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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. NIAID Biodefense Proteomics Program.

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slide1

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

slide3

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
administrative resource activities
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)
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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
slide6
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

administrative center progress to date
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?
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SSS – www.proteomicsresource.org

VBI - proteinbank.vbi.vt.edu/bprc

PIR – pir.georgetown.edu/proteomics

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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
acknowledgements
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