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

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