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					PSI Materials Repository:
   Goals and Progress

              Josh LaBaer
  Director, Harvard Institute of Proteomics
           Harvard Medical School
                 Who are we?
       Harvard Institute of Proteomics

• High-throughput methods for biomarker, antigen
  and interaction discovery; cell-based screens;
  other functional assays
• Clone production—ORF cloning for human genes
  and several microorganisms
• Plasmid repository established 2004
  – Currently >80,000 clones
• Plasmid information curated by a PhD level
  scientist prior to import
• Plasmid Information Database (PlasmID)
• Requests daily, distribute world-wide
                How does it work?
                   Receiving Plasmids




                                            Working sample



Arrive as                      Liquid
  DNA                          Culture
            Transformation &              1 or more on-site
             Robotic Colony                archival sample
                  Pick
                                         • Phage-resistant cells
                                         • Sequence Verified
                                         • Barcode labels
                                         • Automation
                    How does it work?
                      Storing Plasmids
                               BioBank Features
                              • Two -80 freezers
                              • Total sample capacity of 160,000
                              • Samples stored in 2D barcode-
                              labeled tubes
                              • BioBank Software integrated with
                              PlasmID




(Thermo, Zmation)
       How does it work?
        Information Handling




PlasmID: http://plasmid.hms.harvard.edu
Organization of Data in PlasmID


           CLONE

    VECTOR       INSERT

                  GENE
     How does it work?
                  Delivery




On-Line Request




                             Automated Retrieval


Timely Delivery
       Overall Goals of the PSI-MR
• Centralized storage & distribution of information and
  samples for the >100,000 plasmids created at PSI sites

• Quality analysis and control at every step
   –   Barcode labels and Information Tracking at All Steps
   –   Single Colony Selection & Use of Phage-Resistant Bacterial Host Strains
   –   End read Sequencing & Analysis
   –   State-of-the-Art Freezer Storage System (BioBank)


• Scientifically Curated plasmid Information in Oracle
  Database (PlasmID)
   – Saves searchable information about all plasmids
   – Linked to PSI Knowledgebase
   – Ordering directly from website


• Develop terms under which plasmids can be distributed
  under minimally restrictive terms
   – Depositors Agreement and Expedited Process MTA
              Early Goals
• Create points of contact
• Collect & curate info on vectors
• Establish Depositor Agreements
• Establish clone submission format
• Transfer of information to PSI-MR
• Update PlasmID to reflect connection to
  PSI
• Transfer of samples to PSI-MR
• Create PSI-MR website
            Current Goals
Create points of contact
Collect & curate info on vectors
Establish Depositor Agreements
• Establish clone submission format
• Transfer of information to PSI-MR
• Transfer of samples to PSI-MR
• Update PlasmID to reflect connection to
  PSI
• Create PSI-MR website
        Depositors Agreement
• Agreement that sets the terms for distributing
  plasmids deposited by the PSI-MR sites
• Why do we need a DA?
  – Gives the Materials Repository permission to
    distribute the property of others
     • Expressly prohibited by MTAs
  – Appropriately assigns responsibility for the safety of
    distribution
     • MTAs do not address these issues
  – Universal set of operating conditions
  – Establishes the MTA that will accompany the clones
Status of Depositors Agreements
Site     Institution               PSI-X    Status
CESG     University of Wisconsin   PSI-2   completed
JCSG     GNF                       PSI-2   completed
MCSG     WUSTL                     PSI-2   completed
NYSGRC   SGX                       PSI-2   completed
BSCG     LBL                       PSI-1   in process
SESGC    UGA                       PSI-1   completed
         UAH                       PSI-1   in process
ATCG3D   DeCODE                    PSI-2   completed
MCSG     University of Toronto     PSI-2   completed
JCSG     TSRI/Scripps              PSI-2   in process
MCSG     ANL                       PSI-2   in process
NYCMPS   Columbia                  PSI-2   in process
NYSGC    Rutgers                   PSI-2   in process
CHTSB    University of Rochester   PSI-2   completed
         UAB                       PSI-1   in process
CSMP     UCSF                      PSI-2   in process
         NYSBC                     PSI-2   completed
ICSFI    LANL                      PSI-2   in process
                  Current Goals
 Create points of contact
 Collect & curate info on vectors
 Establish Depositor Agreements
    • Continue to work with PSI institutions and PIs to get
      the Depositors Agreement Signed
•   Establish clone submission format
•   Transfer of information to PSI-MR
•   Transfer of samples to PSI-MR
•   Update PlasmID to reflect connection to PSI
•   Create PSI-MR website
           Information Processing

                       Data Processing,
                       Data Validation       Import Files (tab-
Custom Database or                                                Import into PlasmID,
                                                delimited)
Tab-Delimited files                                                 Data Validation
                                                Maps (PDF)
 (formatted files)
                                              Sequence (txt)

                        “Dictionary” of
                          Controlled
                          Vocabulary


                                             Import Files (tab-
   Other Formats                                delimited)
(e.g. Plasmid Maps)   Scientific Curation,      Maps (PDF)
                        Data Validation       Sequence (txt)
Updates to Clone Submission Forms
• Excellent suggestions and input from
  many researchers at several PSI sites
• Five key documents
  1.   Submission Checklist
  2.   SitenameVectors
  3.   clone_files_PSI_table details
  4.   Definitions_for_annotating_CDS_sequences
  5.   Submission Timeline
                     Formatting
Column Header   Required?   Description             Example
UniqueCloneID   Y           PSI site internal ID    917.1.71_GO.880
                                                       (from CESG)
Vector          Y           Vector Name (from
                               table provided)
PDBID           N           Provide a PDB if this   1I6C
                               clone resulted in
                               a structure
NTSeq           Y           text string of the      acggcgcgagtgttgtg
                               inserted                …
                               sequence
CDSstart        Y           start of CDS relative   1
                               to insert NT Seq
CDSstop         Y           Stop of CDS relative    300
                               to NT Seq
                              CDS Definitions
“Fusion” Format
Ex. BamHI or AttL1                Ex. SalI or AttL2     Ex. BamHI or AttL1         Ex. SalI or AttL2

                       YFG               His            GFP                  YFG          Flag
  CDS start                        CDS stop               CDS start                 CDS stop




“Closed” Format
  Ex. BamHI or AttL1                Ex. SalI or AttL2   Ex. BamHI or AttL1         Ex. SalI or AttL2

                       YFG                              GFP                  YFG
    CDS start                        CDS stop             CDS start                 CDS stop


                         Ex. BamHI or AttL1                    Ex. SalI or AttL2

                                              YFG              His
                             CDS start                          CDS stop
PSI-MR
                                                            PSI-MR contacts PSI                            PSI-MR re-arrays
            Send PSI site         PSI-MR reviews data                                PSI-MR receives
                                                              site to send their                            samples, inputs
             submission           and communicates                                    samples, inputs
                                                                   samples                                 data into PlasmID
            checklist and         with PSI site about                                    data, and
                                                                                                           and makes clones
              templates           any changes                                       sequences samples.
                                                                                                             available for
                                                                                                                purchase


                              PSI-MR and PSI site work                              PSI-MR works with
                              together to create computer                            PSI site to acquire
                              compatible formatted files                              suitable samples




           PSI site reviews              PSI site
PSI Site




           documents and              compiles data
           emails PSI-MR               and sends to          PSI site prepares
              with any                 PSI-MR for           samples and sends
              questions                  review                to PSI-MR
Timeline




             ≤ 1 week                2-4 weeks                ≤ 1 week                   2-8 weeks            1 week
                                       2 days
                                     1-2 weeks


                  Data Submission                                                  Sample Submission
                  Current Goals
 Create points of contact
 Collect & curate info on vectors
 Establish Depositor Agreements
    • Continue to work with PSI institutions and PIs to get
      the Depositors Agreement Signed
 Establish clone submission format
    • Send these documents to PSI sites
•   Transfer of information to PSI-MR
•   Transfer of samples to PSI-MR
•   Update PlasmID to reflect connection to PSI
•   Create PSI-MR website
   Data and sample import
# imported      # sequenced      # available
   >2000            ~1400            761

   CESG
  NYSGRC
   JCSG
  ATCG3D


           Bottlenecks
           •Format of data
           •Send data BEFORE samples
           •Timeline
                  Current Goals
 Create points of contact
 Collect & curate info on vectors
 Establish Depositor Agreements
    • Continue to work with PSI institutions and PIs to get
      the Depositors Agreement Signed
 Establish clone info deposit format
    • Send these documents to PSI sites
•   Transfer of information to PSI-MR
•   Transfer of samples to PSI-MR
•   Update PlasmID to reflect connection to PSI
•   Create PSI-MR website
       What’s new on PlasmID
• PSI specific searches
  • TargetDB/PepcDB ID
  • Protein expression, solubility, or purification
  • PDB ID
  • PSI site
• Plasmids linked to PSI Structural
  Genomics Knowledgebase by TargetDB ID
• Credit cards now accepted for all plasmid
  purchases
  • PayPal account NOT required
        PlasmID demo
http://plasmid.med.harvard.edu/PLASMID/
                  Current Goals
 Create points of contact
 Collect & curate info on vectors
 Establish Depositor Agreements
    • Continue to work with PSI institutions and PIs to get
      the Depositors Agreement Signed
 Establish clone info deposit format
    • Send these documents to PSI sites
•   Transfer of information to PSI-MR
•   Update PlasmID to reflect connection to PSI
•   Transfer of samples to PSI-MR
•   Create PSI-MR website
          PSI-MR Web Portal

• Has most up to date clone submission
  templates
• Contains information on how to search for
  and purchase plasmids on PlasmID
• Links to PSI-KB and all PSI Modules and Sites
• FAQs about PSI-MR, Depositors Agreements
  and MTAs
     PSI-MR portal demo
http://www.hip.harvard.edu/PSIMR/index.htm
               Future Goals
• Have all depositors agreements signed
• Expedited Process MTA
• Continue to process data and samples from PSI
  sites
• Work with other PSI sites to start the
  submission process
• Vector information updates from all PSI sites
   – Creating an online vector submission module
        Acknowledgements
                     NIH/NIGMS
                       Jean Chin
  Cathy Cormier
Janice Williamson
  Helen Taycher        PSI KB
    Yanhui Hu        Helen Berman
   Dongmei Zuo      Andrei Kouranov
  Andreas Rolfs       Wendy Tao
    Tina Kelley       Raship Shah
   Mike Collins     John Westbrook
  Jason Kramer
   April Pierce
      Li Chan       All PSI Sites
   Dan Schiwek
     Jason Xu         Funding:
 Stephanie Mohr

				
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posted:10/6/2012
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