HCLSIGUseCases/BiomedicalDataIntegration

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Here’s a set of biomedical data integration we have been working on at Partners. We identified three information queries that might be of interest to biomedical researchers and identified the following scenarios:

  • Current state: The sequence of steps a biomedical researcher would go through today to answer these questions
  • Proposed state (involving Semantic Web Technologies): We have tried to identify where in the current state, SW technology can be applied and what could be the value (steps in red font).

These are at a high level and need more drilling down, so I look to the following feedback: 1. Are the value propositions identified in these use cases feasible? Have I missed any? 1. Any suggestions for “drill down” including examples, queries, databases, etc. would be helpful

The Use Cases are as follows:

What are the SNPs identified in a set of gene expressions. What are the annotations associated with the SNP and the Spot information associated with the gene?
Of those associations between gene expressions and SNP’s that are on the same chromosome (cis), are they preferentially 3’ or 5’?
Can those associations between gene expressions and SNP’s that are on the different chromosome (trans) be explained by known pathways?