G2G

1
G2G

• A Peer-to-Peer Architecture for Gene Expression
  Data

Jason E. Stewart Open Informatics www.OpenInformat
ics.com
2
How I got Here

• Frustrated biologist
• DNA seq (Mac), Standen(Unix/Sun), EMBL (VAX/VMS)
• camel.tar.gz
• Unix Power Tools gt Perl
• Lincoln Stein (DAS, etc.)
• www.OpenInformatics.com

3
Prophecy

• Distributed data
• It's already here
• GenBank/TrEMBL/SwissProt ...
• WormBase/TAIR/FlyBase ...
• Microarray data has no central DB
• ArrayExpress/GEO
• How can we make it most effective?
• Efforts of both biologists and technoligists

4
Punchline

• Ontologies to unify queries
• Controlled Vocabularies not AI
• Object Models (UML)
• Open Source reference implementations
• Wrong-Is-Right
• Queries
• Language XML format parser
• Use cases In rats treated with CFB at 250mg per
  day and pooled, which genes have changed more
  than 2-fold compared to control rats

5
Payoff

• XML-based markup language
• Programming API's Java, Perl, C
• Relational Schema

6
G2G Architecture

• Enables Gene Expression data queries and
  downloads from remote data sources
• Primary focus data discovery
• Technologies
• HTTP/XML
• SOAP/WDSL/UDDI
• MOBY

7
Data in the Big

• 88 hybridization Mouse experiment
• measured data (70Mb), XML ?? Gb
• Number of data sets (few vs. many)
• Contextual data (little vs. large)
• Services (BLAST vs. Clustering)
• Conclusion GE resources will be different than
  DNA sequence oriented ones

8
P2P Metaphor

• G2G not P2P (napster, seti_at_home)
• Uses DNS and central service directory
• Advantages
• Distribution of resources (CPU Bandwidth)
• Distribution of services
• Distribution of annotation (richer)
• Disadvantages
• Authoritative source ??
• Peer review ??

9
Implementing G2G

• Infrastructure
• GeneX
• MAGE/MAGEstk
• Perl/LWP/Apache/mod_perl
• Issues
• Query and response formats (MAGE-ML)
• Creating clients and servers (GeneX)
• Only supports simple queries

10
GeneX (genex.sf.net)

• Open Source gene expression DB
• Laboratory data
• Analysis framework
• Components
• Relational schema
• Data Server Query tools
• Analysis tools
• Perl API
• Active development, two NSF grants

11
MGED (www.mged.org)

• Industry and Academia
• Standards for microarray data
• MIAME (published in Nature Genetics)
• MAGE (mged.sf.net)
• Ontologies (mged.sf.net)
• Queries
• Normalization

12
Review of MIAME

• In MIAME
• Samples Samples used, the extract preparation
  and labeling
• Hybridizations Procedures and parameters
• Array design Each array used and each element
  (spot) on the array
• Measurements Images, quantitation,
  specifications
• ControlsTypes, values, specifications.
• Experimental designThe set of the hybridization
  experiments as a whole

• In MAGE-OM
• BioMaterial
• BioAssay
• ArrayDesign
• BioAssayData
• ExperimentDesign
• ExperimentDesign

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MAGE-OM

• Collaborative effort to develop a common
  representation of gene expression experiments and
  associated annotations.
• Industry Rosetta, Agilent, Affymetrix
• Academic MGED
• UML based model gives rise to
• MAGE-ML XML DTD
• MAGEstk software toolkit
• Java, Perl, C programming language APIs
• XML Reader/Writer
• DB Serializer (future)

14
MAGE-OM Packages

• AuditAndSecurity
• Description
• BioEvent
• BioMaterial
• BioSequence
• HigherLevelAnalysis
• Protocol
• ProtocolApplication

Experiment
BioAssay
BioAssayData
ArrayDesign
DesignElement
Maps
Array
QuantitationType
15
Demo
16
Issues

• User control of local resources
• What queries should be supported
• What services should be supported
• Simple lists of data (current)
• Analyses
• Complex queries with subsetting on genes and
  context

17
How to Help

• MGED (mged.org)
• Ontlogies (mged.sf.net, geneontology.org)
• MAGE (mged.sf.net)
• GeneX, G2G (genex.sf.net)

18
Acknowledgments

• MGED
• Alvis Brazma
• Terry Gaasterland
• MAGE
• Paul Spellman
• Michael Miller
• Charles Troup
• Steve Chervitz, Derek Bernhardt
• Eric Deutsch, Robert Hubley
• Angel Pizzaro

• GeneX
• Jennifer Weller
• Harry Mangalam
• Karen Schlauch
• Michael Pear

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Radical Subversion

• Publicly funded software should be Public
• Www.OpenInformatics.org