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A Framework for Annotating High-Throughput Genome-Wide Screens Josh Moore intelligent Bioinformatics Systems (iBioS) Boston, 28.10.04 Boston, 28 Oct. 04 Outline • Problem • Framework • Tool-Issues Page 2 Boston, 28 Oct. 04 Outline • Problem : MitoCheck • Framework • Tool-Issues Page 3 Boston, 28 Oct. 04 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 Page 4 Boston, 28 Oct. 04 Outline • Problem • Framework : Open Microscopy Environment • Tool-Issues Page 5 Boston, 28 Oct. 04 Framework Page 6 Boston, 28 Oct. 04 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” Basic Architecture • HTTP interface • LSID capable • XML exchange format Page 7 Boston, 28 Oct. 04 Framework Page 8 Boston, 28 Oct. 04 Framework Page 9 Boston, 28 Oct. 04 Outline • Problem • Framework • Tool-Issues : Annotations anyone? Page 10 Boston, 28 Oct. 04 Tool-Issues • Provide RDF layer • Useful for exporting metadata a:Annotation • Suggestion: Annotea • Solves “N-ary” problem a:context a:annotates • Existing tools rdf:type • But “only” Live dc:created dc:modified dc:creator a:body Early Adoption and Demonstration (LEAD) project @prefix a: http://www.w3.org/2000/10/annotation-ns# Page 11 Boston, 28 Oct. 04 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] ... Page 12 Boston, 28 Oct. 04 Tool-Issues Page 13 Boston, 28 Oct. 04 Tool-Issues Page 14 Boston, 28 Oct. 04 Tool-Issues Page 15 http://lsid.limnology.wisc.edu/ Boston, 28 Oct. 04 Tool-Issues • Open: • If not Annotea, what? • Confidence/Trust • Retraction/Negation • Rules • LSIDs in Mozilla Page 16 Boston, 28 Oct. 04 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 Page 17