Access and Analyze Graphs in Oracle Spatial Network Data

Model using Cytoscape

Susie StephensPrincipal Product Manager, Life Sciences

Oracle

susie.stephens@oracle.com

OutlineNetwork Data Model OverviewCase StudiesNDM / Cytoscape Demo

OutlineNetwork Data Model OverviewCase StudiesNDM / Cytoscape Demo

Network ConceptA network is a graph representation for modeling objects of interest and their relationships. It contains the following elements:

Nodes: objects of interestsLinks: relationship between nodesPaths: ordered list of connected links

S1

X2

X1k1· X0

k2 · S1

k3 · S1

X0

Network Data Model OverviewData model for managing graph (link-node) structuresSupports variety of network structures (hierarchical, directed, undirected, random, scale-free)Framework for applying network constraints and rules (e.g. path length, cost, minimum bounding rectangle)

Graph Analysis FunctionsPathway ConnectivityShortest Path/All PathsTracing (Accessibility)Within DistanceNearest Neighbor Minimum Bounding Rectangle Minimum Cost Spanning TreeAbove Analysis With Constraints (Depth, Cost, Distance)

Network SchemaNetwork Metadata

– Name, Type, Node/Link/Path Table InformationNetwork Tables

– Node TableNode_ID, Node_Type, Geometry,…

– Link Table Link_ID, Link_Type, Start_Node_ID, End_Node_ID, Cost, Geometry, …

– Path Table (Path-Link Table)Path_ID, Start_Node_ID, End_Node_ID, Cost, Geometry, Path Links,…

Application Information is added to network schema– Add additional columns in node, link, and path tables directly– Add foreign key(s) to node, link, and path tables

NDM APIs PL/SQL Package: (server-side)

– Network data query and management in Oracle10g– Maintains referential integrity and validation– Supports link/node/path updates

Java API: (mid-tier or client side)– Network loading/storage– Network analysis– Network Creation/Editing

Java Functional Extensibility– Network, Node, Link, Path are Java Interfaces– Application-based network analysis extensions

Visualization ToolsBundled Java visualizer & APIs for 3rd party tools, application development

Cytoscape Oracle Tom Sawyer

OutlineNetwork Data Model OverviewCase StudiesNDM / Cytoscape Demo

Case Study: Metabolic Pathway ModelingIdentify reaction paths between two given chemical compounds

1. ModelingDirected NetworkChemical Compounds as NodesEnzymes as LinksReaction Paths as Paths

2. AnalysisShortest Path AnalysisAll Path Analysis

Pathway Data Definition in NDM

NODE_ID NODE_NAME ACT COSTS SAMPLE_ID ENTRY_ID ----------------------------------------------------------------------------------------------------------------------------------

1 C00022 Y 1 Pyruvate 492 C00122 Y 1 Fumarate 503 C00036 Y 1 Oxaloacetate 514 C05379 Y 1 Oxalosuccinate 525 C00074 Y 1 Phosphoenolpyruvate 536 C00024 Y 1 Acetyl-CoA 547 C00149 Y 1 (S)-Malate 558 C00311 Y 1 Isocitrate 569 C00417 Y 1 cis-Aconitate 5710 C00042 Y 1 Succinate 58

LINK_ID LINK_NAME START_NODE_ID END_NODE_ID ACT COST SAMPLE_ID-------------------------------------------------------------------------------------------------------------------------------------------------1 1.1.1.42 (rn:R00268) 4 19 Y 1 isocitrate dehydrogenase (NADP)2 1.1.1.42 (rn:R00268) 19 4 Y 1 isocitrate dehydrogenase (NADP)3 1.1.1.42 (rn:R00268) 4 20 Y 1 isocitrate dehydrogenase (NADP)4 1.1.1.42 (rn:R00268) 20 4 Y 1 isocitrate dehydrogenase (NADP)5 4.1.1.49 (rn:R00341) 3 19 Y 1 phosphoenolpyruvate carboxykinase (ATP)6 4.1.1.49 (rn:R00341) 3 5 Y 1 phosphoenolpyruvate carboxykinase (ATP)7 1.1.1.37 (rn:R00342) 3 7 Y 1 malate dehydrogenase8 6.4.1.1 (rn:R00344) 1 3 Y 1 pyruvate carboxylase

Node table

Link table

Source: Susumu Goto, Kyoto University

Shortest Path Analysis

Source: Susumu Goto, Kyoto University

NDM Reference“We are glad to hear that Oracle are developing the new Network Data

Model specialized for the bioinformatics field. Efficient and effective pathway analysis will be achieved, especially for pathway computation from large amount of protein interaction and reaction data, using graph

algorithms embedded in the model.”

- Professor and Director Minoru Kanehisa, Bioinformatics Center Institute for Chemical Research Kyoto University

Case Study: Protein InteractionsInfer functions of unknown proteins from their relationships with well-known proteins

1. ModellingUndirected NetworkProteins as NodesInteractions as Links

2. AnalysisNo. of Degrees (Neighboring Nodes)Shortest Path AnalysisWithin-Cost Analysis (Nearest Neighbor Analysis)

NDM Reference"Oracle 10g's Network Data Model feature is great for building a

semantic work infrastructure. Oracle 10g's graphical representation is an excellent tool for planning our Y2H protein interaction data storage

needs and for building a signaling network from our Nature-AfCSMolecule Pages Database."

- Joshua Li, Sr. Computational Scientist, San Diego SupercomputerCenter / UCSD

Case Study: Data IntegrationIntegrate native biological databases by creating rules for network routes. Support multiple ontologies and jump in and out of database space for analysis

1. ModelingDirected NetworksClasses as NodesInteractions as Links

2. AnalysisNo. of Degrees (Neighboring Nodes)Shortest Path AnalysisWithin-Cost Analysis (Nearest Neighbor Analysis)

Integration Architecture

NREF EMBL GO KEGG BIND AFCS

Nodes Edges Graph

NDM layer (semantic layer)

NativeFormats

Data type determines available routesRoutes can be determined using semantics

Distributed Database layer

Network Route

NDM ReferenceOracle Database 10g's spatial network data model will assist in

advancing our research and enable us to accelerate the drug discovery and development process. The incredible amount of research data we generate every day places unique challenges on our database. With integrated data manipulation and analytic tools, our scientists can be

more efficient in processing and running computations. "

- Aram Adourian, Ph.D., vice president, Computational Sciences, Beyond Genomics

RDF Data ModelAn RDF data model to store RDF statements, including reification Java Ntriple2NDM converter for loading existing RDF data An RDF_MATCH function which can be used in SQL to find graph patterns in RDF (similar to SPARQL) Will be release as part of Oracle Database 10.2 later this year

OutlineNetwork Data Model OverviewCase StudiesNDM / Cytoscape Demo

SummaryNDM simplifies network management and analysis by providing an open and generic modelNDM provides reliability, performance and securityA number of visualization tools are integrated with NDM

More InformationNDM Whitepaper

– http://www.oracle.com/technology/products/spatial/pdf/10g_network_model_twp.pdf

NDM Paper published in IEEE with LS Case Studies– http://www.oracle.com/technology/industries/life_sciences

/pdf/ls_ieee_graph.pdfNDM presentation for Life Sciences

– http://www.oracle.com/technology/industries/life_sciences/presentations/biopathways704_graph_modeling.pdf

Cytoscape Plugin– http://www.oracle.com/technology/industries/life_sciences

/ls_sample_code.htmlCytoscape

– http://cytoscape.org/

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