Bioinformatics at NIAIDBiodefense Proteomics Administrative Resource Center

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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
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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.
• Biodefense Emerging Infections Research
  Resource Repository

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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

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Administrative Resource

• Project Management - Social Scientific Systems
  (SSS)
• Meetings and Communications
• Web Portal
• Scientific Coordination - PIR VBI
• Scientific Advisory Working Group (SWG)
• Interoperability Working Group (IWG)
• Data Infrastructure - Virginia Institute of
  Bioinformatics PIR
• Proteomic Database Storage and Retrieval (VBI)
• Data Management and Analysis Tools (PIR/VBI)
• Integrated Protein Knowledge System (PIR)

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Proteomic Data

• 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

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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. Blast Report
• Links Proteins in Experimental Data

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Complete Proteome Tool
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CUPID Core and Unique Protein Identification
system
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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
• Oswald Crasta
• Jeff Chen
• Chengdong Zhang

• Social Scientific Systems
• Margaret Moore
• Terry Brennan
• Paula Yadvish
• National Institute of Allergy Infectious
  Diseases (NIAID/NIH/DHHS)
• Kimberly Stemple
• Joseph Breen

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• The END
• PIR pir.georgetown.edu/proteomics
• SSS www.proteomicsresource.org
• VBI - proteinbank.vbi.vt.edu/bprc
• BEI - www.beiresources.org/