bbn technologies copyright 2009 slide 1 the s*ql plugin for cytoscape visual analytics on the web of...
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BBN Technologies Copyright 2009 Slide 1
The S*QL Plugin for Cytoscape Visual Analytics on the Web of Linked Data
Rusty (Robert J.) Bobrow
Jeff Berliner, Prakash Manghwani
Eric Neumann – Clinical Semantics Group
rusty@bbn.com (617) 873-3601
BBN Technologies Copyright 2010 Slide 2
Biological Network Inference
•Genomics
•Pathways
•Regulatory Networks
•Anatomy and Tissue
•Diseases
•Therapeutics
Experimental Data
BBN Technologies Copyright 2010 Slide 3
The Need for Visualization
Example
Text-Mined Data Set:•Over 1000 nodes:
• genes, processes and compounds
•~8000 links:inhibit, stimulate, interact
Interactions occurring in hepatocytes and adipocytes -- from text-mining
biological literature
BBN Technologies Copyright 2010 Slide 4
Proposed mechanism-derived gene expression signatures and predictive biomarkers; follow-up experiments.
Proposed mechanism-derived gene expression signatures and predictive biomarkers; follow-up experiments.
Biomarker Identification and Validation
Multiple ConditionWhole GenomeMeasurements
Multiple ConditionWhole GenomeMeasurements
ExpressionAnalysis
ExpressionAnalysis
InteractionPathways
RegulatoryNetworks
InteractionPathways
RegulatoryNetworks
Nucleic Acids Research, 2008, Vol. 36KEGG for linking genomes to lifeand the environment
Integrate and interpret experimental data in the context of diverse sources of background knowledge
Integrate and interpret experimental data in the context of diverse sources of background knowledge
Gene DiseaseRelations
Gene DiseaseRelations
The human disease network www.pnas.orgcgidoi10.1073pnas.0701361104
Unsupervised discovery followed by supervised interpretation
Unsupervised discovery followed by supervised interpretation
BBN Technologies Copyright 2010 Slide 5
Knowledge Exploration & Discovery Framework
Less Structured More Structured
Users
Analysis
Search/Query,Navigation
Search/Query,Navigation Hypothesis &
Reasoning ToolsHypothesis &
Reasoning Tools
DataResources Relational DBs,
Knowledge Bases,…
Spreadsheets,XML Docs, …
Web Pages,Podcasts, …
Documents,Images,Video, …
Data & DistributedOperations Tools
Data & DistributedOperations Tools
Integration
Semantic Web& Complementary
Technologies
Visualization
BBN Kineti-GraphTM
Dynamic Data VisualizationData LensesCytoscape, etc.
Supporting the analytic process:- Visualize multiple data sources- Propose and examine patterns within a single data source- Examine implications of selected patterns across multiple displays, data tables- Export selection with descriptive (semantic) meta-data
BBN Technologies Copyright 2010 Slide 6
S*QL Plugin for Cytoscape
SPARQL and SQL access to resources on the web
Linked data visualization and analysis tools
BBN Technologies Copyright 2010 Slide 7
Cytoscape
Open Source Graph Visualization Tool•Large Community Involvement•Multiple Applications
•Protein interactions•Pathways•Genes and diseases•Social networks
•Plug-in architecture ~80 plugins•Analysis, Network and Attribute I/O, Network Inference, Functional Enrichment, Communication/Scripting• Filters• Graph Analyses (cluster algorithms)
BBN Technologies Copyright 2010 Slide 8
Query over the Web
BBN Technologies Copyright 2010 Slide 9
Biopax Pathways
BBN Technologies Copyright 2010 Slide 10
Demonstration Architecture
Users
Analysis
VisualizationBBN Kineti-GraphTM
Dynamic Data VisualizationCytoscapeNetwork View
Integration
DataResources
SPARQL & SQLQuery
Data Selection
SPARQL & SQLQuery
Data Selection
SPARQL & SQLQuery
Data Access
SPARQL & SQLQuery
Data Access
Drug IndicationsTriple Store
Clinical TrialsTriple Store
Analysis/Display Plugins
BBN Technologies Copyright 2010 Slide 11
S*QL Interface
Data Source Navigation
Query Edit Area
Connection Parameters
Destination Merge Operations
Destination Network
BBN Technologies Copyright 2010 Slide 12
RDF Graph:Alternative Drug Applications
768 Entities1050 Associations
Angela Qu et al, 2008Cincinnati Children’s Hospital Medical Center
Systemic Lupus Erythematosus + Tamoxifen
•Genes •Diseases
•Phenotypes•Mechanisms•Compounds
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