Use case discussion: SP 1.5b: Histone code case- semantic data integration

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Use case discussionSP 1.5b Histone code case-
semantic data integration

• Z. Zhao

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Outline

• About the use case
• Challenges
• Agenda

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Histone code case- semantic data integration

• Scenario
• Integrate the genome distribution of histone
  H3K4Me3 and transcription factor binding through
  knowledge models and using a workflow.
• The histone distribution data is obtained from
  ChIP-chip data from the ENCODE project,
  available from the UCSC genome browser.
• Transcription factor binding positions are also
  available from UCSC.

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Analysis

• Process
• Browse data
• Obtain data
• Update data repository
• Browse knowledge
• Annotate knowledge description of histone data
  and transcription factors
• Update knowledge repository
• Integrate histone data and transcription
  factors, using a knowledge model

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A diagram vision
Histone data process
Semantic Integration
Browse
Select
Browse
Annotate
Update
Update
Search
Histone data
Annotated Histone data
Annotated histone data
ChIP-chip data repository
Ontology on histone data
Histone data repository
Match
Browse
Select
Browse
Annotate
Update
Update
Bind
Transcription factor
Annotated transcription factor
Annotated transcription data
Ontology on transcription data
Binded data
Transcription repository
Binded data repository
Transcription data process
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Challenges

• Decompose the processes and wrap them as web/grid
  services

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Agenda

• Validate the process/data decomposition (1 week)
• Define workflows (1 week)
• Implement the services (24 weeks)
• Using the results from the R test case