Rebecca Ernst

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Rebecca Ernst
(funded by EU QLRI-CT-2001-00006)
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PlaNet partners
Institute for Bioinformatics (IBI)/MIPS,
Neuherberg, Germany Flanders Interuniversity for
Biotechnology (VIB), Gent, Belgium
Genoplante-Info, Evry, France Nottingham
Arabidopsis Stock Centre (NASC), Nottingham, GB
John-Innes-Centre (JIC), Norwich, GB Plant
Research International (PRI), Wageningen,
Netherlands Centro Nacional de Biotecnologia
(CNB), Madrid, Spain
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PlaNet
genome and annotation germplasm genome
view sequence insertion sites structural
annotation of genomes and promoters transcription
factors mutants ESTs genetic and physical
mapping Polymorphism
...
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Problems to solve

• data sources are distributed
• copy and paste needed

• output is human readable but cant be read by
  machines

• data transformation into other formats needed
• data not immediately comparable

• user needs to know where to find information
• prior knowledge needed

Applications
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Achievements Standardization

• Data format standardization
• Agreement on common
• Vocabularies
• Ontologies
• reference genome assembly
• identifiers (AGI locus codes)

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Achievements Data Services

• 10 DBs (genome sequence and annotation,
  germplasm, PPIs, sequence insertions, stocks,
  rRNAs, Arrays, mutants,) currently integrated
• 130 PlaNet BioMoby webservices available
  accessing those DBs plus tools (e.g.Blast or data
  transformations)

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Achievements - generic Clients

• 3 generic client applications (gbrowse, AGI Locus
  Report, service aggregator) available for
  interactive requests to PlaNet (browsing)

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gbrowse_moby

• If you have no clue what wuschel is
• Gbrowse_moby is especially useful for browsing
  services in google-style.
• Once you retrieved information you can continue
  with it and click yourself through Planet

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AGI Locus Report
If you want to find everything available about a
gene of interest The AGI Locus Report offers
you all information on a given AGI Code. A link
list providing links to partner DBs and services
which can operate on AGI Codes.
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Service aggregator
If you want to retrieve data without clicking
your way to it. e.g. if you want to retrieve a
blast result you enter the AGI code and the
service aggregator finds its way to retrieve the
sequence and then blast this sequence.
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Achievement specialized Clients
3 specialized client applications (cos marker
client, AtIDB gene report, BioFloWeb) available
for querying Planet services
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Cos marker client

• If you want to find conserved orthologs in a
  given set of genomes
• Select two organisms and find the putative
  othologs between them.

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AtiDB gene report

• If you want to find useful information about a
  gene of interest
• Useful for getting an integrated, up-to date gene
  report on a given gene of interest

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BioFloWeb (Planet gene report)

• Input An AGI code
• Retrieves relevant data from distributed
  databases
• Summarizes and formats the results for easy
  readability
• Configurable
• The user can select what categories of data are
  to be displayed and choose from all possible
  retrieval workflows
• administrators can implement new display modules
  and complex workflows

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MIPS
NASC
JIC
NASC
INRA
CSIC
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Some figures

• 130 services
• 6 clients
• several Taverna workflows for download (currently
  5)
• 100.000 webhits per month
• Service invocations 16543 (May) , 8320 (June
  until now)

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Thanks to

• Klaus Mayer
• Heiko Schoof
• Dirk Haase
• Octave Noubibou
• Tobias Hindemitt
• MIPS (esp. plant group)
• PlaNet partners
• BioMoby consortium
• European Commission

PlaNet is funded by EU QLRI-CT-2001-00006
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there are gt100 services registered !
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with Ontologies
Why BioMOBY?
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Biomoby Principle
phenotype
AGI Codes