1) ReVeaLD is an interactive search platform that allows biomedical researchers to query linked open data sources using natural language queries or a visual interface. 2) It addresses challenges of accessing heterogeneous biomedical data sources by providing a domain-specific language and query templates to form SPARQL queries for multiple data sources. 3) The system was evaluated on tasks involving formulating queries using the domain-specific language concepts and linked open data catalog, and it was found that familiarity with the domain-specific language concepts and a smaller set of concepts improved query formulation times.

1. ReVeaLD: A User-driven Domain specific Interactive
Search Platform for Biomedical Research
Maulik R. Kamdar*, Dimitris Zeginis, Ali Hasnain, Stefan Decker, Helena F. Deus
*maulik.kamdar@deri.org
Motivation
“Are there Drugs with molecular weight
under 400 tested against ‘Colon Cancer’?”
~300 000
compounds
~300 interesting
compounds
Literature
Query databases
Virtual Screening
~ 10 interesting
compounds
(Linked) Data
Challenges
~5 compounds
 Increasing adoption and usability by the non-technical biomedical researcher.
 Awareness of which datasets contain the required data and their data model.
 Heterogeneous biomedical data sources, too dynamic for data centralization.
 High cognitive entry barrier towards the assembly of SPARQL queries.
 Human-readable, domain-specific representation of query results is required.
 Trade-off between expressivity (SPARQL) and usability (NL-Queries).
 Making the User Experience engaging, while providing quality results.
Integrative
Bioinformatics
Hypothesis
Generation
“Do any Publications refer to assays using ‘Aspirin’ as the
primary Drug in treatment of ‘Prostrate Cancer’?
Methods
SPARQL
Query
CanCO - a concise semantic model consisting of
only those concepts and properties which are
relevant to the cancer chemoprevention domain
R
Experimental
Datasets
Rule Templates
chebi:Compound void-ext:subClassOf granatum:Molecule
drugbank:Drug void-ext:subClassOf granatum:Molecule
Transformed
Query
LSLOD
Catalogue
Cataloguing &
Links Creation
Domain Specific Language (DSL)
SELECT * WHERE {<ResourceURI> ?p ?o}
Results are subjected to a set of Graphic Rules, which
follow the Event-Condition-Action paradigm (ECA)
and provide visual representations using Fresnel
Display Vocabulary.
Event: drugbank:targets_844 drugbank:pdbIdPage
<Structure_File> (single triple – can be multiple)
Condition: pdbIdpage (Predicate) + http (Object)
Action: HTTP GET and invoke Resource Renderer
Resource Renderer: GLMol Molecular Viewer
Transformed
Query
Transformed
Query
Transformed
Query
Chebi
DrugBank
UniProt
Others
Life Sciences Linked Open Data
(LSLOD)
Graphic Rules
Federated Query Engine
Results
Concept Map Representation of the DSL
Evaluation
Visual Query Builder Interface (Single-Entity & Advanced Search)
Assays, which identify potential
Chemopreventive Agents with
a Molecular Weight less than 300,
and which Target Estrogen Receptors
 5 Query formulation tasks - single or multiple
concept selection from DSL or LSLOD Catalogue
 Structured on the Tracking Real-time User
Experience (TRUE) methodology, popularly used
to evaluate user experience in computer games.
SPARQL Query
PREFIX
PREFIX
PREFIX
rdfs: <http://www.w3.org/2000/01/rdf-schema#>
granatum: <http://chem.deri.ie/granatum/>
xsd: <http://www.w3.org/2001/XMLSchema#>
SELECT DISTINCT * WHERE
{
?x0_Assay a granatum:Assay ;
granatum:hasInput ?x1_Target ;
granatum:identify ?x2_ChemopreventiveAgent ;
granatum:outcome_method ?x3_outcome_method .
?x1_Target granatum:title ?x4_title .
?x2_ChemopreventiveAgent
granatum:molecularWeight ?x10_molecularWeight ;
granatum:SMILESnotation ?x9_SMILESnotation ;
granatum:hasFormula ?x7_hasFormula ;
granatum:HBD ?x5_Hydrogen_Bond_Donors ;
granatum:HBA ?x6_Hydrogen_Bond_Acceptors ;
granatum:TPSA ?x8_Topological_Polar_Surface_Area .
FILTER regex(xsd:string(?x4_title), "estrogen receptor", "is")
FILTER ( xsd:double(?x10_molecularWeight) < 300 )
} LIMIT
100
Pubchem
Uniprot
Chebi
ReVeaLD – Real-time Visual Explorer and Aggregator of Linked Data (http://reveald.info)
Domain specific Visualizations (resource-dependent)
Usability Hypotheses Evaluated : Does familiarity of the users with the DSL affect
the time needed to formulate the query (intuitive)?
 Does a constrained DSL (smaller DSL), lead to
less time needed for query formulation?
Data Browser Interface (Faceted & Lens-based Data Navigation)
Acknowledgements: This work was funded EU FP7 GRANATUM project, ref. FP7-ICT-2009-6-270139 and Science Foundation Ireland Lion 2
Enabling Networked Knowledge