This presentation is for informational purposes only and may not be incorporated into a contract or agreement.

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1 This presentation is for informational purposes only and may not be incorporated into a contract or agreement.

2 Oracle10g RDF Data Mgmt: In Life Sciences Xavier Lopez Director, Server Technologies Oracle USA, Inc. This presentation is for informational purposes only and may not be incorporated into a contract or agreement.

3 RDF Graphs to Model Systems Life Sciences, Ontologies, Social Networks

4 Applications in Life Sciences

5 BioDASH Demo Source:

6 BioDASH Demo Source:

7 Integrated Bioinformatics Data Source: Siderean Software

8 Seamark Navigator Source: Siderean Software

9 Teranode Source: Teranode

10 Protégé

11 Semantic Web Characteristics 100 s to 1000 s of users Terabytes to Petabytes of unstructured data Rapid evolution of RDF/OWL models Multi-data types (graphs, spatial, images, text) 24x7 systems Address transactional data inputs Overcome isolated systems design Flexibly address future application requirements Decision making based on all available data

12 Why Add Advanced RDF services to Oracle Database? Enable Integrated Operational Systems Support complex workflows (updates,metadata extraction, ontology management, semantic reasoning) Manage huge volumes of data RDF: Billions of Nodes/Links; millions of graphs Apply database benefits to fundamental data management challenges; no scalability boundaries Parallel loading, query, indexing Large graph partitioning Common user management, administration, security

13 Semantic Web Interoperability Challenges Specialty RDF Data Stores Data isolation High systems admin and management costs Scalability problems High training costs Complex support problems RDF/OWL data tightly coupled to specific application Information not aligned with overall business processes RDF/OWL Triples Semantic Data Server Semantic Apps Business Data Enterprise Data Server Business Apps

14 Oracle10g Value Proposition Secure Semantic Data Management Single source of truth for semantic and business information SOA Mediation Services Unparalleled security model and certifications Ontology Engineering ETL Integrated semantic and business queries Leverage proven of RDBMS capabilities Concept Mapping Inferencing Engines Ontology Search

15 RDF Support in Oracle10g R2

16 Oracle 10g RDF Approach: Provide an open and generic RDF data model and analysis platform for semantic applications. Extended existing Oracle10g network data model (NDM) to support RDF object types RDF Data Model with (user-defined) rules to support RDFS inferencing Perform SQL-based access to triples and inferred data Support for user-defined rules, rule bases, rule indexes Combined SQL query of business and RDF graphs Support large graphs (millions & billion of triples) Easily extensible by 3 rd party tools/apps

17 RDF Statements RDF specifies simple descriptions of resources Subject ->Property-> Object triples pers05 Author-of ISBN... Objects are web-resources (URIs) Subject is again an Object: triples can be linked pers05 Author-of ISBN... MIT Author-of ISBN... Publishby Publishby

18 RDF Model :John age 16 Family: (:John :brotherof :Mary) (:John :age 16 ^^xsd:integer) (:Mary :parentof :Matt) (:John :name John ) (:Mary :name Mary ) Reification: (:John :thinks _:S1) (_:S1 rdf:subject :Sue) (_:S1 rdf:predicate :livesin) (_:S1 rdf:object NYC ) claims :Sue brotherof :Mary :Matt parentof livesin NYC

19 RDF Object Type in 10g R2 Two new RDF object types SDO_RDF_TRIPLE SDO_RDF_TRIPLE_S Several constructors and member functions RDF Data Types (URIs, Blank Nodes, Plain, Typed and Long Litterals, Collections Types) Multiple representations of values Reification

20 W3C RDF-Schema Data Model

21 RDFS Inferencing Support Employing symmetry and transitivity characteristics of properties to infer new relationships RDF Statements + RDFS rules Syntax for specifying user-defined rules Enabled by RDFS Example of User defined rules: If John is parentof Suzie And Suzie is parentof Cathy Then John is grandparentof Cathy

22 RDF Query Support SQL-level access to RDF data SPARQL like syntax (W3C) support Extend SQL using Extensibility Framework RDF_MATCH table function Graph pattern specification in query Benefits Leverage powerful constructs of SQL to process RDF Query results Combine with SQL queries without staging

23 Embedding RDF Query in SQL SELECT FROM, TABLE ( RDF Query (expressed as RDF_MATCH Table Function invocation) ) t, WHERE ; Use of RDF_MATCH Table Function allows embedding a graph query in a SQL query

24 RDF Querying Approach New language approach Create new (declarative, SQL-like) languages e.g., RQL, SeRQL, TRIPLE, Versa, SPARQL, RDQL, RDFQL, SquishQL SQL-based approach Introduces a SQL table function SDO_RDF_MATCH that accepts RDF queries

25 SDO_RDF_MATCH Table Func Input Parameters SDO_RDF_MATCH ( Query, graph-pattern (with variables) Models, set of RDF models Rulebases, set of rulebases (e.g., RDFS) Aliases, aliases for namespaces Filter additional selection criteria ) Return type in definition is AnyDataSet Actual return type is determined at compile time based on the arguments for each specific invocation

26 Additional RDF Features Full support for RDF statements and RDF schema Perform SQL search and retrieval of RDF models using graph patterns Search RDF model containing origin of data (provenance) using graph pattern Reification of assertions (statements) Subsumption: Support for subclassof and subpropertyof Syntax for specifying user defined rules Inferencing of RDF schema

27 Additional Platform Features Clustered database servers Partitioning: Oracle table partitioning in support of very large graphs Parallelism: Oracle parallelism to support load, index and query of very large graph models Data Loading: Import and export data in triple formats (e.g. N-triple) using Oracle s SQL Loader utility Versioning Text Search Support for unstructured data types (e.g. XML, spatial, images, georaster imagery, audio, video, text) XML tools (XDB, XQuery) Middleware: Integrated with germane Oracle App Server (BPEL, XSLT, UDDI, portal Oracle Security

28 Performance Metrics Batch Loading 1 million triples loaded in 35 minutes Querying 80M triples RDF_MATCH based query performance is scalable with retrieval cost per result row almost the same as dataset size changes WordNet (0.5M triples) Sub-second query response UniProt (80M triples) Query Results Range: seconds See 2005 VLDP Paper

29 Large-Scale RDF Data: UniProt UniProt 10M, 20M, 40M, 80M triples 6 example queries given with UniProt Number of matches remain constant as dataset size changes (ROWNUM) See VLDB paper results at:

30 UniProt Sample Queries Description Pattern Projection Result limit Q1: Display the ranges of transmembrane regions Q2: List proteins with publications by authors with matching names Q3: Count the number of times a publication by a specific author is cited Q4: List resources that are related to proteins annotated with a specific keyword Q5: List genes associated with human diseases Q6: List recently modified entries 6 triples 5 vars 5 triples 5 vars 1 LIKE pred. 3 triples 2 vars 3 triples 2 vars 7 triples 5 vars 2 triples 2 vars 1 range pred. 3 vars rows 3 vars 10 rows 0 vars 32 rows 1 var 3000 rows 3 vars 750 rows 2 vars 8000 rows

31 Query Response Times RDF_MATCH Performance Scalability Q1 Q2 Q3 Q4 Q5 Q6 10 M Triples 0.86 < 0.01 < M Triples 0.95 < 0.01 < M Triples 0.96 < 0.01 < M Triples 1.03 < 0.01 < Maximum

32 Scalability RDF is Grid-enabled 32 and 64 bit processing Database clustering (RAC) Multiple concurrent read/write sessions Multiple OS and Hardware Platform Support Solaris, Linux, Unix, Windows Back-up & recovery, fail over

33 RDF/OWL Model Security The creator of the application table corresponding to a model can grant privileges to other users To perform DML to a model, a user must have DML privileges for the corresponding application table The creator of a model can grant SELECT privileges on the corresponding database view to other users A user can query only those models for which s/he has SELECT privileges (via corresponding DB views) Only the creator of a model can drop the model Row-level (triple) security planned for future release

34 Rulebase Security Creator of a rulebase can grant privileges on the corresponding database view to other users Performing DML operations requires invoker to have appropriate privileges on the database view Only the creator of a rulebase can drop the rulebase

35 XML Docs Spatial Data Raster Data RDF/OWL/Rule Base Semantic Technology Stack Web-based Enterprise Integrated Query & Visualization Semantic tools Reasoning Engine Mediation Engines TextMetadata Extraction Application Server Rules Engine Semantic Search SQL/Java/XML Semantic Search BPEL Semantic ETL Tools Annotation & Visualization Ontology Construction & Mapping SQL/Java/XML

36 Some Oracle10g RDF Partners Cerebra Siderean Teranode Top Quadrant Stanford University, Protege

37 Why Use Oracle for RDF Mgmt? Improved semantic data management Easier integration with core business data Scales from department to enterprise; from Internet to web services Open programming standards, Java, SQL, XML,.NET XQuery, and emerging W3C standards (SPARQL) All platforms supported: Linux, Unix, Windows Internet enabled architecture for Web delivery Multi-vendor tools support

38 More Information Semantic Technologies Product Manager: Life Sciences Product Manager: