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
CDROM Version: Load the CDROM "Volume 1 Issue 5, VLDB '89-'97" and ...
DVD Version: Load ACM SIGMOD Anthology DVD 1" and ...
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
Contents
References
- [1]
- Serge Abiteboul, Richard Hull:
IFO: A Formal Semantic Database Model.
ACM Trans. Database Syst. 12(4): 525-565(1987)
- [2]
- ...
- [3]
- Carlo Batini, Maurizio Lenzerini, Shamkant B. Navathe:
A Comparative Analysis of Methodologies for Database Schema Integration.
ACM Comput. Surv. 18(4): 323-364(1986)
- [4]
- ...
- [5]
- Val Tannen, Peter Buneman, Shamim A. Naqvi:
Structural Recursion as a Query Language.
DBPL 1991: 9-19
- [6]
- Val Tannen, Peter Buneman, Limsoon Wong:
Naturally Embedded Query Languages.
ICDT 1992: 140-154
- [7]
- Peter Buneman, Leonid Libkin, Dan Suciu, Val Tannen, Limsoon Wong:
Comprehension Syntax.
SIGMOD Record 23(1): 87-96(1994)
- [8]
- Luca Cardelli:
A Semantics of Multiple Inheritance.
Inf. Comput. 76(2/3): 138-164(1988)
- [9]
- ...
- [10]
- ...
- [11]
- Ronald Fagin, Jürg Nievergelt, Nicholas Pippenger, H. Raymond Strong:
Extendible Hashing - A Fast Access Method for Dynamic Files.
ACM Trans. Database Syst. 4(3): 315-344(1979)
- [12]
- Leonidas Fegaras, David Maier:
Towards an Effective Calculus for Object Query Languages.
SIGMOD Conference 1995: 47-58
- [13]
- Nathan Goodman, Steve Rozen, Lincoln Stein:
Requirements for a Deductive Query Language in a Genome-Mapping Database.
Workshop on Programming with Logic Databases (Book), ILPS 1993: 259-278
- [14]
- ...
- [15]
- Zhuoan Jiao, Peter M. D. Gray:
Optimization of Methods in a Navigational Query Language.
DOOD 1991: 22-42
- [16]
- Won Kim:
A New Way to Compute the Product and Join of Relations.
SIGMOD Conference 1980: 179-187
- [17]
- Witold Litwin, Abdelaziz Abdellatif:
Multidatabase Interoperability.
IEEE Computer 19(12): 10-18(1986)
- [18]
- David Maier, Bennet Vance:
A Call to Order.
PODS 1993: 1-16
- [19]
- ...
- [20]
- Masaya Nakayama, Masaru Kitsuregawa, Mikio Takagi:
Hash-Partitioned Join Method Using Dynamic Destaging Strategy.
VLDB 1988: 468-478
- [21]
- ...
- [22]
- ...
- [23]
- Shamkant B. Navathe, Ramez Elmasri, James A. Larson:
Integrating User Views in Database Design.
IEEE Computer 19(1): 50-62(1986)
- [24]
- ...
- [25]
- Atsushi Ohori, Peter Buneman, Val Tannen:
Database Programming in Machiavelli - a Polymorphic Language with Static Type Inference.
SIGMOD Conference 1989: 46-57
- [26]
- Yannis Papakonstantinou, Hector Garcia-Molina, Jennifer Widom:
Object Exchange Across Heterogeneous Information Sources.
ICDE 1995: 251-260
- [27]
- ...
- [28]
- ...
- [29]
- ...
- [30]
- ...
- [31]
- ...
- [32]
- Amit P. Sheth, James A. Larson:
Federated Database Systems for Managing Distributed, Heterogeneous, and Autonomous Databases.
ACM Comput. Surv. 22(3): 183-236(1990)
- [33]
- Amit P. Sheth, James A. Larson, Aloysius Cornelio, Shamkant B. Navathe:
A Tool for Integrating Conceptual Schemas and User Views.
ICDE 1988: 176-183
- [34]
- ...
- [35]
- ...
- [36]
- ...
- [37]
- Philip W. Trinder:
Comprehensions, a Query Notation for DBPLs.
DBPL 1991: 55-68
- [38]
- ...
- [39]
- Philip Wadler:
Comprehending Monads.
Mathematical Structures in Computer Science 2(4): 461-493(1992)
- [40]
- ...
- [41]
- Limsoon Wong:
An Introduction to Remy's Fast Polymorphic Record Projection.
SIGMOD Record 24(3): 34-39(1995)
- [42]
- Limsoon Wong:
Querying Nested Collections.
Ph.D. thesis, Univ. Pennsylvania 1994
- [43]
- ...
Copyright © Sun Mar 14 23:31:24 2010
by Michael Ley (ley@uni-trier.de)