OGSA-DAI-RDF &

Its Ontology Interfaces

Isao Kojima and Masahiro KimotoData Grid Team,

Grid Technology Research Centerhttp://www.dbgrid.org/

http://www.gtrc.aist.go.jp/

AIST（↓） ,Japan

RDF, Ontologies and Meta-Data Workshop at Uk e-Science Centre8th June, 2006

Summary 　　 Implementation of OGSA-DAI RDFOGSA-DAI RDF Prototype Web(Grid) Service based access to RDF databases

– Supports RDFRDF database type to OGSA-DAI database middleware

– RDF handling ActivitiesActivities including SPARQLSPARQL query processing

• Supports Jena and Sesame• Supports RDFS/OWL

– OntologyOntology Interfaces implementation • Based on the Ontogrid’s WS-DAIO initial(old) Proposal Specs

– Schema & Instance Handling Interfaces– Supports Jena– Supports RDFS/OWL

– Current Status and Future Directions

Approach• OGSA-based: Web Service InterfacesOGSA-based: Web Service Interfaces

– Use of Globus Toolkit/WS-RF– Can be combined with other Grid tools (GRAM,MDS,

…..)

• Query Language (SPARQL)Query Language (SPARQL)– W3C Standard Query Language for RDF– Multi-Platform approach

• To support Jena, Sesame,,,,,,, (Oracle?)

• OGSA-DAI:– Activity Framework

• To combine RDF databases other data resources – XMLDBs, Relational DBs(and Files)

• To achieve RDF database workflow programming– DataConversion, Data Transfer,( Web Services)

OGSA-DAI• OGSA-DAI: http://www.ogsadai.org.uk/

– UK e-Science R&D project for grid DB middleware

• Service-based Database Query and Integration– RDB:SQL (Oracle,PostgreSQL,MySQL,DB2,,,)– XML-DB: XPath and XQuery (Xindice,eXist,,,)– Integration tool OGSA-DQP for RDBs

• Supports Grid Middleware– WS-RF(Globus Toolkit 4)– WS-I(OMII)

OGSA-DAI-RDF

Not available for some version

OGSA-DAI Activities: Set of Primitives for Data ProcessingRelational, XML, File Transfer, Data Conversion/Compression

RDF Activities

OGSA-DAI-RDF: Set of RDF Processing ActivitiesOGSA-DAI-RDF: Set of RDF Processing Activities

Implemented Activities (Platform Independent = All activity supports Jena and Sesame)

1. SPARQL QueryStatement 　 Activity– W3C Standard SPARQL for Jena/Sesame

2. RDF Resource(triple)Management Activity– Create/Delete RDF triples,statements

3. RDF Collection(model)Management Activity– Create/Delete/List RDF databases(model,repository)

4. RDF BulkLoad 　 Activity– Bulk loading functions of RDF triples– To achieve common Interface Pattern with Relational, XML-DBs.

5. Ontology Interfaces (based on the Ontogrid’s WS-DAIO initial(old) specs)

- Schema level Activity - Instance level Activity

Query (SPARQL)&

Instance Level(Without ontology)

Appoach

OGSA-DAI-RDF demo(1): Multi-Platform EnvironmentSPARQL GUI Query Interface for Jena/Sesame

– Modified OGSA-DAI DataBrowser OGSA-DAI

Data Service(WS-RF and WS-I)

Sesame

Jena

SPARQL Statement

Result is SPARQL/XML

Format

OGSA-DAI Activity Framework• RDF Activities can be combined with other OGSA-DAI Activities

– Data Compression,Conversion and Transfer– Other database Resources (SQL-DB, XML-DB)

• Activity Programming– Support of Workflow Programming– Simple Distributed Processing

Site1:1.SPAQL query result is converted with XLSTransform Activity2. The converted data is send to site2 by deliverTo Activity

Site2:1.Data is received with delverfrom Activity2.Triples are inserted into the temporary model by ResourceManagement Activity3.Anthoer query is done for this temporary model

Demo(2) : Distributed SPARQL Processing ( to show the power of OGSA-DAI Activity Framework)•Parallel & Synchronized Data Processing over 3 different sites can be programmed with this Framework

Currently Supported Platforms• Jena and Sesame

– RDF(S) and OWL for Jena

• Middleware-> Depends on the Underlying Platforms– Operational Semantics– Functional Limitation

• Supported Implementation Type– On DBMS(RDB as default) – On Memory (Jena)– On File (Sesame)

Can be specified OGSA-DAI resource config file

Dai.data.resource.type=RDF

Function Summary Functions Future

WS-DAI-RDF/OntOGSA-DAI-RDF Notes and

ProblemsData RDF and RDFS •RDF, RDFS and OWL A Single Architecture

to cover OWL

Ontology Interface WS-DAI-Ont •Schema Activity•Instance Activity

Must follow current

WS-DAI-RDFOnt specs

Query Language SPARQL SPARQL QueryStatement Activity

Must have some compatibility with W3C SPARQL protocol

Result Set SPARQL XML Result Format

SPARQL

XML Result Format

Updates Supports basic Update Activity

Graph Management Graph(Collection) Management

Activity

Must cope with

OGSA-DAI resource configuration

Bulk Operation BulkLoad Activity

Factory Operations

Implemented Ontology Interface Activities

• SchemaActivity • InstanceActivityAddConcept

RemoveConcept

GetConcept

GetConcepts

HasConcept

AddSubclassOfRelation

RemoveSubclassOfRelation

GetRelatedConcepts

AddIndividual

RemoveIndividual

GetIndividual

GetIndividuals

HasIndividual

AddInstanceOfRelation

RemoveInstanceOfRelation

GetIndividualParents

Basic Ontology Handling Functions

Parent/ChildAncestor/

Descendant,Sibling,,,,

Basic Instance Handling Functions

Add/RemoveGet/Has,,,Individual

This is only a prototype based on the obsolete specs•To find the usefulness of these kind of interfaces•To get the feedbacks for the future ontology interface discussion•To explore the integrated architecture with Query interface and Ontology Interface•To be a candidate for the second GGF reference implementation

PerformDocument　 Example: NCI Cancer Ontology

Access Example of the Ontology <?xml version="1.0" encoding="UTF-8"?><!-- (c) International Business Machines Corporation, 2002 - 2005.--><!-- (c) University of Edinburgh, 2002 - 2005.--><!-- See OGSA-DAI-Licence.txt for licencing information.-->

<perform xmlns="http://ogsadai.org.uk/namespaces/2005/10/types">

<ontologySchemaManagement name="myActivity"> <getRelatedClasses fromData="rdb" className="http://www.mindswap.org/2003cology.owl#Chemotherapy" lineageRelation="ancestor"> <entry>cancerOntology</entry> </getRelatedClasses> <outputStream name="myActivityOutput"/> </ontologySchemaManagement>

</perform>

NCICancer Ontology

Get the ancestor ofThe class

“Chemotherapy”

Import of NCI cancer ontology using the Activity Framework1. Create a Model on RDB using RDF Collection(model)Management Activity2. Get the data from the NCI site using the OGSA-DAI deliverFromActivity3. Uncompress the file using the OGSA-DAI gZip Activity4. Load the data with our RDF BulkLoad Activity

Execution Examples

1. GetClass

2. HasClass

3. GetRelatedClasses(ancestor)

4. areClassesRelated(Parent?)

Planned ApplicationsGrid Database Integration with OntologyGrid Database Integration with Ontology

Clinical/Bioinformatics Integration(with U-Tokyo)

AIST Geogrid Project (based on GEON)

Specifications• Our system aims to cover OWL and RDF(S)

– We think it is very convenient to cover them in a single framework.• First GGF DAIS specs for RDF will target RDF(S)

– WS-DAI-RDF/Ont architecture should have some extensibility/compatibility for future OWL

– Need to Synchronize R&D and the Spec Discussion

• Must have some compatibility with W3C SPARQL Protocol• Security and Authorization: No idea at now

Implementations • Jena:

– Simple wrapping of Jena Ontology API• Sesame:

– Each interface message is converted to the query representation• On top of the current OGSA-DAI-RDF query module

– Our current approach is based on SPARQL, not SeRQL• Aims to be a yet another implementation of WS-DAI-RDF/Ont• Restricted with Sesame SPARQL implementation• Should wait for the future stable releases

Feedbacks and Problems

Current Implementation & Roadmap

• Current Prototype OGSA-DAI-RDF Activities Query Interface=full function with basic updates Ontology interface= basic functions of WS-DAIO

• Demo Server environment is already set-up– If you have OGSA-DAI 2.1 and download the configuration XML, you can acc

ess our demo site using SPARQL– Current config xsds will be downloadble soon.

• June,2006. 1st Release (without ontology) Version 0.9 Ready to be released now.

Re-designing the interface: Possible inconsistency with future releases.Almost no english document

• Sep. 2006 or Nov. 2006 2nd Release Version1.0 with Stable Spec (with ontology interface????)

Future Directions• Distributed & Scalability

– Distributed Query Processing? – Combine with P2P Query Processing?

(presented yesterday by A.Matono)We think the single site performance is already the matter of the DB vendor

s.Multi-site performance and optimization is our concern

• Applications(related topic will be presented today by S.Mirza)

– Resource Discovery & Management– Service Management for the Semantic SOA.– Database Integration (Geosciences, Clinical-bioinformatics)

• Collaboration– DAIS-RDF/Ont Spec Discussions / Ontogrid Project

(F2F will be tomorrow)

– Semantic Web Group within AIST