Bioinformatics Support for Glycomics Research
This page is a resources page for the Bioinformatics Research Group
that constitutes the
fourth core group
Integrated Technology Resource for Biomedical Glycomics.
The page contains links to the literature as well as to
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 provides a two level view (atoms and molecules), while
Glyde-II provides a four level view (atoms, residues, moieties
Glyde-II provides a flexible means for defining a chemical
structure's partonomy and linkages between the parts in the partonomy.
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).
Bioinformatics Infrastructure to Support Glycomics Research
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
Object Model and
The following query languages are also available:
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
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.
Visualization and Analysis of Biochemical Pathways
The Glycan Browser (GlyB) and visualization tool
leverages the capabilities of GlycoVault,
along with several other technologies
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.
Modeling and Simulation of Biochemical Pathways
A prototype simulation tool, the
Glycomics modeling pathway simulation environment
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
The simulations are generated from information
stored in ontologies as well as pathway and kinetics databases.
Ontology Driven Simulation methodology
utilizing domain ontologies such as
as well as
modeling ontologies such as
is used to generate simulation models of biochemical pathways.