Molecular Integration and Database Project

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Molecular Integration and Database Project

• Planning and Progress

2
SANBI activities

• User specification development
• MID development
• Immunological
• Sequence diversity
• Clinical
• SOP development
• Laboratory and Clinical data management system
  assessment

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CAPRISA Network
DURBAN CENTRE
SANBI
NHLS
UCT
IRENE
SUN
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CAPRISA Network
Molecular Integration Database Web Site
SANBI
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User specification development

• Extensive interviews with user groups
• Visited by Brazilian HIV/Malaria database group
  from Sao Paulo to share expertise
• 45 page detailed user specification has been
  completed
• Integrated database centric
• Other databases within CAPRISA identified as
• Central database
• Molecular Sequence database
• Immunological database
• Behavioural database
• Virological database
• Integration database

6
MID

• Prototype schema developed
• Applications engineers being interviewed
• Pipeline for applications processing and sample
  tracking developed
• Interfaces submitted for review

7
SOP development

• Data submission
• Collation and QC
• Storage
• Backup
• Processing
• Extraction
• 24 individual SOPs under late development
• http//www.sanbi.ac.za/annette/SOPs

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Lab and Clinical data management tools assessment
(time intensive)

• Laboratory
• Commercial packages have been chosen and have
  undergone initial assessments
• One has been discarded
• Another is under onsite testing and technical
  review
• Clinical
• Irene is managing a review and we will perform
  technical due diligence

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Molecular Integration Database

• Sequence module
• Sequence generation/quality control, analysis
• Immunological data module
• separate laboratory records from onsite system
  from which data is realtime extracted via an ODBC
  layer to MID
• Clinical data module
• separate laboratory records from which is
  realtime extracted via an ODBC layer to MID

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Data pipeline

• Production
• Data production record (local database)
• Laboratory experiment
• Specimen collection
• Pipeline applications (molecular data processing)
• Transmission
• Data transmission record
• Information selected for its utility in
  integration with molecular data
• Visualisation
• Analysis
• Relational database tables
• Mined according to analytical needs

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How will the data be sent to SANBI?

• Each data producing center will submit data via
  local database LIMS or equivalent to an account
  user/password accessible. Where no such system
  exists or is not necessary data will be submitted
  via an internet web system.
• Automated, secure submission will be performed
  via realtime ODBC

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Prototype Database Integration
Lims
LIMS
LIMS
Sequence Analysis
Sequence Production
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http//fusion.sanbi.ac.za/caprisa-dev/mocks/
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