Diapositive 1

1
GnpIS Towards an integrated information system
around Plant genomes

1INRA Unité de Recherche en Génomique-Info, chez
Infobiogen 523 place des terrasses 91000 Evry,
FRANCE 2Laboratoire de Génomique et Bioinformatiq
ue, Biogemma, 1 rue Pierre Fontaine, 91058 Evry
Cedex, FRANCE 3Bayer CropSciences 5 rue Pierre F
ontaine, 91058 Evry Cedex, FRANCE
4INRA Unité de Recherche Protéomique, 2 place
Pierre Viala, 34060 Montpellier, FRANCE
Emmanuelle Karsenty1, Delphine Samson1, Erik
Kimmel1, Farid Chetouani1, Frédéric Sapet1,
Michael Alaux1, Fabrice Legeai1, Cyril Pommier1,
Sebastien Reboux1, Cédric Bouttes4, Guillaume
Kerboul2, Bruce Thomas2, Eric Perche3, Nicolas
Sajot2, Laurent Viau3, Denis Scala2, François
Artiguenave1
The INRA URGI (Unité de Recherche en
Génomique-Info) is a bioinformatic platform which
collects data of projects coming from Génoplante
partners (INRA, CNRS, CIRAD, IRD, Bayer
CropScience, Biogemma) since 2000. It maintains a
restricted site for the partners
(https//genoplante.infobiogen.fr, ask
urgi-support_at_versailles.inra.fr for an account)
and for all, a public Web site
http//urgi.infobiogen.fr. The platform stores a
nd organizes the data to make them accessible to
all partners. It provides a user-friendly
environment to biologists for visualization and
analysis of the data. The URGI information syste
m is a web based system composed of several
applications (in Java and Perl) built above a
relational database (Oracle) that includes
integrated schemas for sequence data (EST, mRNA),
mapping data (genetic maps, QTL maps), expression
data, proteomic data and polymorphism data.
The GnpIS information system is composed of 6
modules 1) GnpSeq, the URGI EST, mRNA sequenc
e database which contains home-made clusters,
contigs and annotations 2) GnpMap, the home-made
mapping database (See Poster M2 GnpMap)
3) GnpGenome, a multispecies database containing
genomic sequences and their annotation. (See
Poster M2 GnpGenome) 4) GnpArray, the home-made
MIAME compliant expression database (See Poster
M2 GnpArray) 5) GnpSNP, the home-made polymorph
ism (SNP/DIP/STR) database (See Poster M2
GnpSNP) 6) GnpProt, the proteomic database (See P
oster M2 GnpProt)

• Technology
• RDBMS Oracle 8.1.7, PostgreSQL 8.1
• Database modeling UML (Rational Rose,
  Poseidon)
  
• Upload, integration tool Perl/CGI or Java
• Web interface
• Perl/CGI (GnpSeq, GnpGenome)
• Server-side technology Java J2EE servlets and
  JSP under the Struts framework
  
• Object/Relationnal Mapping tool (Hibernate) and
  Data Access Object/Service design pattern to
  encapsulate database access

Ongoing developments The ongoing developments ar
e the creation of an interoperability between the
databases modules. These allow integrated queries
involving all kind of data. The integration have
begun with the development of a new database
schema (Aster) composed of the common tables of
the Gnp modules. Clone, Sequence, cross referen
ces databanks (XREF) objects are main entities in
the integration system to crosslink with GnpSeq
(EST clone/sequence), GnpMap (mapped EST Marker).
The database fusion of GnpSeq and GnpMap is now
done in Aster. Web interfaces release are planned
for summer 2006.
GnpIS query interface
Simplified schemas
Aster schema
2) GnpMap
Authentification
Protocol
Anchoring
PCR
Trait
Marker
GnpSeq 2006 Database summary
Amplicon
QTL
Loci
Population
Primer
Lines
Assignment
Map
5) GnpSNP
SubSNP
Batch
SNP
Allel
Legend ------- and in developmen
t SNP single nucleotide polymorphism DIP d
eletion insertion polymorphism
STR short tandem repeat
Further work . the fusion in Aster of GnpSNP (Li
nes, Population and PCR, Amplicon, Primer)
. the fusion in Aster of GnpArray data (cDNA
/oligo spot/gene lists) and GnpGenome (BAC or
pseudomolecule clones), planned for the end of
the year. . The development of the complete web
integrative interface to query the global
information system . Links with SIREGAL (Systèm
e dinformation sur les ressources génétiques)
INRA URGI project . Links with CNRGV (Centre nati
onal de ressources génomique végétale) INRA
Toulouse project
Dépôt APP (Genoplante Valor) GnpSeq Deposit
number IDDN.FR.001.21009.000.D.P.2002.000.10300
Publication GénoPlante-Info (GPI) a collection
of databases and bioinformatics resources for
plant genomics. Nucleid Acids Research, 2003, Vo
l.31, No.1, 179-182.Genoplante partners
restricted Web site https//genoplante.infobiogen
.fr URGI Contact urgi-contact_at_versailles.inra.fr
INRA URGI and Genoplante public Web site http/
/urgi.infobiogen.fr Genoplante administrative Web
site http//www.genoplante.com
Site ANR http//www.gip-anr.fr