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Transcript 
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
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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
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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
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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]
...
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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
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