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A Framework for Annotating High-Throughput Genome-Wide Screens

A Framework for Annotating High-Throughput Genome-Wide Screens. Josh Moore intelligent Bioinformatics Systems (iBioS). Outline. Problem Framework Tool-Issues. Outline. Problem : MitoCheck Framework Tool-Issues. Problem. MitoCheck (EU FP6)

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A Framework for Annotating High-Throughput Genome-Wide Screens

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

  2. Outline • Problem • Framework • Tool-Issues

  3. Outline • Problem : MitoCheck • Framework • Tool-Issues

  4. 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

  5. Outline • Problem • Framework : Open Microscopy Environment • Tool-Issues

  6. Framework

  7. 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

  8. Framework

  9. Framework

  10. Outline • Problem • Framework • Tool-Issues : Annotations anyone?

  11. a:Annotation dc:created a:context dc:modified dc:creator a:annotates rdf:type a:body @prefix a: http://www.w3.org/2000/10/annotation-ns# 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

  12. Tool-Issues • Hypothetical Query: select ?gene where (?annotation1, a:annotates, ?image) (?annotation1, rdf:type, ex:Phenotype) (?annotation1, a:body, ex:somePhenotype) (?annotation2, a:annotates, ?image) (?annotation2, rdf:type, ex:KnockedOutGene) (?annotation2, a:body, ?gene); • Result Bindings:[?gene ex:gene00001][?gene ex:gene19404]...

  13. Tool-Issues

  14. Tool-Issues

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

  16. Tool-Issues • Open: • If not Annotea, what? • Confidence/Trust • Retraction/Negation • Rules • LSIDs in Mozilla

  17. Acknowledgements • Open Microscopy Environment (www.openmicroscopy.org) • 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

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