Glycomics Ontology

"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."