BIRD
BIRD System (BIRD): Biological Integration and Retrieval Data was designed by Hoan Nguyen at LBGI laboratory (POCH Team) of IGBMC[1] Strasbourg
Contents
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
Kownledge Discovery in Biological Database
Data flow of the mining procedure (FindDeviations)
DB2 Miner Intelligent (API)
Finding deviations
Finding groups with similar characteristics (ClusterTable procedure)
You can find groups with similar characteristics by using the ClusterTable procedure. When to do it: The database might contain patient data including demographic data, for example: v Gender v Age v Profession v Family statusThe information might also include the income or the socio-demographic group of the customer
Finding relationships (FindRules procedure) You can find relationships in your data by using the FindRules procedure.
Predicting future behavior (PredictColumn procedure)
The database might contain customer data. In the tables or views of your database, there might be one column that you are particularly interested in. In the clinical data, you can find relations between symptoms and diseases. With this information, you can predict the potential diseases of new patients
Use cases
Transciptomic
Protein Protein Interaction Pattern
BIRD System in Action
Décrypthon Data Center
Overview
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
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
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
Origin BIRD System
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.
Conceptual 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.
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.
Query Engine
Data Integration
The creation of a database goes through some principal stages : Initially the relational schema system (meta-model) is created when BIRD is installed. In the second phase, the configuration module creates the business data model including SQL and Java codes corresponding to the predefined metadata given by the XML configuration. Then, the system analyzes some integration rules to select the data files and proceed to their conversion and loading into the relational tables .
Architecture
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)---
