A Data Transformation System for Biological Data Sources

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Technical Reports (CIS)
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Buneman, Peter
Hart, Kyle
Overton, Chris
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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.

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1995-02-24
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University of Pennsylvania Department of Computer and Information Science Technical Report No. MS-CIS-95-10.
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