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Yen Low edited this page May 2, 2014 · 4 revisions

Participants

  • Yen Low
  • Adrien Coulet

NCBO Hackathon final pitch

https://www.dropbox.com/s/8gr91nqlukmmt5u/nobpresentation.pptx

Aims

  1. Given a hypothetical drug-disease association, propose a mechanism using known drug-gene and disease-gene interactions. Simplify and visualize the proposed pathway.

  2. Based on the proposed pathways, suggest new drug-disease associations as potential new indications for drugs.

Methods:

  1. Interrogate bio2rdf for drug-gene and disease-gene associations.
  2. Exploit known protein-protein interactions (IntAct) to expand the list of genes associated with drug or disease. This expanded gene list may explain potential mechanism pathways between the drug and disease.
  3. Visualize the drug-gene(s)-disease pathways using www.relfinder.com (requires a sparql endpoint as input)
  4. Infer disease (e.g. new indication) enriched by the expanded genes associated with drug of interest.

###Summary of Day 1's tasks:

  1. Extract relevant data sources (CTD, IntAct).
  2. Ensure common identifiers are used (MeSH DOID for drugs, disease; GeneID -> UniProtID)

###Summary of Day 2's tasks

  1. Extract the data relevant for 2 use cases
  2. Create a sparql endpoint of collated data http://s2.semanticscience.org:12090/sparql
  3. Visualize paths between drug-disease with www.relfinder.com