An extensible web interface for databases and its application to storing biochemical data

TL;DR

This paper introduces a flexible web-based database interface built in Prolog, demonstrating its use for biochemical data management and integration with statistical tools, highlighting ease of development and extensibility.

Contribution

The paper presents a generic, schema-transparent web interface for databases implemented in Prolog, showcasing its application to biochemical data and integration with R for statistical analysis.

Findings

Efficient schema-transparent interface created with minimal programming effort.

Prolog's features facilitate seamless integration of relational databases and structured documents.

The system effectively supports biochemical and genomic data management and analysis.

Abstract

This paper presents a generic web-based database interface implemented in Prolog. We discuss the advantages of the implementation platform and demonstrate the system's applicability in providing access to integrated biochemical data. Our system exploits two libraries of SWI-Prolog to create a schema-transparent interface within a relational setting. As is expected in declarative programming, the interface was written with minimal programming effort due to the high level of the language and its suitability to the task. We highlight two of Prolog's features that are well suited to the task at hand: term representation of structured documents and relational nature of Prolog which facilitates transparent integration of relational databases. Although we developed the system for accessing in-house biochemical and genomic data the interface is generic and provides a number of extensible features. We describe some of these features with references to our research databases. Finally we outline an in-house library that facilitates interaction between Prolog and the R statistical package. We describe how it has been employed in the present context to store output from statistical analysis on to the database.