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Schema Driven Assignment and Implementation of Life Science Identifiers (LSIDs)
Speaker:
Professor Daniel P. Miranker
Institute of Cell and Molecular Biology
Department of Computer Sciences
University of Texas at Austin
Time: 3-4pm, Monday, Nov. 20
Location: Room 517, New Life Science Building, Peking University
Abstract:
Life science identifiers (LSIDs) is a global unique identifier protocol adopted by the Object-Management group (OMG). LSIDs are intended to help rationalize the unique archival requirements of biological data. These requirements include guaranteeing that the data will be available, unchanged, forever. Also, that there is meta-data describing the data. The Semantic Web’s RDF representation of ontologies is a preferred representation of that meta-data.
We describe an implementation architecture such that existing data managed by a relational database management system (e.g. Microsoft SQL Server) may be integrated with the LSID protocol as an add-on layer. and thus made available as Semantic Web content. The approach requires a database administrator to specify an export schema detailing the content and structure of the archived data, and a mapping of the existing database to that schema. A compiler may translate these specifications making it easy to integrate existing databases with the Semantic Web.
Bio:
Daniel P. Miranker is a Professor of Computer Science at the University of Texas atAustin. He was recently awarded a joint appointment with the University of TexasInstitute for Cell and Molecular Biology. He earned a PhD (1986) in Computer Science atColumbia University and a BS (1979) in Mathematics at MIT.Professor Miranker has worked strictly in Bioinformatics since his return to academia in2001 after founding Liaison Technology Inc., a company whose products are used tomanage catalog content and real-time supply chains. Miranker leads two projects. Themolecular biological information system, MoBIoS, (pronounced mobius), a nextgeneration database management system for life-science data. MoBIoS’ methodsintegrate biochemical criteria into core database algorithms, enabling interactive searchand mining of large life-science databases. Miranker is also the database lead for theMorphster project, an effort to integrate 2 and 3 dimensional image data with ontologies(semantic web) in support of systematic biology.Prior to his foray into commercial software development, Professor Miranker was bestknown for his work in the evaluation of rule-based programs, most notably the TREATalgorithm. A central theme in the work is the mapping of Artificial Intelligence searchproblems to relational database primitives. This work culminated in his paper, “A LowerBound Theorem for Indexing Schemes and Its Application to Multidimensional RangeQueries", for which he earned the Best Paper Award at the Seventeenth Symposium onPrinciples of Database Systems (PODS-98).
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