Bioinformatics at NIAID-Biodefense Proteomics Administrative Resource Center

1. Bioinformatics at NIAID-Biodefense Proteomics Administrative Resource Center Peter McGarvey Ph.D. Senior Bioinformatics Scientist, Project Manager Protein Information Resource (PIR) Georgetown University Medical Center

3. NIAID Biodefense Proteomics Program • 7 Proteomics Research Centers: Identifying Targets for Therapeutic Interventions “..discovering targets for potential candidates for the next generation of vaccines, therapeutics, and diagnostics” • Administrative Resource Center: Support research centers, public distribution of results and protocols ..establish a Scientific Advisory Group, Interoperability Working Group and promote awareness of the project so scientists worldwide can utilize these resources. • Social & Scientific Systems • PIR, Georgetown University Medical Center • Virginia Bioinformatics Institute, Virginia Tech • Biodefense & Emerging Infections Research Resource Repository

4. Administrative Resource Activities • Project Management (SSS) • Meetings and Communications • Web Portal • Scientific Coordination (PIR/VBI) • Scientific Advisory Working Group (SWG) • Interoperability Working Group (IWG) • Data Infrastructure (VBI/PIR) • Proteomic Database: Storage and Retrieval (VBI) • Data Management and Analysis Tools (PIR/VBI) • Integrated Protein Knowledge System (PIR)

5. Albert Einstein College of Medicine(PI - George Orr) • T. gondii, C. parvum • Caprion Pharmaceuticals(PI - Eustache Paramithiotis) • B. abortus • Harvard Institute of Proteomics(PI - Joshua LaBaer) V. cholerae, B. anthracis • Myriad Genetics(PI - Jerry Lanchbury) • B. anthracis, Y. pestis, F. tularensis, Vaccinia • Pacific Northwest National Laboratory(PI - Richard Smith) • S. typhimurium, S. typhi, Vaccinia, Monkeypox • Scripps; Burnham Institute(PI - Peter Kuhn) • SARS CoV • University of Michigan(PI - Philip Hanna) • B. anthracis

6. Mass Spectrometry: LC-MS/MS LC-FTICR Bio-arrays and Y2H: Affymetrix Arrays Protein Arrays Random & Directed Y2H Screens 1-D & 2-D Gels Structural Proteomics: High resolution NMR/X-ray crystallography Other Experimental Data: RNAi & KO data ORF clones for complete proteomes Mutant proteins Antibody Screens Phagocytosis mapping using fluorescence Protein localization information, EM Methodology: Sample Prep Methodology Experimental protocols Novel technologies Proteomic Data

8. Administrative Center Progress to date • Scientific Working Group(SWG) • Outside experts to advise the project • Interoperability Working Group(IWG) • Adopt MIAPE/MIAME and community standards. • Adopt relevant ontologies • Prototypes for Web Interfaces • SSS – www.proteomicsresource.org • PIR – pir.georgetown.edu/proteomics • VBI - proteinbank.vbi.vt.edu/bprc • Documentation: Use Cases > Req. >> Design • Outreach – What are your suggestions?

9. SSS – www.proteomicsresource.org VBI - proteinbank.vbi.vt.edu/bprc PIR – pir.georgetown.edu/proteomics

10. 4 5 2 1 3 Master Catalog • Sophisticated Text Searches • Customizable Information Matrix • Report Retrieval • 1. UniProtKB Protein Report • 2. iProClass Protein Report • 3. BioThesaurus Name Report • 4. PIRSF Family Report • 5. UniRef50 Cluster Report • Links Proteins in Experimental Data

12. Complete Proteome Tool

13. CUPID Core and Unique Protein Identification system

14. PIR – Georgetown University Cathy Wu Peter McGarvey Hongzhan Huang Raja Mazumder Darran Natale Zhang-Zhi Hu Xin Yuan Baris Suzek Virginia Bioinformatics Institute Bruno Sobral Jeff Chen Oswald Crasta Social & Scientific Systems Margaret Moore Terry Brennan Paula Yadvish National Institute of Allergy & Infectious Diseases (NIAID/NIH/DHHS) Kimberly Stemple Joseph Breen Acknowledgements

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