boston, 28.10.04 a framework for annotating high-throughput genome-wide screens josh moore...
TRANSCRIPT
Boston, 28.10.04
A Framework for Annotating High-Throughput
Genome-Wide Screens
Josh Mooreintelligent Bioinformatics Systems (iBioS)
Page 2
Boston, 28 Oct. 04 Outline
• Problem
• Framework
• Tool-Issues
Page 3
Boston, 28 Oct. 04 Outline
• Problem : MitoCheck
• Framework
• Tool-Issues
Page 4
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 5
Boston, 28 Oct. 04 Outline
• Problem
• Framework : Open Microscopy Environment
• Tool-Issues
Page 6
Boston, 28 Oct. 04 Framework
Page 7
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”
• HTTP interface
• LSID capable
• XML exchange format
BasicArchitecture
Page 8
Boston, 28 Oct. 04 Framework
Page 9
Boston, 28 Oct. 04 Framework
Page 10
Boston, 28 Oct. 04 Outline
• Problem
• Framework
• Tool-Issues : Annotations anyone?
Page 11
Boston, 28 Oct. 04 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
a:Annotation
dc:created
dc:modified
a:bodyrdf:type
dc:creatora:annotates
a:context
@prefix a: http://www.w3.org/2000/10/annotation-ns#
Page 12
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 13
Boston, 28 Oct. 04 Tool-Issues
Page 14
Boston, 28 Oct. 04 Tool-Issues
Page 15
Boston, 28 Oct. 04 Tool-Issues
http://lsid.limnology.wisc.edu/
Page 16
Boston, 28 Oct. 04 Tool-Issues
• Open:
• If not Annotea, what?
•Confidence/Trust
•Retraction/Negation
•Rules
•LSIDs in Mozilla
Page 17
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