ReVeaLD: A User-driven Domain Specific Interactive Search Platform for Biomedical Research

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  • 1. ReVeaLD: A User-driven Domain Specific Interactive Search Platform for Biomedical Research Maulik R. Kamdar, Ali Hasnain, Helena F. Deus Copyright 2011 Digital Enterprise Research Institute. All rights reserved. Enabling Networked Knowledge
  • 2.         Enabling Networked Knowledge
  • 3. “Are there Drugs with molecular weight~300 000 under 400 tested against ‘Colon Cancer’?”compounds ~300 interesting compounds ~ 10 interesting compounds Query databases Virtual Screening ~5 compounds Literature (Linked) Data Hypothesis Generation “Do any Publications refer to assays using ‘Aspirin’ as the primary Drug in treatment of ‘Prostrate Cancer’? Enabling Networked Knowledge
  • 4.  Enabling Networked Knowledge
  • 5.      Enabling Networked Knowledge
  • 6.  Enabling Networked Knowledge
  • 7.  Hasnain et. al., EKAW 2012 Enabling Networked Knowledge
  • 8. CanCO Query Query Logging Saved Queries SPARQL Query Engine ?molec a Granatum:Molecule RDFization Transformation Experimental Chebi:Compound void-ext:subClassOf Granatum:Molecule Datasets Rule Templates DrugBank:Drug void-ext:subClassOf Granatum:Molecule Transformed Transformed Transformed TransformedSocial Collaborative Query Query Query Query Workspace LSLOD Catalogue Chebi DrugBank UniProt Others ?molec a Chebi:Compound Cataloguing & Links Creation ?molec a DrugBank:Drug Life Sciences Linked Open Data (LSLOD) Enabling Networked Knowledge
  • 9.   Availability: http://srvgal78.deri.ie:8080 Enabling Networked Knowledge
  • 10.  Enabling Networked Knowledge
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  • 14. PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>PREFIX granatum: <http://chem.deri.ie/granatum/>PREFIX uniprot: <http://bio2rdf.org/ns/uniprot:>PREFIX dc: <http://purl.org/dc/elements/1.1/>SELECT DISTINCT * WHERE {?x0_Journal_Citation a uniprot:Journal_Citation ; uniprot:pages ?x1_pages ; dc:identifier ?x2_identifier ; uniprot:volume ?x3_volume ; uniprot:date ?x4_date ; uniprot:author ?x5_author ; rdf:void ?x6_void ; granatum:title ?x7_title .FILTER( regex( xsd:string( ?x7_title ), "mouse", "is" ) ) .} Enabling Networked Knowledge
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  • 16.      Enabling Networked Knowledge
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  • 21.    Enabling Networked Knowledge
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