GLYDE-II

The purpose of GLYDE-II is to provide an XML standard that is suitable for exchanging structural information regarding a broad range of biomolecules, especially glycoconjugates. GLYDE-II supports the representation of chemical structrures at different levels of granularity using a object model to formally define molecular partonomy and linkages between the parts.

The GLYDE-II standard is based on a connection table formalism using XML syntax. The syntax of a GLYDE-II document is fully defined by its schema (either a DTD or XML Schema), which provides a framework we call PARCCHMENT (PARtonomy of CHeMical ENTities). PARCHMENT allows the complete structure of biological molecules (including complex glycans) to be completely and unambiguously specified at several level of granularity. Semantic constraint on structures are enforced when translating to our Glycomics Object Model (GOM) or GlycO. For more information see GLYDE-II - GLYcan structural Data Exchange using Connection Tables

GLYDE-II Schema

Currently the syntax for GLYDE-II is given in the form of a Document Type Definition (DTD). It defines various structural types such as atoms (free and bound), residues, moieties, molecules and aggregates, etc. as well as their linkages. The latest version is GLYDE-II_v1.0.0.DTD

Glycomics Object Model (GOM)

The Glycomics Object Model (GOM) provides a convenient way to translate GLYDE-II XML documents into other forms such as GlycO OWL instances. The object model was design using UML and classes were coded in Java. The correspondence with GLYDE-II is nearly one-to-one, as shown in the UML Class Diagram for GOM.

Examples of GLYDE-II XML Documents

Examples: