A Data Transformation System for Biological Data Sources

Peter Buneman, Susan Davidson, Kyle Hart, Chris Overton, L. Wong

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well as sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data.
Original languageEnglish
Title of host publicationProceedings of 21st VLDB Conference
PublisherMorgan Kaufmann
Pages158-169
Number of pages12
ISBN (Print)1-55860-379-4
Publication statusPublished - 1 Sep 1995

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