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Representing Flow Cytometry Experiments within FuGE
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Representing Flow Cytometry Experiments within FuGE
Josef Spidlen1, Peter Wilkinson2, and Ryan Brinkman1
1BC Cancer Research Centre, Vancouver, BC, Canada2University of Montreal, Montreal, QC, Canada
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How can we accurately model “complex” flow cytometry
experiments in an exact manner?
FCS parameter(e.g., FL1)
Reagent
Reporter(e.g., PE)
Detector(e.g., Anti-CD4)
Cell population(e.g., CD4+)
Filter settings?
Emission spectra?
Compensation? ?
?
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Why would we even want to?
• Sharing experimental details• Understanding third party experiments
– Collaboration– Independent validation
• Common and sharable software tools– High-throughput data processing– New data processing methods
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FuGE
• Functional Genomics Experiment Object Model– A model of the common components of functional
genomics experiments– FuGE is developed by members of MGED/PSI with
input from ‘cross-omics’ experimentalists– Aims to help the development of data standards– Should allow some cross-compatibility between
different ‘omics’ experiments
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What is FuGE?
• An object model in UML– An XML Schema (generated from UML)– A software API (created from UML)– ER schema (generated from UML)
• Milestone 3 UML2 - August 2006• Current state: Version 1.0 candidate
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Benefits of shared model components
• Queries over common annotation– Samples, hypotheses, protocols
• Shared software for experimental annotation and analysis– Reduced development and learning times through the
sharing of consistent practice– Eased integrating of functional genomics data
• Developing standards for each technique is a hard problem– Shared resources could alleviate problems
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FuGE
Common
Bio
Description
Audit
Ontology
Protocol
Reference
Investigation
Data
Material
ConceptualMolecule
Common:• General data format management• Auditing• Referencing external resources• Protocols
Bio:• Investigation structure• Data• Materials (organisms, solutions, compounds)• Theoretical molecules e.g., sequences
FuGE structure
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Using FuGE in practice
1. Extend UML with domain-specific components
• Encapsulate details in classes/attributes• Use “generic” classes with text-based
descriptions
2. Reference a FuGE entry for investigation structure and bio samples description
3. Define ontologies and use FuGE as it is for experimental metadata
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FuGE extensions• MAGE V2
– Format for microarray data and annotations• GelML
– Gel electrophoresis, format for methods and results• spML
– Sample processing: liquid chromatography, capillary electrophoresis, …• CPAS
– Computational Proteomics Analysis System – set of bioinformatics tools to help scientists store, analyze, and share data from experiments and clinical trials
• PRIDE – Proteomics Identification Database contemplating FuGE for data format
• Metabolomics community – considering• MIACA (Minimum Information About a Cellular Assay) – considering
• Flow Cytometry– FuGE was chosen as core for flow cytometry object model during
FICCS OMWG Development Workshop (Dallas, October 2006)
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FuGE – Main Abstract Classes
• Everything is “Describable”– Text based description– Ontology reference– Custom properties (keyword / value pairs)
• Most classes are “Identifiable”– “Identifiable” is “Describable”– Unique identifier– Name, database references
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FuGE Protocol Types
1. Material treatment:Flow sample preparation
2. Data acquisition:Cytometer generates FCS
3. Data and material acquisition:Flow sorting
4. Data transformation:Compensation, gating, scaling, visualization
MaterialMaterial
DataMaterial
DataData
DataMaterial
Material
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Flow Cytometry – DataFuGEFlow
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Flow Cytometry – MaterialFuGEFlow
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Flow Cytometry – ProtocolFuGEFlow
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Computational ProtocolFuGEFlow
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Computational ProtocolFuGEFlow
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Computational ProtocolFuGEFlow
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FuGEFlow
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Conclusions
• Initial work on extending FuGE has been done– Can be downloaded using subversion from
https://svn.sourceforge.net/svnroot/flowcyt/ – Pretty high level so far
• Need to incorporate more details• Need to validate the model
– Encoding various use cases– An iterative approach needed
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Acknowledgement
• Members of the FICCS OMWG– Keith Boyce, Ryan Brinkman, Jennifer Cai, Mark
Dalphin, Megan Kong, Jamie Lee, Yu (Max) Qian, Richard Scheuermann, Peter Wilkinson, and others.
• Introduction to FuGE based on original presentations from FuGE development team – Angel Pizarro, Andrew Jones, Paul Spellman, Michael
Miller, and others.