Experiences Applying Metadata to Bioinformatics
Terence Critchlow, Tom Slezak
Center for Applied Scientific Computing
Lawrence Livermore National Laboratory
P.O. Box 808, L-561, Livermore, CA 94551
{critchlow, slezak}@llnl.gov
Ron Musick*
iKuni, Inc
Palo Alto, CA 94304
musick@ikuni.com
Abstract
Bioinformatics is facing the daunting challenge of providing
geneticists and biologists effective, efficient access to data
currently distributed among dynamic, heterogeneous data sources.
Complicating the problem is hte speed at which the underlying science
and technology evolve, leaving the terminology, databases and
interfaces to catch up. As the genomics community moves from
sequences to functional genomics, the pressure to find a solution is
increasing. Realistically addressing this problem, whether through a
data warehouse, multi-database, federated database, or other approach,
requires development of a scalable, flexible infrastructure that can
quickly adapt to meet user needs in this extremely dynamic
environment. This is best accomplished by extensively using meta-data
to reduce the application's maintenance costs. Using the DataFoundry
project as an example, this paper discusses the first steps and
practical problems of developing a metadata-based infrastructure
capable of meeting the demands of an active scientific community. It
also demonstrates how much bioinformatics must still progress before
it can truly satisfy its users.
Appeared in
Information Sciences, Volume 139 (1-2), November 2001.
Look at the Paper (pdf.gz)
Companion paper appeared in
Fifth Joint Conference on Information Sciences, Vol 2. February 2000, Atlantic City NJ.