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Whypothesis
Yen Low edited this page May 2, 2014
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- Yen Low
- Adrien Coulet
https://www.dropbox.com/s/8gr91nqlukmmt5u/nobpresentation.pptx
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Given a hypothetical drug-disease association, propose a mechanism using known drug-gene and disease-gene interactions. Simplify and visualize the proposed pathway.
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Based on the proposed pathways, suggest new drug-disease associations as potential new indications for drugs.
- Interrogate bio2rdf for drug-gene and disease-gene associations.
- 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.
- Visualize the drug-gene(s)-disease pathways using www.relfinder.com (requires a sparql endpoint as input)
- Infer disease (e.g. new indication) enriched by the expanded genes associated with drug of interest.
###Summary of Day 1's tasks:
- Extract relevant data sources (CTD, IntAct).
- Ensure common identifiers are used (MeSH DOID for drugs, disease; GeneID -> UniProtID)
###Summary of Day 2's tasks
- Extract the data relevant for 2 use cases
- Create a sparql endpoint of collated data http://s2.semanticscience.org:12090/sparql
- Visualize paths between drug-disease with www.relfinder.com