical Pathways
• GlyB Software
• GlyB Paper

Modeling and Simulation of Biochemical Pathways

A prototype simulation tool, the Glycomics modeling pathway simulation environment (Glympse), is under development that will simulate biochemical pathways using Hybrid Petri Nets. Ordinary discrete Petri Nets are used for Qualitative Modeling, while Petri Nets with continuous places are used for Quantitative Modeling. The simulations are generated from information stored in ontologies as well as pathway and kinetics databases. The Ontology Driven Simulation methodology utilizing domain ontologies such as GlycO and SBO as well as modeling ontologies such as DeMO and DeSO is used to generate simulation models of biochemical pathways.

• Literature on Simulating Biochemical Pathways
• Glympse Software
• Glympse Paper