Expression Data Generation and Collection at MPIMG and RZPD

1
Expression Data Generation and Collection at
MPIMG and RZPD

• Resource Center within the
• German Human Genome Project
• Steffen Schulze-Kremer

2
Background History

• 1987
• first spotting system (EMBL,ICRF)
• 1989
• complex cDNA Hybridisations to arrays
• 1989 onward
• distribution of arrays in reference library system

3
RZPD Database Objectives (since 95)

• To support dissemination of variety of biological
  materials
• Clones
• Filters
• Pools
• To collect and redistribute biological primary
  data
• Hybridisations
• Sequences
• Phenotypes

4
RZPD Database Coverage

• Biological Information
• Clones
• Libraries
• Genes
• Sequences
• Hybridisation
• Logistic Information
• Clone storage
• Library re-arraying
• Filters

• Accounting Information
• Customers
• Orders / requests
• Affiliation (DHGP?)
• Price lists
• Information Integration
• Confidential information
• Links to other databases
• Query
• Visualisation

5
RZPD Database Contents (Oct 5/99)

• Biological Information
• 27.582.866 clones
• 17.280.664 master clones
• 319 libraries
• 47.209 filters
• 581.219 sequences
• 24.366 hybridisations
• 352.806 Blast hits
• 187.952 distinct targets hit

• Accounting Information
• 5551 registered users
• 1228 organisations
• 630 German
• 598 foreign
• RZPD orders (in RLDB)
• 15.980 clones (4405)
• 3610 filters (1468)
• 1118 pools (0)
• Submissions
• 38.042 sequences (DHGP)
• 15.589 sequences (other)

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Graphical Filter Display Tool
7
Database Components

• Oracle / Unix
• DEC Alpha 8 Processor Server
• Secure Web Server
• protects confidential information during transit
• different roles available
• customised views
• OPM Tools
• some 80 object classes
• class browser
• query editor

8
OPM Schema Browser
9
Hybridisation Data in RZPD
10
Laboratory Database at MPIMG
11
Dictionaries
12
Owned Objects
13
Result Experiment

• Lab Database Development Team at MPIMG
• Dr. Arif Malik, Axel Nagel, Dr. Holger Eickhoff

14
RZPD Distribution Service, Database
Bioinformatics Team (www.rzpd.de)

• Distribution Service
• Nadja Pohl, Eva Partsch, Patience Frederick,
  Maryam Sabet
• Registration
• Radka Kochan
• System Administration
• Klaus Dobrindt, Robert Fürst
• Data Submission
• Dr. Andreas Hewelt
• Protein Structure Factory
• Dr. Jörn Quedenau, Ursula Meyhoefer

• Database Managers
• Karsten R. Heidtke, Peter Neubert
• Web Designer
• Iris A. Bertram
• Application Programmers
• Elisabeth Maschke, Ralf Mühlhaus
• Students
• Falco Ripsas, Katja Wegner
• Informatics Manager
• Dr. Steffen Schulze-Kremer