1. Representing Flow Cytometry Experiments within FuGE Josef Spidlen 1, Peter Wilkinson 2, and Ryan Brinkman 1 1 BC Cancer Research Centre, Vancouver, BC, Canada 2 University of Montreal, Montreal, QC, Canada

2. 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? ? ?

3. 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

4. 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

5. 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

6. 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

7. FuGE Common Bio Description Audit Ontology Protocol Reference Investigation Data Material Conceptual Molecule 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

8. 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

9. 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)

10. 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

11. 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 Material DataMaterialData Material

12. Flow Cytometry – Data FuGE Flow

13. Flow Cytometry – Material FuGE Flow

14. Flow Cytometry – Protocol FuGE Flow

15. Computational Protocol FuGE Flow

16. Computational Protocol FuGE Flow

17. Computational Protocol FuGE Flow

18. FuGE Flow

19. Conclusions Initial work on extending FuGE has been done –Can be downloaded using subversion from https://svn.sourceforge.net/svnroot/flowcyt/ 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

20. 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.