DKFZSWLSWorkshop

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A Framework for Annotating High-Throughput Genome
-Wide Screens
Josh Mooreintelligent Bioinformatics Systems
(iBioS)
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Outline

• Problem
• Framework
• Tool-Issues

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Outline

• Problem MitoCheck
• Framework
• Tool-Issues

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Problem

• MitoCheck (EU FP6)
• 5D images from genome-wide screens (RNAi)
• Multiple images for each human gene
• 10-100 TB of data over the next 4 years
• Goal Automated classification of phenotype

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Outline

• Problem
• Framework Open Microscopy Environment
• Tool-Issues

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Framework
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Framework

• OME defines a set of information common to all
  biological microscopy, a format for storing this
  information, and a mechanism for sharing it with
  other software
• HTTP interface
• LSID capable
• XML exchange format

BasicArchitecture
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Framework
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Framework
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Outline

• Problem
• Framework
• Tool-Issues Annotations anyone?

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Tool-Issues

• Provide RDF layer
• Useful for exporting metadata
• Suggestion Annotea
• Solves N-ary problem
• Existing tools
• But only Live Early Adoption and Demonstration
  (LEAD) project

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Tool-Issues

• Hypothetical Query select ?gene where
  (?annotation1, aannotates, ?image)
  (?annotation1, rdftype, exPhenotype)
  (?annotation1, abody, exsomePhenotype)
• (?annotation2, aannotates, ?image)
  (?annotation2, rdftype, exKnockedOutGene)
  (?annotation2, abody, ?gene)
• Result Bindings?gene exgene00001?gene
  exgene19404 ...

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Tool-Issues
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Tool-Issues
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Tool-Issues
http//lsid.limnology.wisc.edu/
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Tool-Issues

• Open
• If not Annotea, what?
• Confidence/Trust
• Retraction/Negation
• Rules
• LSIDs in Mozilla

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Acknowledgements

• Open Microscopy Environment (www.openmicroscopy.or
  g)
• Jason Swedlow (U. Dundee)
• Ilya Goldberg (NIH)
• MitoCheck Project (www.mitocheck.org)
• EMBL/Ellenberg Pepperkok Labs
• DKFZ/iBioS (www.dkfz.de/ibios)
• Roland Eils
• Karl Rohr
• Stefan Frank