TableMaker: An ad hoc Query Tool for Relational Databases Page: 4

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queries against the underlying database. The wizard
walks the researcher through the process of selecting
the correct tables to search, specifying the correct
search criteria, and selecting the desired attributes for
display by presenting a series of increasingly more
specific questions.
3 Results
3.1 PlantGDB instance of TableMaker
The TableMaker tool has been implemented with
PlantGDB, a web-based database of plant molecular
sequences that are downloaded from GenBank and
reorganized for analysis and retrieval using MySQL
[4]. TableMaker was connected to PlantGDB in order
to provide researchers with robust searching and
reporting capabilities
(http://www.bioextract.org/genbank/home/index.j sp;
all examples discussed in the text are demonstrated at
this site). With the TableMaker tool, researchers can
execute queries that are not possible to execute at
GenBank (e.g. "show me all the plant promoter
sequences" or "show me all the species names in the
family Poaceae"). Figure 1 demonstrates an example
of using TableMaker at http://www.plantgdb.org to
retrieve all the annotated long terminal repeat (LTR)
sequences found in plant retroelements. Because all
the necessary information for locating LTR is stored in
the backend PlantGDB database, a few clicks on
TableMaker at PlantGDB will execute the
corresponding SQL statements and obtain the
database-query results easily.
3.2 Other TableMaker Usage
To demonstrate the applicability of TableMaker
to diverse databases, we have implemented
TableMaker versions of the MINT and Panzea
databases for protein-protein interactions and
comparative genomics, respectively [5, 6]. These
TableMaker instances can be accessed at
http://biota.usd.edu/mint/ and
http://biota.usd.edu/panzea/.
4 Future Work
The TableMaker is a generalized Web-based ad hoc
query tool that is designed to help users easily query a
relational database. There are several areas within the
TableMaker system that we would like to expand.
Currently, the system is primarily designed to connect
to MySQL databases. Because the TableMaker system
uses standard the JDBC API to connect to the
underlying database, it is able to connect to other
Database Management Systems (DBMS) such
PostgreSQL or Oracle but additional functionality

needs to be added to take advantage of specific DBMS
characteristics.
The queries in TableMaker could be expanded to
include other table joining mechanisms such as right
outer join and cross join to enrich the functionality of
the current inner and left join operations. Providing a
graphical view of the underlying database (i.e.
simplified schema) might also enrich to the
TableMaker by helping the user understand the
structure of the data.
Adding an administrative module for defining
views of the system would be another addition that
would make the system easier to use. This module
could provide a GUI for defining aliases, hiding
elements, and defining table relationships.
Lastly, it is very easy in SQL to construct queries
that return a huge amount of data, such as when
querying large tables, or when tables are joined
without giving appropriate join conditions. These
types of queries have the potential to bring down a
database server. Although the TableMaker system has
a "time-out" mechanism to terminate queries taking a
excessively long period of time, further action should
be taken to more effectively handle this problem.
5 Acknowledgements
The development of TableMaker was supported
in part by National Science Foundation grants DBI-
0321600 and DBI-0606909 to V.B. and C.L.
6 References
[1] Galperin,M.Y. The Molecular Biology Database
Collection: 2007 update. Nucleic Acids Res., 35, D3-D4,
2007.
[2] Baxevanis,A., The Molecular Biology Database
Collection: an online compilation of relevant database
resources. Nucleic Acids Res., 28, 1-7, 2000.
[3] Schuler,G.D. et al., Entrez: molecular biology
database and retrieval system. Methods Enzymol., 266, 141-
162, 1996.
[4] Duvick, J. et al., PlantGDB: a resource for
comparative plant genomics. Nucleic Acids Res., 36, D959-
D965, 2008.
[5] Chatr-aryamontri,A. et al., MINT: the Molecular
INTeraction database. Nucleic Acids Res., 35, D572-D574,
2007.
[6] Zhao,W. et al., Panzea: a database and resource for
molecular and functional diversity in the maize genome.
Nucleic Acids Res., 34, D752-D757, 2006.

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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/m1/4/ocr/: accessed May 23, 2019), University of North Texas Libraries, Digital Library, https://digital.library.unt.edu; crediting UNT College of Arts and Sciences.

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