Progress of Biodefense Proteomic Research Program on SWG Recommendations

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Progress ofBiodefense Proteomic Research
Program onSWG Recommendations
Scientific Working Group (SWG) Meeting at The 4th
Annual Programmatic Meeting Salt Lake City,
Utah May 31, 2007 Cathy H. Wu, Georgetown
University Medical Center Resource Center for
Biodefense Proteomics Research
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SWG-Recommended Action Items

• Define Metrics for Measuring Success
• Initial Ideas of Metrics
• Expectation of NIAID on PRC (Proteomics Research
  Center) /RC (Resource Center) Contracts
• Define Deliverables and Stakeholders/User
  Community
• Deliverables for the User Community
• Initial List of Stakeholders
• Outreach
• Resource Center as Public Face
• Publicize Deliverables of the Program
• Outreach in Meetings

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I. Define Metrics for Measuring Success

• A. Initial Ideas of Metrics
• Papers published by PRCs/RC
• RC Project Catalog tracks papers related to
  submitted data (11 papers)
• Citations of all papers are on the publications
  page (40 papers)
• Publication citations/web links from the user
  community
• Have established reciprocal links with several
  collaborators
• Forthcoming tracking citations/links from user
  community
• Licenses/patents/grants resulted from this
  program
• Partnership with industry and vaccine,
  diagnostics, therapeutics enabled
• To be tracked by NIAID

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• B. Expectations of NIAID on PRC/RC Contracts
• Progress/success as defined in contracts/SOWs
• Timely dissemination PRC-specific submission
  protocols and release plans
• RC tracks and disseminates all deliverables
  (data, reagents, technology)

• Sample data release plan
• Data
• List of proteins (text data)
• List of candidate targets or validated proteins
  (text data)
• Reagents
• Clones to be submitted to BEI
• Antibodies to be submitted to BEI
• Protocols
• Clone production
• Methods for obtaining quantitative global protein
  measurements
• Data release time frame
• (to be produced by contractor and agreed upon by
  the project officer)
• Contractors and/or collaborators must submit
  data, reagents and protocols within 2 months of
  target validation or 6 months of conclusion of
  the study whichever is sooner.

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II. Define Deliverables and Stakeholders

• A. Deliverables for the User Community
• Data, Reagent, Technology
• Master Protein Directory
• About 23,000 proteins from all experimental
  results mass spec (13,000), microarray (6000),
  clone (8500), protein interaction (100),
  structure (5)
• Annotated key proteins as potential targets
  (3000 with comments)
• Master Reagent Directory
• About 12,000 reagents clone (12,000), antibody
  (22), bacterial strain (7), arraychip (1)
• Technology Directory
• Infectious disease surveillance (1), protein
  structural determination (2), visual exploration
  of proteomics data (1)
• SOPs (28) and experimental data sets (27) at
  proteomic data center
• MS peptide data, microarray MIAME data, clone
  sequence
• Forthcoming FTP direct download of all
  experimental data files

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• B. Initial List of Stakeholders
• PRCs and other biodefense programs, e.g.,
  NIAID-funded BRCs (Bioinformatics Resource
  Centers) and RCEs (Regional Centers of
  Excellence)
• Biomedical community, e.g., microbiology,
  proteomics
• Bioinformatics and computational community
• RC (reciprocal) links/data exchange with related
  resources BRCs (ERIC, NMPDR, PATRIC), PlasmID,
  PFGRC, BEI, IEDB
• Data submission to and integration with public
  repositories PDB (protein structure), GenBank
  (DNA sequence), ArrayExpress (microarray),
  UniProt (function annotation)
• Adopt common standards and promote
  Interoperability
• Forthcoming PRIDE (mass spec)

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III. Outreach

• A. Resource Center as Public Face
• Provide resource availability and tracking
• Web portal (http//www.proteomicsresource.org/)
  central information source for reagents, data,
  and protein targets
• Resource tracked by project catalog and
  directories
• Alert system to notify subscribers the
  availability of new data
• Provide data representation and analysis
• Data infrastructure - integrated deliverables
  from 7 PRCs data methods/protocols/reagents/tec
  hnologies
• Value-added annotation and integrated analysis
  tools
• Enabling scientific understanding and target
  discovery more than sum of individual components

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• A. Resource Center as Public Face
• Provide usage/user tracking
• Monthly average in the last six months

Session an estimate of number of
visitors Pageview an estimate of number of pages
viewed Hit an estimate of number of successful
request
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• B. Publicize Deliverables of the Program
• Educate users what are our deliverables and how
  to use them
• Develop use cases/tutorials to show utility of
  the data/resources
• Develop advertising/PR documents
• Newsletters and brochures
• Posters, software demos and meeting exhibits
• Forthcoming web tutorials/use cases
• Develop web of activities (e.g., PRCs linking to
  RC)
• Branding (e.g., one common web page for PRCs)
• All PRC web sites have linked to RC

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• C. Outreach in Meetings
• Invite collaborators to attend the annual program
  meeting
• BRCs, RCEs, BEI, IEDB attending PRC annual
  program meetings
• Invited talks at 2007 BRC and NHLBI proteomics
  annual meetings
• Host pre-symposium and/or booth at related
  conferences
• Presentations/demos e.g., HUPO (proteomics), ASM
  (microbiology and biodefense) , ISMB
  (bioinformatics)
• USHUPO-2007 NIAID Biodefense Workshop
• USHUPO-2008 Biodefense Structure Proteomics
  Workshop

• USHUPO 3rd Annual Conference, Seattle, WA, March
  6, 2007
• Current Challenges and Opportunities in
  Proteomics
• Moderator Joseph Breen, NIAID
• Kimberly Stemple, NIAID - NIAID proteomics and
  related programs addressing challenges and
  opportunities
• Joshua Adkins, PNNL - Towards a proteomics data
  resource for the salmonella and orthopox research
  communities with emphasis on therapeutic targets
• Philip Hanna, U Michigan - Integrated proteomics
  and gene expression analysis of host-pathogen
  interactions
• Cathy Wu, Georgetown U - Integrated proteomic
  bioinformatics Challenges and solutions for
  NIAID biodefense proteomics