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Semantics and Services enabled Problem Solving Environment for Trypanosoma cruzi

Semantics and Services enabled Problem Solving Environment for Trypanosoma cruzi. PI: Amit Sheth, LexisNexis Ohio Eminent Scholar, Wright State U. with Rick Tarleton, Distinguished Professor, Univ. of Georgia, and Mark Musen, Professor (Biomedical Informatics); Division Head (BMIR)

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Semantics and Services enabled Problem Solving Environment for Trypanosoma cruzi

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  1. Semantics and Services enabled Problem Solving Environment for Trypanosoma cruzi PI: Amit Sheth, LexisNexis Ohio Eminent Scholar, Wright State U. with Rick Tarleton, Distinguished Professor, Univ. of Georgia, and Mark Musen, Professor (Biomedical Informatics); Division Head (BMIR) Semantic & Services enabled PSE (ssPSE) Funding expected 1Q2008: Collaboration with National Centers for Biomedical Computing (R01) National Heart, Lung, and Blood Institute; National Institutes of Health

  2. Partners & Partner Institutions • Kno.e.sis Center (Dr. Amit Sheth, key contributor: Satya Sahoo) • Tarleton Lab, Cellular Biology, University of Georgia (Dr. Rick Tarleton) • Computer Science, University of Georgia (Dr. Prashant Doshi) • NCBO/Stanford Medical Informatics Center (Dr. Mark Musen, Dr. Natasha Noy)

  3. Project Overview • Facilitate T.cruzi research through an ontology driven Problem Solving Environment • Biological Objectives: • Identification of vaccine, diagnostic, and therapeutic targets for T.cruzi caused Chagas disease • Chagas disease affects 18 million people in Latin America • Computer Science Objectives • Dynamic integration of local and public multimodal data to answer biological questions • Suite of intuitive and comprehensive interfaces for usability and easy adoption by biologists

  4. Proposed T.cruzi PSE System Architecture OWL OWL OWL OWL OPEN BIOMEDICAL ONTOLOGIES (OBO) OPEN BIOMEDICAL DATABASE (OBD) OWL Multiple Ontology Alignment mappings T.cruzi Semantic Data annotations GO ProPreO T.Cruzi Lifecycle Metabolic Pathways SEMANTIC WEB SERVICES SAWSDL OWL-S T.Cruzi Problem Solving Environment (PSE) BPEL4WS UDDI ONTOLOGY RESOURCE Sd Asdasd Sdaasda Asdada Asd Web Service Registry Data & Service Annotation T.Cruzi Query Interface Web Process Composition BioPORTAL

  5. Computer Science Research • Phased development of a suite of ontologies for parasitic organisms such as T.cruzi • Extension of BioPAX ontology for T.cruzi human specific life cycle pathways • Extension of ProPreO ontology to incorporate RT-PCR procedure and incorporate microarray data analysis • Investigate novel methods for ontology alignment and merging • Extension PROMPT tool with our work on semantic mappings

  6. Computer Science Research (contd.) • Semantic annotation of experimental data with ontological concepts • Extension of Integrated Semantic Information and Knowledge System (ISiS) to T.cruzi specific experimental datasets • Extension of NCBO Open Biological Data initiative (OBD) and integration with ISiS • Semantic Web services (SWS) based scientific workflows • SWS discovery, composition • Ontology driven entity identification and relationship extraction from biomedical text • Complex query processing and visualization • SPARQ2L for partially defined patterns in the search query • Intuitive Web based query interface

  7. T.Cruzi PSE Query Interface – Semantic Annotation of Experimental Data

  8. Preliminary Work to build upon • Ontologies • ProPreO ontology • EnzyO Ontology • Standards • SAWSDL • Tools/Systems • SAWSDL4J & Woden APIs • SemBOWSER • Past projects: • The Integrated Technology Resource for Biomedical Glycomics

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