Nottingham Arabidopsis Stock Centre

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Microarrays
UKCROP.NET
Bioinformatics
Seeds, DNA, mutants and natural variants
Nottingham Arabidopsis Stock Centre
Funded by the bbsrc
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Other databases and applications
Transcriptomics database
DB2
Germplasm database
MySQL
MySQL
Other databases and applications
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large files / difficult mining
Bioinformatics
Arrays 2002 500 expts 2003 1000 expts Each
22K objects
User friendly
connect
AGR 25,000 genes Variable sub-objects (e.g.
clones, sequence)
Seeds 1991 200 objects 1999 20,000
objects Today 450,000 objects
Complex objects / difficult curation
Difficult visualisation
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Order seed
Mutants, ecotypes, other germplasm
Germplasm database
Image
Description of phenotype
Blast for similar sequences
DNA sequence
Other similarmutants / genes
AGR
Protein sequence
Microarray database
Spot historiesScatter plots
Expression profiles
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Germplasm

• NASC is based at the University of Nottingham and
  provides seed and information resources primarily
  to Europe.
• The Americas are served by ABRC and both centres
  serve the rest of the world together.
• Stocks
• 1991 200 lines
• 2002 200,000 lines
• Now 450,000 lines represented
• Distribution
• - 25,000 tubes of seed a year to mainly
  European countries.
• Approximately 20 of our users get seeds for
  free, the rest enjoy an average price of about
  2 euros per line
• All of these seeds can be ordered through our
  online catalogue at http//arabidopsis.info.

   
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Distribution of NASC Users in Europe

• Almost 3000 users throughout Europe (and the
  rest of the world)

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Functional genomics seed tools donors
International statistics for openly distributed
genetic resources.
Seed tools recipients (May 2002-Apr 2003)
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What do the Seed Donors get ?

• Security we preserve the seeds under the best
  possible conditions for longevity and germination
  frequency.
• Stability Funded from 1991-2007 (and
  counting). Any seeds donated can be recovered if
  local stocks get compromised or lost (or just
  lose their germination state) many years after
  they have been donated.
• Publication many journals now require seeds to
  be donated to the stockcentres before
  publication. We give donors a NASC code on
  receipt of the seeds.
• Less work we distribute on the donors behalf,
  and their name is associated with the donated
  stock forever.
• Publicity we associate stocks with documents
  from your lab, e.g. instructions on use,
  observations etc, even logos if that is what the
  donor wants.

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http//ukcrop.net/
UKCrop.net

• A consortium of plant genome databases.
• Established in 1996.
• Develop, manage, and distribute information
  relating to comparative mapping and genome
  research in crop plants.
• The 6 projects comprising UK CropNet are
  located at
• Institute of Grassland Environmental Research
  (IGER) in Aberystwyth
• John Innes Centre (JIC) in Norwich
• Nottingham Arabidopsis Stock Centre (NASC) at
  the University of Nottingham
• Scottish Crop Research Institute (SCRI) in Dundee

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• 5 species-specialised UK databases
• Arabidopsis
• Barley
• Brassica
• Forage grasses
• Millet
• 2 broad species UK databases
• ComapDB
• CropseqDB
• 25 external world databases mirrored

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http//ukcrop.net/agr
AGR

• The Arabidopsis Genome Resource, based at NASC.
• built as a part of the UKCrop.net project.
• holds sequence and mapping data for
  Arabidopsis.
• promotes comparative analysis between
  Arabidopsis and crop plants.
• integrated with the Arabidopsis stock
  catalogue.

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http//ukcrop.net/agr
OR USE SEQUENCE / BLAST
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http//arabidopsis.org.uk/insertwatch
Insert Watch / Blast

• InsertBlast (http//arabidopsis.org.uk/blast.html)
  
• Since 2000 allows searching of insert
  sequences matching a gene of users interest.
• Linked to NASC stock catalogue
• - users can order the corresponding
  insert-containing stock.
• InsertWatch (http//arabidopsis.org.uk/insertwatch
  )
• Since 2000 automated searching of new sequenced
  insert populations. Matches are e-mailed.

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Affymetrix service
Browsing, downloading, automated delivery by CD
(AffyWatch), searching, scatterplots, spot
histories, mass downloads, gene swinger.. etc
Data tools
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Caution !
Array data are CLUES !!
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ArrayExpress
As part of the Affy service Your data submitted
to ArrayExpress (required for publication) under
your name.
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Bioinformatics
EMBL
Genomics (AGR)
Insert data insert germplasm (JIC)
Germplasm DNA data
TAIR
NASCproteomicsDB
MIPS
Proteomics (Cambridge)
ArrayExpress
ABRC

• NASCarrays
• Local generation
• Spotted arrays
• Affymetrix gene chips

CRIME TranscriptomicsDB
Metabolomics (Long Ashton)
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PLANET

• EU consortium to generate a federated set of
  databases for plant genomics (Arabidopsis as
  first focus)
• Started 2002
• Goal is federation on a distributed model (inc
  GRID or GRID-like approach as it becomes
  possible)
• 2003 the selected model became web-services /
  BioMOBY
• Pick up the leaflet and look at the posters
  please !!!!

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Future plans
BioMoBY

• Explores ways to represent, distribute and
  discover biological data. 
• Data providers agree on a standard defining how
  their data and tools are represented.
• A 'registry' tracks which data sources implement
  which services.
• Scripts consult registry to determine which data
  sources to query for which data type or
  operation.
• We intend to make our data fully BioMOBY
  compliant.

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MOBY-Services

• Accepts MOBY Object(s) as queries via SOAP
• Returns MOBY Object(s) in response via SOAP
• Service provider registers with MOBY Central
• "Port"
• Service Type (from service hierarchy)
• URL of service
• Human-readable description

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Mock Response Sequence XML for Apetala3
ltMOBY Authority"ncbi.nlm.nih.gov"
log"Query/ID" id 1334543gt ltSequence
namespace"GenBank/Acc" idD21125.1gt ltCrossRefe
rencegt ltObject namespace"PubMed/ID
id"7948893"/gt ltObject namespace
"SwissProt/ID" id"BAA65.1"/gt ltObject
namespace "TAIR/Locus" id"AP3"/gt ltObject
namespace "GO/Acc id"GO0001835"/gt
ltObject namespace "EMBL/ID"
id"AF056541"/gt lt/CrossReferencegt ltLengthgt876lt
/Lengthgt ltSequenceStringgtgatcaatcca tgttagtttc
taactgtggc caacttagtt . lt/SequenceStri
nggt lt/Sequencegt lt/MOBYgt
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Where does new info come from?

• SERVICE AMPLIFICATION

Sequence
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Future plans
NASC Data made available to PLANet

• Phenomics data will be made available to PLANet
• XML file for each seed generated
• Transcriptomics data generated in-house will be
  made available to PLANet
• Any other external database can also use the
  services as they become available for internal or
  public use.
• e.g. would you like to enhance YOUR database
  by adding germplasm data pulled by AGI code from
  our database without going through our pages ?
• i.e. Data YOUR WAY when YOU want it in YOUR
  format and layout.

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Near future - Ensembl
Arabidopsis
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Internal NASC ENSEMBLdevelopment plan 2003/4
launch
Two lanes of Affy. Thisll be where links to
NASCarrays go
AGI codes go here
SWISSProt trEMBL
APPROVED
Lanes for germplasm, CATMA, for Inserts
(several), for SNPs, for repeat regions, for
ESTs, for ABRC clones, for other species
homologiesetcetc.
Arabidopsis Unigene available
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Nottingham Arabidopsis stock centre
Taking from the data and seed rich and giving to
the data and seed poor
Bioinformatics / Curation team David Craigon
Affy DB Graeme Gill Germplasm Curation Janet
Higgins Affy / CATMA QC curation Emma Humphreys
Germplasm curation Nick James Germplasm
DB John Okyere Affy analysis Beatrice
Shildknecht Planet/BioMoby Guo-an Sun AGR DB
Seeds
Bioinformatics
Molecular Biology
Bold here in York
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The future ?
Its already here