reveald: a user-driven domain-specific interactive search platform for biomedical research
TRANSCRIPT
Enabling Networked Knowledge
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX granatum: <http://chem.deri.ie/granatum/>
PREFIX 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
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.
ReVeaLD: A User-driven Domain specific Interactive
Search Platform for Biomedical ResearchMaulik R. Kamdar*, Dimitris Zeginis, Ali Hasnain, Stefan Decker, Helena F. Deus
Acknowledgements: This work was funded EU FP7 GRANATUM project, ref. FP7-ICT-2009-6-270139 and Science Foundation Ireland Lion 2
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
Methods
Results
Challenges
Concept Map Representation of the DSL Visual Query Builder Interface (Single-Entity & Advanced Search)
Data Browser Interface (Faceted & Lens-based Data Navigation)Domain specific Visualizations (resource-dependent)
Evaluation
SPARQL Query
Motivation
~5 compounds
~300 000
compounds~300 interesting
compounds
~ 10 interesting
compounds
Lite
ratu
re
Virtu
al S
cre
en
ing
Qu
ery
data
ba
ses
Hypothesis
Generation
(Linked) Data
“Are there Drugs with molecular weight
under 400 tested against ‘Colon Cancer’?”
“Do any Publications refer to assays using ‘Aspirin’ as the
primary Drug in treatment of ‘Prostrate Cancer’?
Integrative
Bioinformatics
Domain Specific Language (DSL) Federated Query Engine Graphic Rules
CanCO - a concise semantic model consisting of
only those concepts and properties which are
relevant to the cancer chemoprevention domain
SPARQL
Query
Chebi DrugBank UniProt Others
Life Sciences Linked Open Data
(LSLOD)
Transformed
QueryTransformed
Query
Transformed
Query
Transformed
Query
chebi:Compound void-ext:subClassOf granatum:Molecule
drugbank:Drug void-ext:subClassOf granatum:Molecule
RRule Templates
LSLOD
Catalogue
Cataloguing &
Links Creation
Experimental
Datasets
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.
ReVeaLD – Real-time Visual Explorer and Aggregator of Linked Data (http://reveald.info)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?
Pubchem
Chebi
Uniprot
Assays, which identify potential
Chemopreventive Agents with
a Molecular Weight less than 300,
and which Target Estrogen Receptors