BIRD

BIRD System : Biological Integration and Retrieval Data was designed by Hoan Nguyen at LBGI laboratory (POCH Team) of IGBMC[1] Strasbourg

What is the BIRD System

BIRD System Overview

The BIRD System was designed to manage large collections of biological data (Bird_Databases_List) and to perform intensive computation and simulation. BIRD has inherited some of the idealogy of the Saada project [2]. A generic configurable data model has been designed and allows the simultaneous integration of genomics, transcriptomics and ontology datasets using a limited number of product mapping rules provided by the user (operator or system administrator). The integration rules allow the easy creation of a database according to semantic topics and real requirements. BIRD is driven by a high level query engine (BIRD-QL), based on SQL and a full text engine allowing the biologist to quickly extract knowledge without programming. Thanks to such an engine, the system is capable of generating sub-databases in accordance with the real requirements of a given project.

The hosted data can be accessed by the community using various methods such as a Web interface, Http Service, an API Java or a BIRD-QL Engine Query.

The BIRD System is developed using the Java technology and uses the IBM DB2 as the data server, as well as the Websphere Federation Server for virtual databases. The web application is hosted either by a Tomcat Server or by a WebSphere Application Server.

The BIRD System is not only a data retrieval tool, but also provides a platform for Knowledge Discovery in Biological Databases or an inductive database. We use the IBM Intelligent Miner (association rules, classification, ..) in order to develop the data mining model. The user can then use BIRD-QL for mining pertinent information or for analyzing the relational patterns based on the descriptive patterns available in the BIRD-QL engine.

The first goal of the Bird System is the implementation of the Décrypthon Data Center in the framework of the Décrypthon Programme (AFM/CNRS/IBM ) [3]

BIRDQL Biological Query Language

The heterogeneous data integrated in the BIRD System are represented by several relational tables. The exploitation of these data by SQL queries is not obvious and can only be performed by expert developers or computer scientists.

In this context, building complex queries with SQL involves the use of joins (technical term) to select data in multiple tables. This complexity can be hidden by HTML forms, but many types of queries cannot be specified with HTML forms.

We have therefore developed our own query language (BIRDQL), which is a new biological query language that allows the biologist or clinician to create data retrieval protocols without requiring exhaustive knowledge of the data sources and their architecture. BIRDQL makes it possible for biologists to easily express queries and to extract knowledge using classical constraints and scientific functions (StructuralDistance,SequencePattern,AssociationRule...).

BIRDQL in not a mathematically complete language but instead is an idiom that is adapted to the GUI and is human readable enough to be modified by hand. see more BIRDQL