BIRD

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

What is BIRD System

Scientific Context

Since 2000, thanks to the availability of the human genome and the rapid progress of biotechnologies and information technologies, numerous large biomedical datasets have been generated. Thus, modern biomedical information corresponds to a high volume of heterogeneous data that doubles in size every year (Statistics NCBI) and that covers very different data types, including patient data (from phenotypic, environmental or behavioral origins), gene data (including genome environment, gene expression status, enzymatic activity, gene product modification…) and the processes, protocols or treatments used to generate the information. In this context, systemic approaches are now being developed to analyze and compare this huge amount of information, in order to identify genes and to predict their functions in the cascade of events and networks involved for example, in the emergence of a disease. This requires the development of dynamic and powerful systems to store, assemble, integrate and process very large datasets from different sources. Recently, the Decrypthon initiative (Decrypthon), resulting from a collaboration between AFM/CNRS/IBM, has been instigated, firstly to develop a computing grid that connects hundreds of processors installed in various data-processing centres of French universities and, secondly to provide a facilitated access to the data for the scientific biological community. In the framework of the Decrypthon initiative, several biomedical projects are in progress requiring on the one hand, a strong computational capacity and on the other hand, the deployment in the grid environment of a data integration system able to manage automatically large volumes of heterogeneous data and to quickly process complex queries and versioning management.

BIRD System Overview

BIRD System (Nguyen et al, CORIA 2008, Hermes Edition) was designed to manage large collections of biological data and to intensive computation and simulation. BIRD heritages somes main idea of 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 the database according to semantic topics and real requirements. BIRD is driven with a high level query engine, 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 to generate the sub-bank of data in accordance with the real requirement.

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.

BIRD System is developed with the Java technology. BIRD System uses IBM DB2 for data server; Websphere Federtion Server for virtual databases. The web application is hosted by a Tomcat Server or by a WebSphere Application Server.

BIRD System is not only a retrieval data system but also a plate-forme of Kownlegde Discovery in Biological Database. We use IBM Miner Intelligent (association rules, classification, ..) in order to develop the data mining model.

The first goal of Bird System is to implementation of the Décrypthon Data Center [3] [4] in the framework of Décrypthon Programme (AFM/CNRS/IBM ) [5]

DATABASES List

GENBANK, EST, WGS, REFSEQ, PDB, UNIPROT, UCSC, INTERPRO, GO, TAXONOMY, MACSIM, EVI-GENORET (local user), STRING (local user), UMD Data (local user), ...

BIRDQL Biological Query Language

BIRDQL in few words

The heterogeneous data integrated in BIRD System are represented by several relational tables. The exploitation of these data by SQL queries is not obvious except for developers or computer scientist experts.

Building queries with SQL in this context is not easy with because that requires to use joins (terme technique) to select data in multiple tables. This complexity must be hidden by HTML forms but a lot of queries can not be setup with HTML forms.

We proposes own query language (BIRDQL), there is new standard biological query language allowing the biologist or clinician to create data retrieval protocols without exhaustive knowledge of the data sources and their architecture. BIRD System is driven with a high level query engine: BIRDQL, which makes it possible for biologists to express easily queries and to extract knowledge by classical constraints and scientific functions (StructuralDistance,SequencePattern,AssociationRule...).

BIRDQL in not a mathematically complete language but indeed an idiom adpated to the GUI, human readable enough to be modified by hand.

BIRDQL Grammar

ID <list of id/ac/query_id > DB <bank names>

WH Field[6] Contains (kw1 & kw2) | kw_n

WH PATTERN <function SequencePattern() >

WH PATTERN <function DiagonalMolecule()>

WH PATTERN <function InteractionProtein()>

WH PATTERN <function AssociationRule()>

FD <Field[7] out>

LM <n>

FM Fasta/Flat/Xml/CSV/Simple/Object/OID

BIRDQL example

Two other examples below also show how to use the BIRD-QL syntax.

Example 1: simple query, search and fasta format generation

ID * DB UNIPROT

WH DE contains "synthetase" & "tyrosyl"

WH OX contains 382

FD AC, ID,DE,OX,SQ

FM FASTA

Result

>Q92PK5 | SYY_RHIME | Tyrosyl-tRNA synthetase (EC 6.1.1.1) (Tyrosine--tRNA ligase) (TyrRS). | 382 MSEFKSDFLHTLSERGFIHQTSDDAGLDQLFRTETVTAYIGFDPTAASLHAGGLIQIMMLHWLQATGHRPISLMGGGTGMVGDPSFKDEARQLMTPETI...

Example 2: complex query

ID * DB GENBANK, REFSEQ

WH OC Contains "Eukaryote"

WH DR Contains "GO"

WH GENE contains "GF100027"

FM FASTA

The query above allow to search in Genbank and RefSeq, the Eucaryotic sequences containing the GF100027 gene with a cross reference in GeneOntology.

Example 2: complex query

ID * DB GENBANK, REFSEQ

WH OC Contains "Eukaryote"

WH DR Contains "GO"

WH GENE contains "GF100027"

FM FASTA

The query above allow to search in Genbank and RefSeq, the Eucaryotic sequences containing the GF100027 gene with a cross reference in GeneOntology.

Example 3: mining in EST

ID * DB GBEST

WH TISSUE_TYPE contains "retina"

WH DEV_STAGE contains "adult"

LM 100

FD AC,DE,OX,OC,tissue_type,dev_stage,chr

FM FLAT

Example 4: Mining in EST

ID CJ133635,CJ133593,CJ133659 DB GBEST

WH DE contains "AMINOTRANSFERASE"

WH OC contains "Eukaryota" & not "Metazoa"

WH TISSUE_TYPE contains "retina"

FD AC,DE,OX,OC,tissue_type,dev_stage,chr

FM FLAT

Example 5: Mining in EST

ID * DB GBEST

WH TISSUE_TYPE contains "colon"

WH DEV_STAGE contains "adult"

LM 100

FD AC,DE,OX,OC,tissue_type,dev_stage,chr,os

FM FLAT

Example 6: Mining In PDB

ID * DB PDB

WH DE contains "ERYTHRINA CORALLODENDRON LECTIN IN COMPLEX"

WH OS contains "ERYTHRINA CORALLODENDRON"

WH RESO contains 1.90

LM 10

FM FASTA

Example 7: running SQL Native (authorized user)

ID * DB STRING

WH SQLNATIVE select * from items.proteins

Limit 100

FM CSV

Example 8: Association rules (authorized user)

ID * DB protein_interaction

WH PATTERN AssociationPattern(Right(protA,ProtB,ProtC),Left(ProtK),sup=30,conf=90))

FD ID,Rules

FM FLAT

Data Access Protocoles

Data Browsing at Décrypthon Data Center

Database content can be browsed from BIRD System WEB Node ENS-Lyon: [8] Node IGBMC: [9]

Data Selection by BIRD-QL Service

Data can also be selected with BIRD-QL queries; Expert users can however modify queries by hand. Trois query service are available:

     1. curl -F upload=@your_bird.ql 'http://bird.u-strasbg.fr:8080/bird/bsearch?service=birdql'

     2. http://bird.u-strasbg.fr:8080/bird/bsearch?service=birdql&query=your_birdql
     Example:  http://bird.u-strasbg.fr:8080/bird/bsearch?service=birdql&query=
                ID * DB Uniprot--WH DE contains "histone"--LM 10--FD AC,DE--FM FLAT
               http://bird.u-strasbg.fr:8080/bird/bsearch?service=birdql&query=
                ID * DB Uniprot--WH DE contains "Helianthinin"--LM 10--FM FASTA

     3. BIRD-QL Editor (in pres).

User can use this engine for intensive computation, download [birdql cmd].

Simple Services-Bank ID

Service : http://bird.u-strasbg.fr:8080/bird/bsearch?db=<database>&accession=<ac or id>&field=<DE,OS..> &format=<fasta/flat>

Example 1: get EST

     http://bird.u-strasbg.fr:8080/bird/bsearch?db=gbest&accession=Cj133605&field=DE,OS,OC,TISSUE_TYPE,DEV_STAGE

Example 2: get Protein :

     http://bird.u-strasbg.fr:8080/bird/bsearch?db=uniprot&accession=Q23456

Example 3: get PDB :

    http://bird.u-strasbg.fr:8080/bird/bsearch?db=pdb&accession=1XDS

Example 4: get Fasta :

    http://bird.u-strasbg.fr:8080/bird/bsearch?db=pdb&accession=1XDS&format=fasta

WEB Server

   http://bird.u-strasbg.fr:9080/BirdSystem/HomePage.do   (firefox)

API JAVA - BIRDQL Client

The API is an Interface of programming which defines the way in which a data-processing component can communicate with another. The API Java of BIRD contains useful reusable classes by external modules of access to the databases. It has functions (methods) returning the data selected under various formats. The user of high-level can use the API to develop new functionalities exploiting of the data. It can also be used to make personalized graphic interfaces and Web Services. The codes Java below illustrate the exploitation of BIRD API. BIRDQL Engine doesn’t return data but just OIDs of selected records. The content of the record must then be searched by the API.

// API BIRD

Import org.igbmc.bird.* Class ExampleUtilisationAPI {

 InterfactDB birddb  = new InterfaceDB(“my-bird”)
 // BIRD-QL
     String birdql = ” ID * DB UniProt
                     --WH OS contains "Mus mus"
                     --WH OC contains "Eukaryota" & not "Metazoa"
                     --FM OID”
 Vector OID=birddb.queryengine.run(birdql);  
 For { i=1 to OID.size()   }
  { // result treatment
    UniProt obj=(UniProt)birddb.getObject(OID[i]);
            ….
  }

// BIRDQL CLient

java org.igbmc.bird.datadiscovery.BirdQLClient birdql nameServer outFile

@birdql  : file name contains your bird-ql query

@nameServer: name of BIRD Server (d1.crihan.fr or bird.u-strasbg.fr)

@outFile  : file name, the result will be print to this file

BIRD business intelligence

Use cases

Transciptomic

Protein Protein Interaction Pattern

BIRD System in Action

Décrypthon Data Center

Overview

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BIRD System is core of Décrypthon Data Center.

  Sharing of large scare biological data for applications (Macsim, MS2PH, Macgos, Ordali..)   
  runing on Décrypthon Grid.
  Managing of generated data (result) on grid   

  Sharing of data and services for scientific community
  http://bird.u-strasbg.fr:9080/BirdSystem/HomePage.do

File:Bird ddc.jpg

Macsim uses BIRDQL engine

MACSIMS:Multiple Alignment of Complete Sequences Information Management System (Thompson et al, 2006).MACSIMS provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist .

Macsim gets direct connection with Bird database

GPS uses BIRDQL engine

http://nucleic.fr

Gscope utilise BIRD

Gscope peut se mettre maintenant en connexion directe avec Bird

• proc BirdFromQueryText {Texte {OutFile ""} {BirdUrl ""}}
• proc BirdFromQueryFile {Fichier {OutFile ""} {BirdUrl ""}}

Bird sait intégrer les fiches infos d'un projet Gscope. On peut alors les interroger directement par http ou par Gscope ou, mieux, par des affiches avec la commande BirdGscopeSearch

BIRD Development

BIRD Implementation

Origin BIRD System (SAADA)

BIRD was based on main principe of Saada project [10].

  SAADA - Systèm d’Archivage Automatique des Données Astronomiques
  First Goal : Archive & Exploitation of Data of  the European XMM Newton satellite  [11].The 2XMM catalogue of X-ray sources, 
    the largest of its kind ever, has now been released.
  In a PhD Framework (2002-2005, Prototype Saada V.1.3) of Dr.NGUYEN  at University of Strasbourg I,Supported by the  
   CNES[www.cnes.fr] and the Alsace Region,  Supervised by Dr. Michel and Dr.Motch. 

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Data Model

In order to automatically integrate heterogeneous data, we have designed several business data model corresponding to the real format of the data banks. Figure below illustrates the conceptual data model of the BIRD system. It can simultaneously host several bank types. Each type can itself concern several User Defined banks having the same format. Thanks to this conceptual model, BIRD can host different versions of a given data bank and manage them so that the programs launched on grid computing within an application can exploit the same data version during their computation time.

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Conceptual data model

The data model of a data bank is predefined in an XML configuration file . This metadata is used to create the Java and SQL code. The code generation is launched at the moment of the configuration of the BIRD data bank or at data loading or reloading. In the example given figure 3, the metadata of Genbank are used to create Genbank-EST, Genbank-Refseq.

This Figure illustrates the business model for Genbank. Each bank can have several associated entries. Each entry has its associated information like Dbref, SEQData, FTSource,... According to our design, the Java classes of the business models are automatically generated by BIRD. Only instances of classes inherited from super ObjectPersistence will be recognized by the BIRD API. This super class contains common attributes and methods for all generated classes.

Architecture

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Key Technologies

Relational Core store

  IBM DB2 WareHouse V9.1 
  WebSphere Federation Server 

WEB Server & Services

  IBM WebSphere Application Server ( main Portal)
  Tomcat Server (services, non graphic)
  Hibernate and JSF-Java Server Face 
  Object Relational Mapping 
  Web component

XML & JAVA

Project Distribution

  Not net to public

Publications

To cite BIRD System, please use the following publication;

1. Nguyen H., Berthommier G., Friedrich A., Poidevin L. ,Ripp R. , Moulinier L. and Poch O. Introduction du nouveau centre de données biomédicales Décrypthon, CORIA 2008.

2. "Conception of the BIRD System" is preparing for .....

3. "BIRDQL-A new Biological Query Language " is preparing for....

Contact

  Nguyen Ngoc Hoan,PhD
  IGBMC Strasbourg
  1 rue Laurent Fries
  BP 10142
  67404 Illkirch CEDEX / France 
  Mail:nguyen@igbmc.fr
  Tel: 0033 388653302

--Nguyen 15:07, 16 February 2008 (CET)---