Richard H. Scheuermann, Ph.D.
November 5, 2012
Support for Systems Biology Datain IRD/ViPR
www.viprbrc.org www.fludb.org
Bioinformatics Resource Centers (BRCs)
Genome Sequencing
Centers
GenomicsFunctional Genomics Proteomics
Structural Genomics
Systems Biology Other
“omics”PathogenFunctionalGenomics
Center
ProteomicsResearchCenters
StructuralGenomicsCenters
ClinicalProteomics
Centers
SystemsBiologyCenters
Databases/Bioinformatics Resource Centers
Human Microbiome
Project
To address key questions in microbiology and infectious disease
To identify new targets and develop new strategies for vaccines, diagnostics and therapeutics
NIAID Genomics Program
Host/Pathogen Interaction
SystemsBiology
“Omics” Data Management
BiosamplesCells/organisms
TreatedSamples
PrimaryData
ProcessedData Matrix
Biosets1.
Pathogentreatment
Assay 1Data
processingData
interpretation
Project
BiosamplesCells/organisms
TreatedSamples
PrimaryData
ProcessedData Matrix
Biosets2.
Assay 2
“Omics” Data Management
BiosamplesCells/organisms
TreatedSamples
PrimaryData
ProcessedData Matrix
Biosets1.
BiosamplesCells/organisms
TreatedSamples
PrimaryData
ProcessedData Matrix
Biosets2.
Pathogentreatment
Assay 1Data
processingData
interpretation
Project
Metadata
Assay 2
Data Submission Workflows
Study metadata
Experiment metadata
Primary results
Analysis metadata
Processed data matrix
Free text metadataGEO/PRIDE/PNNL/SRA/MetaboLights
ViPR/IRD/PATRIC
Host factor bioset
pointer
submission
submission
pointer
Systems Biology sites
Host Factor Data
8 Studies To Date
X
Associated Biosets
Bioset Example
Cross-experiment Comparison
Boolean Combinations
Search for Specific Genes
Summary of Current “Omics” Support
• Structured metadata about study, experiments, analysis methods
• Series of derived biosets• Boolean analysis of biosets from different
experiments• Biosets based on expression patterns• Search for expression patterns of specific genes• Access to complete data matrix
Future Development Plans
• Proteomics, metabolomics and lipidomics data• Integration of RNA expression, protein
abundance and metabolite abundance• GO enrichment analysis• Pathway/network visualization and analysis– Protein interaction networks, e.g. BioGRID– Pathways, e.g. BioCyc
GOenrichment
Networkvisualization
GOGOGOGOGOGOGOGOGOGOGOGOGOGO
Acknowledgement
• Lynn Law, U. Washington• Richard Green, U. Washington• Peter Askovich, Seattle Biomed• Brett Pickett, U.T. Southwestern/JCVI • Jyothi Noronha, U.T. Southwestern• Eva Sadat, U.T. Southwestern• Entire Systems Biology Data Dissemination Task
Force, especially Jeremy Zucker• NIAID (Alison Yao and Valentina DiFrancesco)
31
• U.T. Southwestern– Richard Scheuermann (PI)– Burke Squires– Jyothi Noronha– Victoria Hunt– Eva Sadat– Brett Pickett– Yun Zhang
• Vecna– Chris Larsen– Al Ramsey
• LANL– Catherine Macken– Mira Dimitrijevic
• U.C. Davis– Nicole Baumgarth
• USDA– David Suarez
• Sage Analytica– Robert Taylor– Lone Simonsen
• U. Washington– Michael Gale
• Northrop Grumman– Ed Klem– Mike Atassi– Jon Dietrich– Patty Berger– Jawwad Cheema– Zhiping Gu– Sherry He– Wenjie Hua– Wei Jen– Sanjeev Kumar– Xiaomei Li– Jason Lucas– Bruce Quesenberry– Barbara Rotchford– Prabhu Shankar– Hongbo Su– Bryan Walters– Sam Zaremba– Liwei Zhou
• U. Washington– Lynn Law– Richard Green
• IRD SWG– Gillian Air, OMRF– Carol Cardona, Univ. Minnesota– Adolfo Garcia-Sastre, Mt Sinai– Elodie Ghedin, Univ. Pittsburgh– Martha Nelson, Fogarty– Daniel Perez, Univ. Maryland– Gavin Smith, Duke Singapore– Dave Stallknecht, Univ. Georgia– David Topham, Rochester– Richard Webby, St Jude
• ViPR SWG– Richard Kuhn, Purdue– Raul Andino, UCSF– Slobodan Paessler, UTMB Galveston– X.J. Meng, VBI– Colin Parrish, Cornell– Elliot Lefkowitz, UAB– Carla Kuiken, LANL– David Knipe, Harvard– Matthew Henn, Broad Institute– Richard Whitley, UAB– John Young, Salk Institute
Acknowledgments
N01AI40041N01AI2008038
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