Beatrice Schildknecht NASC

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Beatrice SchildknechtNASC
PLANET A European Plant Genome Database Network
September 2004
QLRI-CT-2001-00006
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Overview

• What is PlaNet?
• PlaNet data
• Who are we?
• What data do we have?
• NASC data
• PlaNet architecture
• BioMOBY
• PlaNet website

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Currently .
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The Problem

• Information is massively distributed
• Beyond just NASC, MIPS
• Researchers and bioinformaticians need this data
  out there
• Expertise is also massively distributed
• There is no interface to this dispersed pool of
  knowledge

The solution? .we must build something simple
enough for the bench biologist to use
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What is PlaNet?

• PlaNet is a distributed, shared effort among
  bioinformatics groups and molecular biologists in
  the EU, to generate a federated and integrated
  set of databases for plant genomics
• Focused on Arabidopsis at first.
• Goal is to provide a centralised platform to
  integrate heterogeneous data into a comprehensive
  user interface.

Poster and leaflets available-gt please have a
look !!!!
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PlaNets aims

• To develop and deliver a high level plant genome
  database for the systematic exploration of
  Arabidopsis and other plants.
• fulfils
• Easy to use interface
• Comprehensive data resource
• Rapidly discovers all relevant data
• Requires no prior knowledge by end-user
• Enables machine-to-machine discovery of service
  contract and execution
• SIMPLE and minimally disruptive to service
  providers existing methodologies
• ..........

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The PlaNet solution
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PlaNet partners

• Nottingham Arabidopsis Stock Centre (NASC)
• Institute for Bioinformatics (MIPS), Germany
• Flanders Interuniversity for Biotechnology
  (VIB), Belgium
• Genoplante-Info, France
• John-Innes-Centre (JIC), England
• Plant Research International (PRI), Netherlands
• Centro Nacional de Biotecnologia (CNB), Spain

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PlaNet data
(NASC) Arabidopsis germplasm (NASC) Arabidopsis
Ensembl genome browser (NASC) Affymetrix
Microarray data (MIPS) Arabidopsis genome and
annotation (JIC) sequence insertion sites in
Arabidopsis (VIB) structural annotation of
genomes and promoters (VIB) ribosomal RNA
sequences (CSIC) Arabidopsis transcription
factors (PRI) Arabidopsis mutants
database (Genoplante) Arabidopsis Flanking
Sequence Tags (FSTs) (Genoplante) EST and
sequence db (Genoplante) genetic and physical
mapping (Genoplante)

• Stock Catalogue
• AtEnsembl
• NASCarrays
• MAtDB
• AtIDB
• PlantCARE
• rRNAdb
• REGIAdb
• WAtDB
• FLAGdb
• ESTdb
• mappingDB
• Polymorphism DB

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PlaNet Services
June, 2004
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Web Services at NASC
Arabidopsis Image
Experiment Description
NASC code
Phenotype information
EMBL Accession
Global Keyword
Arabidopsis Insert
Slide Name
Experiment Name
Arabidopsis ecotype name
Protocols
Genes -AGI codes
BioSource Information
Expression Data
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Germplasm
Stocks 1991 200 lines 2002 200,000
lines Now 500,000 lines Distribute 33,000
tubes of seed a year to mainly European
countries.
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Transcriptomics

• Focus is on plant experiments, however we have
  processed Affymetrix hybridisations for a range
  of species.
• All data from our Affymetrix service is submitted
  to NASCArrays- The NASC Affymetrix database.
• So far 90 experiments have been run by NASC for
  customers.
• Database is fully MIAME-compliant.
• And now data is available via PlaNet web
  services.

See http//affymetrix.arabidopsis.info, or email
affy_at_arabidopsis.info
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From Sample to Hybridised Array
Labelling protocol
Extraction protocol
Labelled RNA
RNA extract
Hybridisation protocol
Treatment
Hybridised mix
Control
Affymetrix chip
Biological sample
Scanning
Hybridisation parameters
Analysis
Adopted from Miller et al, Conforming to MIAME
www.man.ac.uk
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PlaNet Architecture
Central access point
User Interface / Web display
xml
xml
applications
BioMOBY
Access point for other programs
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BioMOBY

• BioMOBY is an international research project
  involving biological data hosts, biological data
  service providers, and coders.
• Aim is to explore ways to represent, distribute
  and discover biological data. 
• BioMoBY is led by Mark Wilkinson.
• Sept. 2001 The beginnings of the "MOBY"
  specification for database interoperability are
  established at this meeting.

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MOBY components
MOBY
Service provider
The data
MOBY Objects
MOBY Services
MOBY Client
MOBY Central
Service requestor
Service Registry
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How it works.
Service requestor
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BioMOBY Implementation

• Written in Perl
• API and supporting code is relatively stable
• v0.8 API released July, 2004
• MOBY Central web service registry publicly
  available
• PlaNet has its own Central
• Over 100 services currently active (PlaNet has
  over 70)

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PlaNet Website

• Homepage http//www.eu-plant-genome.net
• Mailing lists Planet_at_gsf.de

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PlaNet Client
Homepage http//www.eu-plant-genome.net
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Nottingham Arabidopsis Stock Centre http//Arabido
psis.info
Thanks to
Germplasm Dr Emma Humphreys Victoria Haslam Mr
Graeme Gill Muriel Topham Lubomira Kacinova
Nicola Leftley Celia Hansen Stuart Jones
Linda Lucas Alan Mortimore Dhaval Patel
Director - Dr Sean May Molecular Biology Dr John
Okyere Zoe Emmerson Henrik Townsend
Bioinformatics Mr David Craigon Dr Nick
James Mr Simon Mr Pablo Minguez Paniagua Mr
Warren Read
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