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Semantic Integration of Glycomics Data and Information

Semantic Integration of Glycomics Data and Information. W.S. York, A. Sheth, K. Kochut, J.A. Miller, C. Thomas, M. Nagarajan, S. Sahoo, K. Gomadam, X. Yi, and K. Verma. Complex Carbohydrate Research Center and Large Scale Distributed Information Systems Laboratory at the

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Semantic Integration of Glycomics Data and Information

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  1. Semantic Integration of Glycomics Data and Information W.S. York, A. Sheth, K. Kochut, J.A. Miller,C. Thomas, M. Nagarajan, S. Sahoo, K. Gomadam, X. Yi, and K. Verma Complex Carbohydrate Research Center andLarge Scale Distributed Information Systems Laboratory at the University of Georgia The 1st Human Disease Glycomics/Proteomics Initiative (HGPI) Workshop August 23 and 24, 2004 Osaka, Japan

  2. NIH Integrated Technology Resource for Biomedical Glycomics Complex Carbohydrate Research Center The University of Georgia • Michael Pierce - CCRC • Al Merrill - Georgia Tech • Kelley Moremen - CCRC • Ron Orlando - CCRC • Parastoo Azadi – CCRC • Stephen Dalton – UGA Animal Science • Will York - CCRCAmit Sheth, Krys Kochut, John Miller UGA Large Scale Distributed Information Systems Laboratory

  3. One definition of an ontology is "a specification of a conceptualization that is designed for reuse across multiple applications." By a conceptualization, we mean a set of concepts, relations, objects, and constraints that define a semantic model of some domain of interest. An ontology is a specification of a conceptualization in the sense that it is a formal encoding of the concepts, relations, objects, and constraints within that semantic model. Peter D. Karp, Vinay K. Chaudhri and Jerome Thomere http://www.ai.sri.com/~pkarp/xol/xol.html

  4. TAMBIS BioPAX GlycO EcoCyc GlycO is a populated ontology: Schema + Facts Knowledge Representation and Ontologies KEGG Thesauri “narrower term” relation Disjointness, Inverse,part of… Frames (properties) Formal is-a CYC Catalog/ID DB Schema UMLS RDF RDFS DAML Wordnet OO OWL IEEE SUO Formal instance General Logical constraints Informal is-a Value Restriction Terms/ glossary GO SimpleTaxonomies ExpressiveOntologies Ontology Dimensions After McGuinness and Finin

  5. Glycotree N. Takahashi and K. Kato (2003)Trends in Glycoscience and Glycotechnology, 15: 235-251.

  6. b-mannosyl residue

  7. a-mannosyl residue 4 b-mannosyl residue

  8. a-mannosyl residue 4 N-acetyl b-glucosaminyl residue 9

  9. Automatic Semantic Annotation of Text: Entity and Relationship Extraction KB, statistical and linguistic techniques

  10. Conclusions • New Domain Formalized (Glycomics) • Existing Tools, (Protégé), Commercial Technology (Semagix Freedom) and W3C Standards (OWL, RDF, LSID) • Populated Ontology (Schema + factual knowledge: > 1M instances) • New Tools and Capabilities are being Developed • Richer Ontological Representation: OWL extended to capture probabilistic relationships • Emergent Semantics (for community participation; notions of observation, hypothesis, truth) • Provenance • Automatic Annotation of Experimental Data and Literature • Blended Semantic Searching and Browsing • Workflows (for organized multi-step analysis) and Knowledge Discovery to explore research hypotheses and discover new relationships • Platform for Open Sharing and Community Participation

  11. Acknowledgements LSDIS Amit ShethKrys KochutJohn Miller Chris ThomasMeenakshi NagarajanSatya SahooKarthik GomadamXiaochuan YiKunal Verma CCRC-UGA Mike PierceKelley MoremenStephen DaltonRon OrlandoParastoo Azadi The National Institutes of HealthThe National Center for Research Resources

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