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Wednesday, May 19, 2010

LifeDB Autonomous Data Integration System Trial Release

LifeDB Autonomous Data Integration System Trial Release

It is with great excitement and anticipation that we
announce the release of LifeDB Autonomous Data Integration
system [1] for Life Sciences data management and workflow
querying. LifeDB has its own SQL-like query language
called BioFlow [2, 3] using which, most arbitrary
online deep web resources and tools can be used to develop
applications completely dynamically and on an ad hoc basis.
The goal in LifeDB is to allow application development by
end users using SQL-like declarative query language without
having to worry about schema heterogeneity and geographical
distribution of resources. LifeDB relies on two basic fully
autonomous sub-systems: FastWrap [4, 5] for wrapper
generation and table annotation, and OntoMatch [6] for
schema mapping. BioFlow supports horizontal and vertical
integration and autonomous record linkage through entity
identification and resolution. It is based on an extended
parameterized relational algebra called Integra [7] that is
capable of blurring the distinctions between web documents
and traditional SQL tables by uniformly treating both as

To support end user application development, we have also
developed a visual application development system called
VizBuilder [8] that allows writing BioFlow applications
visually without any knowledge of BioFlow. In our current
LifeDB release, VizBuilder is included as an alternate

Currently, LifeDB is in a trial phase while it undergoes
internal validation. We believe LifeDB is performing within
its design parameters. We invite interested researchers in
Databases and Life Sciences to register for LifeDB as end
users. Registered users will be able to either download
LifeDB binary for local use, or use LifeDB in our server
with limited user data space. Currently, our goal is to
compile bug reports, if any, and fix the currently unknown
bugs before its final release. Full information on LifeDB
can be found at http://integra.cs.wayne.edu:8080/lifedb.

Our laboratory is fully committed to supporting registered
users and their applications on a long term basis on our
Wayne State Server. Registered users will have their own
data space in our server to store their data, applications
and other resources. For high-end users, we will also
consider offering dedicated processors to support computation
intensive applications, resource permitting. We are
considering a novel resource sharing model and it will be
announced when we finalize our plan and acquire the needed
resource. LifeDB will be an open source system for the
community, following the release of its final version. We
are now compiling user requests for data space over the
next 3-6 months based on which we plan to acquire the needed
hardware to support our users. A request for needed space
(and dedicated processor, subject to agreement) may be made
through an e-mail to the PI at jamil@cs.wayne.edu. Please use
subject heading "LifeDB Resource Request."

Publications related to LifeDB and other projects can be found
at our Integration Informatics Lab home page at
http://integra.cs.wayne.edu. A comprehensive LifeDB user manual
is also available for end users. The user manual will include
test examples and design parameters under which LifeDB is
designed and expected to function well.

LifeDB has been funded in part by National Science Foundation
grants SEIII IIS 0612203 and MRI CNS 0521454.


[1] Anupam Bhattacharjee, Aminul Islam, Mohammad Shafkat Amin,
Shahriyar Hossain, Shazzad Hosain, Hasan Jamil and Leonard Lipovich,
"On-the-fly Integration and ad hoc Querying of Life Sciences
Databases using LifeDB", 20th Database and Expert Systems
Applications, Linz, Austria, August 2009.

[2] Hasan Jamil, Bilal El-Hajj-Diab, "BioFlow: A Web-based
Declarative Workflow Language for Life Sciences", IEEE International
Workshop on Scientific Workflows, Hawaii, United States, July 2008.

[3] Hasan Jamil, Aminul Islam, "The Power of Declarative
Languages: A Comparative Exposition of Scientific Workflow Design
using BioFlow and Taverna", IEEE SCC International Workshop on
Scientific Workflows, Los Angeles, California, July 2009.

[4] Mohammad Shafkat Amin, Hasan Jamil, "FastWrap: An Efficient
Wrapper for Tabular Data Extraction from the Web", IEEE
International Conference on Information Reuse and Integration,
Las Vegas, Nevada, United States, August 2009.

[5] Mohammad Shafkat Amin, Anupam Bhattacharjee, Hasan Jamil,
"Wikipedia Driven Autonomous Label Assignment in Wrapper Induced
Tables with Missing Column Names", ACM International Symposium on
Applied Computing, Sierre, Switzerland, March 2010.

[6] Anupam Bhattacharjee, Hasan Jamil, "OntoMatch: A Monotonically
Improving Schema Matching System for Autonomous Data Integration",
IEEE International Conference on Information Reuse and Integration,
Las Vegas, Nevada, United States, August 2009.

[7] Shazzad Hosain, Hasan Jamil, "An Algebraic Language for Semantic
Data Integration on the Hidden Web", IEEE International Conference
on Semantic Computing, Berkeley, California, United States,
September 2009.

[8] Shahriyar Hosain, Hasan Jamil, "A Visual Interface for
on-the-fly Biological Database Integration and Workflow Design
using VizBuilder", International Workshop on Data Integration in
Life Sciences (DILS), Manchester, United Kingdom, July 2009.
URL: http://integra.cs.wayne.edu

Contact Person: Hasan Jamil (jamil@cs.wayne.edu)