In computer science, an ontology is a data model that represents a domain and is used to reason about the objects in that domain and the relations between them. Ontologies are used in artificial intelligence, the semantic web, and software engineering as a form of knowledge representation about the world or some part of it. Ontologies generally describe:

• Individuals: the basic or "ground level" objects
• Classes: sets, collections, or types of objects
• Attributes: properties, features, characteristics, or parameters that objects can have and share
• Relations: ways that objects can be related to one another

The Glycomics Ontology GlycO is the focused domain ontology we are developing for the glycobiology domain. GlycO is a formal representation of key concepts and relationships related to the biosynthesis and biological functions of complex carbohydrates, including glycoproteins, glycolipids, and polysaccharides. GlycO is intended to act as a framework for classification of and reasoning about glycans, the biomolecules they interact with, and the cellular machinery that synthesizes them. The GlycO schema exploits the expressiveness of advanced representation languages, such as the Web Ontology Language OWL, to restrict relationships between these concepts and objects, thus facilitating the classification of the objects.

Glycan structures from various partially overlapping sources have been incorporated into GlycO, requiring the use of sophisticated techniques to disambiguate and transform the structural information.

GLYDE is an XML standard format to represent glycan structures. The GLYDE format provides a means by which computers running diverse software applications that use different internal formats for representation of glycan structures can share this information. GLYDE thus provides a robust interface between distributed databases and computational resources, such as the GlycO (the Glycan Ontology).

GLYDE version 1 uses a tree structure to represent glycan structure. Our interactions with international collaborators and our experience in developing GlycO has led to the conclusion that a more flexible format is needed, and we are developing GLYDE version 2 using an adjacency table format that is consistent with the improved GlycO ontology schema.

ProPreO, part of the ontology suite, is being developed as a comprehensive process ontology that models experimental proteomics. The current version of ProPreO contains 390 concepts and 30 relationships, along with more than 3 million data instances. ProPreO describes proteomics experiments using three top-level concepts: (a) data (b) material object and (c) task. The organization of concepts in this manner facilitates the annotation of high-throughput experimental data, allowing contextually relevant parameters and parameter collections (such as mass spectral data) to be efficiently identified, extracted, and analyzed by software applications.

The vast amounts of data routinely generated by high-throughput glycoproteomics experiments requires efficient computational methods for information management, retrieval, and analysis. The workflow protocols that we have developed are designed to use semantic technology for the annotation of the experimental process and the data that it produces. This semantic annotation will make it possible to identify contextually relevant data sets and will facilitate knowledge discovery by computational reasoning with the data.

One of the workflows we have developed for high throughput glycoproteomics uses multiple computational resources, located on multiple machines running different operating systems. Software applications are invoked in a specific order and the resulting data is automatically transferred to specific computers for further processing. The Simple Object Access Protocol (SOAP) was used to implement these tasks in a distributed environment. SOAP is the XML-based language used by Web Services to communicate.

OntoVista is a tool for the visualization of complex (representationally rich) biological and biochemical ontologies. The most important feature of OntoVista is that it can generate semantically enhanced graphs that display relationships in a way that is familiar to experts in a particular domain. When used with its powerful querying and navigation capabilities, OntoVista facilitates the extraction of information from the ontology and provides visual queues that aid the user in discovering knowledge that may be inferred.

Protege, a free ontology development toolkit, can also be used to visualize an ontology. All ontologies discussed in this presentation are available in the "ontologies" folder (with an .owl extension).

• Satya S. Sahoo, Christopher J. Thomas, Amit P. Sheth, Cory Henson, William S. York, GLYDE - An expressive XML standard for the representation of glycan structure, Carbohydr Res. 2005 Dec 30;340(18):2802-7. Epub 2005 Oct 20. PMID: 16242678. Paper
• James A. Atwood III, Satya S. Sahoo, Gerardo Alvarez-Manilla, Daniel B. Weatherly, Kumar Kolli, Ron Orlando and William S. York, "Simple modification of a protein database for mass spectral identification of N-linked glycopeptides" Rapid Commun. Mass Spectrom. 2005; 19: 1-5.
• Satya S. Sahoo, Christopher J. Thomas, Amit P. Sheth, William S. York, Samir Tartir, "Knowledge Modeling and its Application in Life Sciences: A Tale of two Ontologies", 15th International World Wide Web Conference, Edinburgh, Scotland, May 23 - May 26, 2006 (Acceptance Rate: 11%). Paper
• Satya S. Sahoo, Amit P. Sheth, William S. York, John A. Miller, "Semantic Web Services for N-glycosylation Process", International Symposium on Web Services for Computational Biology and Bioinformatics, VBI, Blacksburg, VA, May 26-27, 2005. Abstract
• Christopher Thomas and Amit Sheth, "On the Expressiveness of the Languages for the Semantic Web - Making a Case for 'A Little More", in E. Sanchez (Editor), "Fuzzy Logic and the Semantic Web", Elsevier, March 2006. Paper
• Satya S. Sahoo and Amit Sheth, "Bioinformatics applications of Web Services, Web Processes and role of Semantics", Semantic Web Processes and Their Applications. J. Cardoso, A. Sheth, Editors. Springer, 2006.
• Amit Sheth, Keynote Address: "Semantic Web applications in Financial Industry, Government, Health care and Life Sciences " at AAAI Spring Symposium on Semantic Web meets eGovernment (SWEG'06), March 27-29, 2006, Stanford University, CA. Presentation
• Amit Sheth, "Semantics Enabled Industrial and Scientific Applications: Research, Technology and Deployed Applications", First Online Metadata and Semantic Research Conference, November 21-30, 2005. Presentation I, II, III
• Amit Sheth, "Semantics for Scientific Experiments and the Web-the implicit, the formal and the powerful," Featured Talk, BISCSE 2005: Forging New Frontiers, "Where Fuzzy Began," Berkeley CA, November 2-6, 2005. Presentation

• Christopher J. Thomas, Amit P. Sheth and William S. York. Modular Ontology Design Using Canonical Building Blocks in the Biochemistry Domain. Submitted to FOIS 2006 - International Conference on Formal Ontology in Information Systems. Paper
• Ravi Pavagada, Christopher J. Thomas, Amit P. Sheth and William S. York. Show Me What You Mean! Exploiting Domain Semantics in Ontology Visualization. Submitted to InfoVis 2006 - IEEE Information Visualization Symposium IEEE. Paper