Database Research Group (CIS)

Document Type

Conference Paper

Date of this Version

September 1995

Comments

Postprint version. Published in Proceedings of the 21th International Conference on Very Large Data Bases, September 1995, pages 158-169.
Publisher URL: http://hdl.library.upenn.edu/1017/11047

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.

Date Posted: 04 June 2007

This document has been peer reviewed.