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Integrated Proteomic Bioinformatics: Challenges and Solutions for NIAID Biodefense Proteomics

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Proteomic Informatics Challenges. Data Management ... Utilization by the broad biomedical community for hypothesis generation and testing ... – PowerPoint PPT presentation

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Title: Integrated Proteomic Bioinformatics: Challenges and Solutions for NIAID Biodefense Proteomics


1
Integrated Proteomic Bioinformatics Challenges
and Solutions for NIAID Biodefense Proteomics
www.proteomicsresource.org
(Web Posters 59, 68)
US HUPO-2007 Proteomics Workshop Seattle,
WA March 6, 2007 Cathy H. Wu, Ph.D. Director,
Protein Information Resource (PIR) Professor,
Georgetown University Medical Center
2
NIAID Biodefense Proteomic Program
Organism
Data Type
Research Center (PRC)
Admin Resource Center (AC)
3
Challenges
  • Challenges
  • Working with seven Proteomic Research Centers
    (PRCs) with different technologies, pathogens,
    processes, and data types
  • Seamless integration of three institutions that
    make up the Admin Resource Center (AC)
  • Effective dissemination of newly discovered
    information to the scientific community
  • Dissemination Requirements
  • Timely Dissemination
  • Submission Protocol and Data Release Plan
  • Standards and Interoperability
  • Adopt common standards HUPO PSI, caBIG VCDE
  • Define a core set of metadata and map to
    CV/ontology
  • Recommend preferred IDs
  • Define data storage requirements
  • Value-Added Annotation
  • Rich Annotation Capture experimental results and
    scientific conclusion
  • Integration with related resources and major
    public repositories

4
Integration at Admin Resource Center
  • Scientific Coordination Scientific Working Group
    Interoperability Working Group
  • Data Infrastructure Proteomic database, data
    management and analysis tools
  • Web Portal Central information source for
    reagents, data, and validated protein targets

5
Proteomic Catalog www.proteomicsresource.org
6
Protein and Reagent Information
7
Data Specific Links with Related Resources
Find proteins in the colonization pathway
containing epitopes known to illicit immune
responses
8
Data Exchange with Related Resources
NIAID BRC (Bioinformatics Resource Center)
9
Integrative Analysis Homologous Virulence
Factors
Currently 99 Proteins from 3 Organisms Related to
Colonization Pathway
  • Results Include Orthologous and Paralogous
    Proteins
  • 19 from an MS/MS study of the Salmonella
    typhimurium proteome under various growth
    conditions by Pacific Northwest National
    Laboratories.
  • 10 from Microarray Studies of the Bacillus
    anthracis Life Cycle by University of Michigan.
  • 9 from Clones of the Bacillus anthracis Proteome
    by Harvard Institute of Proteomics. (7 overlap
    with microarray study).
  • 68 from Clones of Vibrio cholerae Proteome by
    Harvard Institute of Proteomics.

10
Integrative Analysis Host-Pathogen Interaction
  • 15 proteins detected in mouse macrophages
  • Infected with 2 different bacteria (Salmonella
    typhimurium, Bacillus anthracis)
  • From 2 different experiments Using 2 different
    methods (MS/MS, Microarray)
  • In 2 different labs (PNNL, U Michigan)

Mouse macrophage data forthcoming Brucella
abortus MS/MS data from Caprion
11
Scientific Coordination Integration
  • Scientific coordination and integration
  • Coordination within NIAID Biodefense Proteomic
    Research Program NIAID, PRCs, AC, IWG, SWG
  • Integrated deliverables data
    methods/protocols/reagents/technologies
  • Integration with other NIAID Biodefense Programs
    Bioinformatics Resource Centers (BRCs), IEDB
    (Immune Epitope Database), PFGRC (Pathogen
    Functional Genomics Resource Center), BEI
    (Biodefense and Emerging Infectious Research
    Resources Repository)
  • Integration with other proteomic resources and
    well-curated databases/major public repositories
    (e.g., UniProtKB)
  • Enabling scientific understanding and target
    discovery
  • More than sum of individual components
  • Proteomics and beyond (Genomics, Transcriptomics,
    Proteomics, Interactomics, Metabolomics,
    Structural Genomics)

12
Acknowledgements
  • PIR Georgetown University
  • Cathy Wu
  • Peter McGarvey
  • Hongzhan Huang
  • Raja Mazumder
  • Jian Zhang
  • Yongxing Chen
  • Virginia Bioinformatics Institute
  • Bruno Sobral
  • Chengdong Zhang
  • Stephen Cammer
  • Rebecca Will
  • Social Scientific Systems
  • Margaret Moore
  • Margie Odle
  • Nathalie Fike
  • Shiquan Hu
  • Siyu Li
  • Terry Brennan
  • National Institute of Allergy Infectious
    Diseases (NIAID/NIH)
  • Kimberly JoJo Stemple
  • Joseph Breen
  • Malu Polanski

Supported by National Institutes of Allergy and
Infectious Disease NIH Contract
HHSN266200400061C
13
Proteomic Informatics Challenges
  • Data Management
  • Large volume of data and Heterogeneous data from
    disparate sources
  • Data update consistency and integrity
  • Data Standards
  • Capturing common metadata for data integration
  • Common standards for data exchange and
    dissemination
  • ID mapping a problem
  • Data Integration and Analysis
  • Quantitative comparisons between labs, data types
    and methods
  • Functional interpretation in the context of
    pathways and protein networks
  • Utilization by the broad biomedical community for
    hypothesis generation and testing
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