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QGB: a system for querying sequence database fields and features

G C Overton¹, J S Aaronson, J Haas

¹Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia 19104-6145, USA.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|January 1, 1994

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We created QGB, a system for complex queries on biological sequence databases. It enhances data accuracy by inferring missing features and correcting errors in sequence information.

Area of Science:

Bioinformatics
Computational Biology
Genomic Databases

Background:

DDBJ/EMBL/GenBank databases store vast amounts of biological sequence data.
Querying complex structural features within these databases presents significant challenges.
Existing query systems may lack the capability to infer relationships or deduce missing information.

Purpose of the Study:

To develop a general system, QGB, for advanced querying of DDBJ/EMBL/GenBank databases.
To enable complex queries over structural sequence features using an SQL-like syntax.
To introduce novel methods for inferring missing features and identifying data inconsistencies.

Main Methods:

Developed a query system (QGB) with an SQL-like syntax and extensions for complex data types.

Related Experiment Videos

Utilized a customized Definite Clause Grammar (DCG) in Prolog to implement a parse tree for sequence structure.

Employed the parse tree construction to deduce missing features and infer relationships.

Main Results:

QGB facilitates complex queries on sequence structural features.
The system can deduce missing features and infer relationships from the FEATURE TABLE.
Parse tree construction identifies and potentially corrects inconsistencies and errors in the FEATURE TABLE.

Conclusions:

QGB offers a powerful and versatile approach to querying biological sequence databases.
The system enhances data integrity by inferring and correcting feature information.
The use of logic grammars provides an effective framework for representing and processing sequence data.