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Bioinformatics for Glycan Expression

Integrated Technology Resource for Biomedical Glycomics: Technological Research and Development Project IV, A Project funded by NIH

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Ontology Visualizing tool - GlycOViz

Contact person: Meenakshi Nagarajan nbmeena@uga.edu

GlycOViz is an ontology browser for viewing and browsing the Glycomics Ontology.

The default view of the ontology is a tree view similar to that of Protege. Also available is a TouchGraph representation of the ontology. The different frames and tabs are logically interconnected. When the user clicks on a class in the tree view, it comes into focus in the graph view and vice versa. At the same time, the properties tab and the instances tab are updated with the properties and instances of the selected class. The natural language description and provenance information of a particular class or instance is always displayed in a text area at the bottom of the applet. Overall, the tool combines the advantages of both a hierarchical structure, provided by the tree view, and a graph structure, provided by the TouchGraph™ interface.

GlycO can be downloaded as an executable JAR file. The JAR file contains the compiled code for GlycOViz. It also includes the required third party JAR files. For the installation and configuration instructions and how to use GlycOViz, please refer to the User's Manual. Licensing information, API documentation and source code for the tool will be available shortly.

Downloading and launching the GlycOViz Ontology Browser

Download the jar file
If the jar file downloads as a zip file, rename the file to have a .jar extension instead of a .zip
Double click on the jar file to launch the application

GlycoViz 0.5 alpha - Ontology Visualizing tool

User Manual - Downloading, Launching and using GlycOViz

 

Ontologies to visualize

GlycO

GlycO (for "Glycomics Ontology"), represented using OWL is being populated with extensive domain knowledge that embodies semantically rich descriptions of carbohydrate structures, glycan binding relationships, glycan biosynthetic pathways, and the developmental biology of stem cells.
Provenance, i.e., the sources of the information and the processing history of curated and non-curated data, is also incorporated into the ontology description and knowledge base.

The current release version 0.5 of GlycO contains 573 classes and 113 types of named relationships. It has been semi-automatically populated with more than 480 N-Glycans. In order to assure correctness on the lower levels of granularity, several hundred instances that act as building blocks for glycans have been inserted manually.
GlycO imports EnzyO to extend its range over the enzymes and reactions present in the Glycan biosynthesis pathways.

GlycO version 0.5

EnzyO

EnzyO (for "Enzyme Ontology"), is also represented using OWL. It has been populated with rich descriptions of enzyme structures and reactions, thus embodying a deep knowledge of the domain. Many disparate sources of information were used during the creation and population of EnzyO, thus it may be held as a comprehensive source of knowledge that will allow for the efficient retrieval of semantically relevant enzyme information. Since the two domains are so highly intertwined, GlycO.

EnzyO version 0.2

Figure 1: GlycOViz snap shot

Tutorial and related Web Resources

Jorge Cardoso and Amit Sheth, Semantic Web Processes: Semantics Enabled Annotation, Discovery, Composition and Orchestration of Web Scale Processes, 4th International Conference on Web Information Systems Engineering (WISE 2003), December 10-12, 2003, Rome, Italy. PowerPoint-show PDF

Jorge Cardoso and Amit Sheth, Semantic Web Processes , Net Object Days 2003 and MATES03 , September 23, 2003, Erfurt , Germany. Abstract Extended Abstract Powerpoint -show PDF

Cardoso, Bussler, Sheth, Fensel: Semantic Web Services and Processes : Semantic Composition and Quality of Service, International Federated Conferences: DOA/ODBASE/CooPIS 2002, Irvine, CA, October 28-29, 2002. Tutorial Web Resource on Semantic Web Process

John Miller's Web Resource on Web Services for Bioinformatics


Funding: Bioinformatics of Glycan Expression (one of the four components of the "Integrated Technology Resource for Biomedical Glycomics," appox. $6 million+), National Institute of Health, July 1, 2003 - June 30, 2008.