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Applying the Semantic Web at UCHSC - Center for Computational Pharmacology

Applying the Semantic Web at UCHSC - Center for Computational Pharmacology. Ian Wilson. Projects with semantics at UCHSC-CCP. Integrated Neuroscience Initiative on Alcoholism (INIA) Analysis Suite Ongoing project to support the INIA consortium (30+ universities geographically dispersed)

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Applying the Semantic Web at UCHSC - Center for Computational Pharmacology

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  1. Applying the Semantic Web at UCHSC - Center for Computational Pharmacology Ian Wilson

  2. Projects with semantics at UCHSC-CCP • Integrated Neuroscience Initiative on Alcoholism (INIA) Analysis Suite • Ongoing project to support the INIA consortium (30+ universities geographically dispersed) • First release at the Neuroscience 2004 conference – Microarrays only at the moment • NLP Enrichment Opportunities • Recent funding September 2004 – NLM • Data integration framework for life science knowledge-bases

  3. INIA SemWeb Opportunities • Conversion of LISP-CM based signal transduction knowledge-base to OWL • Application framework to link the semantics of our data – e.g. MAGE, fMRI, etc. • Exploring ‘scientific workflow’ tools to enable composition of semantically annotated web services – easy UI for the investigator • myGrid project – also presenting at the conference • Issues with the granularity of semantics

  4. NLP Enrichment Opportunities • Using Direct Memory Access Parsing (DMAP) – ‘conceptual parsing’ supported by ontologies • Developing Protege plug-in to support NLP annotations – gold standard development • Text sources • Entrez GeneRIFs • 255 character summary of gene function derived from PubMed • Gene Ontology Definitions

  5. Data Integration Framework • Creating RDF wrappers for several bioinformatics data sources • Using NCBI, GO, Uniprot, etc. as test cases • Alignment of several bio-ontologies – extending when appropriate • Investigating/benchmarking several triple stores and browsers • Kowari, Jena, Sesame • Lightweight JSP, Longwell • Mappings are not always straight forward

  6. Why integrate? • Current architecture is not maintainable • Web tiered databases • Data models in flux • Web client interfaces in flux • Everyone has a different client interface and data model design • CLI tools • 500+ services/databases & Growing • Cutting and pasting • Large number of steps • Frequently repeated – info now rapidly added to public databases • Don’t always get results

  7. Semantic Web Concerns • Inference • Modeling default reasoning and negation in OWL? • Reification is not sufficient for context – • Quads • Named graphs • DL’s are good for certain tasks, but • Need other logics in the life sciences • closed world reasoning – e.g. rules • Scalability • Need to constrain search in RDF space

  8. Conclusion • Always looking for collaborators • Questions?

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