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

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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

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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

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S*QL Plugin for Cytoscape

SPARQL and SQL access to resources on the web

Linked data visualization and analysis tools

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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)

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Query over the Web

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Biopax Pathways

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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

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S*QL Interface

Data Source Navigation

Query Edit Area

Connection Parameters

Destination Merge Operations

Destination Network

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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