Ontologies

This subproject involves the creation several ontologies relevant to the overall project goals. One of the main efforts is to develop the Glycomics Ontology (GlycO), which 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. The following two are furthest along in their development.

GlycO

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. The GlycO schema exploits the expressiveness of OWL-DL to place restrictions on relationships, thus making it suitable to be used as a means to classify new instance data. These logical restrictions are necessary due to the chemical nature of glycans, which have complex, branched structures that cannot be represented in any simple way. Glycans are thus distinguished from DNA (e.g., genes) and proteins, which can be represented (at least in their most basic forms) as simple character strings. The structural knowledge in GlycO is modularized, in that larger structures are semantically composed from smaller canonical building blocks. In particular, glycan instances are modeled by linking together several instances of canonical monosaccharide residues, which embody knowledge of their chemical structure (e.g., β-D-GlcpNAc) and context (e.g., attached directly to the Asn residue of a protein). This bottom-up semantic modeling of large molecular structures using smaller building blocks allows structures in GlycO to be placed in a biochemical context by describing the specific interactions of its component parts with proteins, enzymes and other biochemical entities.

Glycan Ontology

You can download the most recent version of the GlycO schema and the populated GlycO.

EnzyO

EnzyO describes enzymes and enzyme-catalyzed reactions.EnzyO (for Enzyme Ontology) 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.The current version of EnzyO has a total of over 8000 enzyme and reaction classes. The downloadable version contains only a subset of reactions and enzymes that are involved in the N-Glycan biosynthesis pathway.
Since the two domains are so highly intertwined, GlycO imports EnzyO, thus ensuring modularity also at the level of glycan biosynthesis.

You can download the most recent version of EnzyO

ReactO

ReactO bridges EnzyO and GlycO by storing the enzymatic reactions that are catalyzed by the enzyms in EnzyO to generate a structure stored in GlycO.

You can download the most recent version of ReactO

ReferO

ReferO is a ontology that allows to reference any entry in on of the other ontologies (EnzyO, ReactO, GlycO) with literature references and references to databases or other ontologies. ReferO also contains comments for entries in the ontologies.

You can download the most recent version of the ReferO schema or the entire populated ReferO ontology

References

  1. Sahoo, S.S., C. Thomas, S. Tartir, W. York, and A. Sheth. 2006. Knowledge modeling and its applications in life sciences: A tale of two ontologies. The World Wide Web Conference 2006, Edinburgh, Scotland, May 22-26, 2006. Cited by 36
  2. Thomas, C.J., A.P. Sheth, and W.S. York. 2006. Modular ontology design using canonical building blocks in the biochemistry domain. In: Proceedings of the International Conference on Formal Ontology in Information Systems. IOS Press, Baltimore, Maryland, November 9-11, 2006. Cited by 16
  3. Sahoo, S.S., C. Thomas, A.P. Sheth, and W.S. York. 2005. GlycoO and ProPreO: A case study of two deep domain life sciences ontologies. Large Scale Distributed Information Systems Laboratory Technical Report, University of Georgia, September.