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|Glycomics Ontology | GLYDE | Proteomics Process Ontology | Glycoproteomics Workflow | Ontology Visualization|
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:
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.Would you like to know more? Or see a demo? Or see a presentation? Or see a poster? GLYDE: Glycan Data Exchange
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.Would you like to know more? Or see a presentation? ProPreO: Proteomics Process Ontology
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.Would you like to know more? Or see a presentation? Or see a poster? Glycoproteomics Workflow
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.Would you like to see a presentation? Or see a poster? OntoVista: Ontology Visualization
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.Would you like to know more? Or see a presentation?
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).Read Protege tutorial Install Protege 2005-2006 Publications & Presentations