ACM SIGMOD Anthology VLDB dblp.uni-trier.de

A Data Transformation System for Biological Data Sources.

Peter Buneman, Susan B. Davidson, Kyle Hart, G. Christian Overton, Limsoon Wong: A Data Transformation System for Biological Data Sources. VLDB 1995: 158-169
@inproceedings{DBLP:conf/vldb/BunemanDHOW95,
  author    = {Peter Buneman and
               Susan B. Davidson and
               Kyle Hart and
               G. Christian Overton and
               Limsoon Wong},
  editor    = {Umeshwar Dayal and
               Peter M. D. Gray and
               Shojiro Nishio},
  title     = {A Data Transformation System for Biological Data Sources},
  booktitle = {VLDB'95, Proceedings of 21th International Conference on Very
               Large Data Bases, September 11-15, 1995, Zurich, Switzerland},
  publisher = {Morgan Kaufmann},
  year      = {1995},
  isbn      = {1-55860-379-4},
  pages     = {158-169},
  ee        = {db/conf/vldb/BunemanDHOW95.html},
  crossref  = {DBLP:conf/vldb/95},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

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 conjunctionwith the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data.

Copyright © 1995 by the VLDB Endowment. Permission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage, the VLDB copyright notice and the title of the publication and its date appear, and notice is given that copying is by the permission of the Very Large Data Base Endowment. To copy otherwise, or to republish, requires a fee and/or special permission from the Endowment.


Online Paper

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Printed Edition

Umeshwar Dayal, Peter M. D. Gray, Shojiro Nishio (Eds.): VLDB'95, Proceedings of 21th International Conference on Very Large Data Bases, September 11-15, 1995, Zurich, Switzerland. Morgan Kaufmann 1995, ISBN 1-55860-379-4
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