TableMaker: An ad hoc Query Tool for Relational Databases Page: 1
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TableMaker: An ad hoc Query Tool for Relational
C. Lushbough', J.Duvick2, Q. Dong3, D. Jennewein', J. Reynoldson', and V. Brendel4
'Department of Computer Science, University of South Dakota, Vermillion, SD 57069, USA
2 Department of Genetics, Development and Cell Biology, Iowa State University, Ames IA 50011, USA
3 Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
4Department Genetics, Development and Cell Biology, and Department of Statistics,
Iowa State University, Ames, IA 50011, USA
Abstract: Most Web servers hosting biological data limit
users to a defined set of search options and output formats
that are short of the whole range of options available to
users with direct database access. However, to make full use
of the wealth of data in the database resource, it is desirable
to have an intermediate solution that provides a broad
range of flexible query and output options through a Web
TableMaker is a generalized Web-based ad hoc query
tool that connects to relational databases using the Java
Database Connectivity (JDBC) API. It allows researchers to
build sophisticated queries and select data items for display
in tabular format through a menu-driven query building
interface, without requiring users to type Structured Query
Language (SQL) statements. A query wizard is included for
additional ease of use.
Availability: TableMaker is available through SourceForge
at https://sourceforge. net/projects/tablemaker.
Contact: Carol.Lushbough@usd. edu
Keywords: Ad Hoc Query, Relational Database.
The number of molecular biology resources
available on the Internet is growing rapidly, with 960
public databases indexed in 2007  compared to
approximately 260 in 2000 . These database
resources store vast amounts of diverse data. Such data
includes genetic and genomic data, molecular
structures, metabolic pathways, and gene expression
data. In order for biologists to access the information
stored within these databases, web-accessible
Graphical User Interfaces (GUIs) are typically
provided in the form of text-input fields, checkboxes,
selection menus, etc., used for constructing queries.
Designing online query tools for a broad clientele
often involves compromises between the clarity of the
interface and the complexity of the underlying
database. While meeting the needs of the majority of
researchers, such query tools may be inadequate for
some. For example, users of GenBank's Entrez
sequence data search tool 
(http://www.ncbi.nlm.nih.gov/) might want to access
information regarding "tissue type", e.g., "retrieve all
the EST sequences from maize leaf tissue" for
studying gene expression patterns. Despite the fact that
"tissue type" information is stored in GenBank, it
cannot be accessed online because "tissue type" is not
one of the designated search fields.
Another limitation of many interfaces to data
resources is the lack of ability to generate flexible
tabular reports from query results. Similar to the query
limitation described above, the available output
options are also usually fixed by the Web designers,
whereas users may want to specify what attributes of a
particular record should be included in the output. In
addition, the query output format may be inconvenient
for data export and parsing for further analysis.
One option for overcoming these limitations is to
allow direct access to the backend database system.
However, this solution is not practical for researchers
who are not familiar with the internal database
language (typically SQL). Therefore, a generalized but
easy-to-use solution is desirable. We present
TableMaker, an ad hoc web-based query tool that
connects to any relational database and provides a
simple but powerful interface for database queries and
data display. With TableMaker, researchers are able to
build sophisticated queries and select data items for
display without being required to know SQL. Usability
is further enhanced by means of a customizable query
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Lushbough, Carol; Duvick, Jon; Dong, Qunfeng; Jennewein, Douglas; Reynoldson, Joe & Brendel, Volker. TableMaker: An ad hoc Query Tool for Relational Databases, paper, July 2008; [USA]. (https://digital.library.unt.edu/ark:/67531/metadc78297/m1/1/: accessed April 21, 2019), University of North Texas Libraries, Digital Library, https://digital.library.unt.edu; crediting UNT College of Arts and Sciences.