SemSorGrid4Env FP7-223913 Deliverable D4.2v1 ...

SemSorGrid4Env FP7-223913

Deliverable D4.2v1 Implementation and Deployment of the Ontology-based Data Integration Service – Phase 1 Jean-Paul Calbimonte and Oscar Corcho Universidad Politécnica de Madrid

December 18, 2009

Status: Final Scheduled Delivery Date: December 31, 2009

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Executive Summary The realisation of the Semantic Web vision, where data is available understandable and processable by computers, has launched several initiatives that aim at providing semantic access to traditional data sources. In recent years streaming data sources have become increasingly available thanks to advances in ubiquitous data capturing technologies such as sensor networks. The required transparent integration of heterogeneous sources of this kind has brought new challenges to the research community. In the context of the SemSorGrid4Env project and its Work Package 4 (WP4), we propose the design, implementation and deployment of a Semantic Integration Service for streaming and stored data sources. The design of this service follows an ontology-based approach that extends previous works on data access for relational databases. This deliverable focuses on a core component of the semantic Integrator: the Ontology-based streaming data access module. To the best of our knowledge there is still no bridging solution that allows connecting ontologybased mappings and streaming data access technologies coherently in order to answer to the requirements of i) establishing mappings between ontological models and streaming data source schemas, and ii) accessing streaming data sources through queries over ontology models. In summary our approach consists in creating an Ontology-based Streaming Data Access service that can receive requests over an ontological view and transforms them into queries for acquisitional or event-based stream sources or stored sources. The results of these queries can be integrated following a query plan and returned as RDF triples in terms of the global ontology. This module, named StreamMapster, extends the ODEMapster [BG06] engine that provided ontology-based access for databases, and uses the language for Stream-to-ontology mappings S2O [CC09]. An implementation of the proposed solution is presented, so that we can provide some evidence of the applicability of our approach. This first deliverable of the implementation will be completed and presented as part of the entire integration solution in future releases. This first initiative is expected to constitute the basis for future efforts related to data integration, linked streaming data and distributed processing of continuous queries.

D4.2v1 Implementation and Deployment of the Ontology-based Data Integration Service – Phase 1

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Note on Sources and Original Contributions The SemSorGrid4Env consortium is an inter-disciplinary team, and in order to make deliverables self-contained and comprehensible to all partners, some deliverables thus necessarily include state-of-the-art surveys and associated critical assessment. Where there is no advantage to recreating such materials from first principles, partners follow standard scientific practice and occasionally make use of their own pre-existing intellectual property in such sections. In the interests of transparency, we here identify the main sources of such pre-existing materials in this deliverable: •

Chapter 1 contains material adapted from [CC09]


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Document Information Contract Number Full title Project URL Document URL

EU Project officer Deliverable Task Work package Date of delivery Code name Nature Distribution Type Authoring Partner QA Partner Contact Person

FP7-223913 Acronym SemSorGrid4Env SemSorGrid4Env: Semantic Sensor Grids for Rapid Application Development for Environmental Management www.semsorgrid4env.eu http://www.semsorgrid4env.eu/home.jsp?content=/sew/viewTerm&content=instance.jsp&_sew _var_name=instance&_sew_instance=D4.2+v1&_sew_instance_set=SemSorGrid4Env&_origin =%2Fhome.jsp Antonios Barbas Number D4.2 Name Implementation and Deployment of the Ontology-based Data v1 Integration Service Number T4.2 Name Implementation and Deployment of the Ontology-based Data Integration Service Number WP4 Contractual 31 December Actual 31 December 2009 2009 D4.2 v1 Status draft final ; Prototype Report ; Specification Tool Other Public ; Restricted Consortium UPM UNIMAN Jean-Paul Calbimonte Email

Abstract (for dissemination)

jpcalbimonte@delici Phone +34913363670 Fax +34913524819 as.dia.fi.upm.es Thanks to the increasingly available ubiquitous data capturing technologies such as sensor networks, new requirements for streaming data access solutions have surfaced. One of these is the integration of heterogeneous streaming data sources. In the context of the SemSorGrid4env project and its Work Package 4 (WP4), we propose the design, implementation and deployment of a Semantic Integration Service for streaming and stored data sources. The design of this service follows an ontology-based approach that extends previous works on data access for relational databases. This deliverable focuses on a core component of the semantic Integrator: the Ontology-based streaming data access module.

This module, named StreamMapster, extends the ODEMpaster engine that provided ontologybased access for databases, and uses the language for Stream-to-ontology mappings S2O. An implementation of the proposed solution is presented, so that we can provide some evidence of the applicability of our approach. This first deliverable of the implementation will be completed and presented as part of the entire integration solution in future releases. This first initiative is expected to constitute the basis for future efforts related to data integration, linked streaming data and distributed processing of continuous queries.

Keywords Data Integration. Semantic integration Version log/Date Change 0.1 / 01 December 2009 Initial Draft 0.2 / 14 December 2009 Revised text 0.3 / 15 December 2009 Comments from QA 0.4 / 18 December 2009 Revised text

Author J.-P. Calbimonte J.-P. Calbimonte J.-P. Calbimonte & O. Corcho J.-P. Calbimonte


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Project Information This document is part of a research project funded by the IST Programme of the Commission of the European Communities as project number FP7-223913. The Beneficiaries in this project are: Partner Universidad Politécnica de Madrid

Acronym UPM

(Coordinator)

Contact Prof. Dr. Asunción Gómez-Pérez Facultad de Informática Departamento de Inteligencia Artificial Campus de Montegancedo, sn Boadilla del Monte 28660 Spain #@ [email protected] #t +34-91 336-7439, #f +34-91 352-4819

The University of Manchester

UNIMAN

Prof. Carole Goble Department of Computer Science The University of Manchester Oxford Road Manchester, M13 9PL, United Kingdom #@ [email protected] #t +44-161-275 61 95, #f +44-161-275 62 04

National and Kapodistrian University of

NKUA

Athens

Prof. Manolis Koubarakis University Campus, Ilissia Athina GR-15784 Greece #@ [email protected] #t +30 210 7275213, #f +30 210 7275214

University of Southampton

SOTON

Prof. David De Roure University Road Southampton SO17 1BJ United Kingdom #@ [email protected] #t +44 23 80592418, #f +44 23 80595499

Deimos Space, S.L.U.

DMS

Mr. Agustín Izquierdo Ronda de Poniente 19, Edif. Fiteni VI, P 2, 2º Tres Cantos, Madrid – 28760 Spain #@[email protected] #t +34-91-8063450, #f +34-91-806-34-51

EMU Limited

EMU

Dr. Bruce Tomlinson Mill Court, The Sawmills, Durley number 1 Southampton, SO32 2EJ – United Kingdom #@ [email protected] #t +44 1489 860050, #f +44 1489 860051

TechIdeas Asesores Tecnológicos, S.L.

TI

Mr. Jesús E. Gabaldón C/ Marie Curie 8-14 08042 Barcelona, Spain #@ [email protected] #t +34.93.291.77.27, #f ++34.93.291.76.00


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Table of Contents

1

2

Introduction ............................................................................................................................. 1 1.1

System Objectives ............................................................................................................ 1

1.2

System Description .......................................................................................................... 2

1.2.1

Relationship to SemSorGrid4Env Architecture ........................................................ 2

1.2.2

The StreamMapster Processor .................................................................................. 3

Source Code............................................................................................................................. 4 2.1

StreamMapster ................................................................................................................. 4

2.1.1

Dependencies ............................................................................................................ 5

3

Input Files ................................................................................................................................ 6

4

Installation and Execution ....................................................................................................... 9

5

4.1

Build ................................................................................................................................. 9

4.2

Configuration ................................................................................................................... 9

4.3

Execution........................................................................................................................ 10

Bibliography .......................................................................................................................... 12


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Index of Figures Figure 1.1: Semantic Integrator service .......................................................................................... 2


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Glossary C‐SPARQL Continuous SPARQL IRI Internationalized Resource Identifier. DQP Distributed Query Processor. DSMS Data Stream Management System. OWL The Web Ontology Language. A W3C standard for specifying ontologies. R2O Relational-to-Ontology mapping language. RDBMS Relational Database Management System. RDF The Resource Description Framework. A W3C standard for modeling Web resources metadata. S2O Stream-to-Ontology mapping language. SNEE Sensor Network Engine. A query compiler for the SNEEql language. SNEEql Sensor Network Evaluation Query Language for querying streams of data. SPARQL SPARQL Protocol and RDF Query Language for querying RDF documents. SPARQLSTR Extended C-SPARQL language SQL Structured Query Language for querying relational databases. UNIMAN University of Manchester. UPM Universidad Politécnica de Madrid. URI Uniform Resource Identifier. WP Work Package. XML Extensible Markup Language


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1 Introduction One of the SemSorGrid4Env 1 Work Package 4 (WP4) objectives is to design and implement a Semantic Integration Service for the SemSorGrid4Env project [CCG09]. This deliverable focuses on the implementation of a prototype of the Ontology-based streaming data access component of the Semantic Integration Service. This document is organised as follows: In Chapter 1, we set the context of this work package, by introducing the prototype objectives and description (see Section 1.2 and Section Error! Reference source not found. respectively). In Chapter 2, we describe the source code and its dependencies. Chapter 3 provides details about the test input given to the prototype. Finally in Chapter 4, we indicate how to install, configure and run the prototype.

1.1 System Objectives The main objectives of the presented prototype are to: •

Provide a first implementation of the StreamMapster query translator, using the new S2O extended version of the R2O [BCG05] mapping language, capable of transforming queries in terms of an ontology into SNEEql [BGF+08, GGF+09a] queries.

•

Implement the required streaming extensions to SPARQL[PS08] (SPARQLSTR ) 2 support for the StreamMapster engine, as a replacement of ODEMQL[Bar06].

•

Provide a first implementation of basic time window support for streaming queries in StreamMapster.

•

Implement a first integration with the out-of-network version of the SNEE system [GGF+09b], for ontology-based streaming data access.

1

Semantic Sensor Grids for Rapid Application Development for Environmental Management, http://www.semsorgrid4env.eu.

2

Extensions of the C-SPARQL[BGJ08] language, as described in [CC09].


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1.2 System Description 1.2.1 Relationship to SemSorGrid4Env Architecture As it is explained in the SemSorGrid4Env architecture document [GGF+09], the Semantic Integrator is one of the core middleware components of the system and is designed to implement the Integration and Query Interfaces. The Integration interface allows consumers to specify which sources they want to integrate as a single virtual source, using a mapping definition. The Query Interface allows queries over this integrated view, using a declarative query in terms of a global ontology [GGF+09, CCG09]. In Figure 1.1 we show the components of the Semantic Integrator. The prototype presented in this document corresponds to the Query canonisation component displayed in the figure. This component is in charge of receiving a SPARQLSTR query [CC09] qr over an ontological view, and using a S2O [CC09] mapping document generates a SNEEql [BGF+08] query Qc that is sent to a distributed query processing engine that ultimately interacts with the data source (e.g. a sensor network). The distributed query processing engine will make use of the SemSorGrid4Env data services infrastructure to obtain the data from the sources.

Figure 1.1: Semantic Integrator service


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This first stage of the implementation and deployment of the Semantic Integrator is labelled as Phase 1. Subsequent phases will include the rest of the components depicted in the figure.

1.2.2 The StreamMapster Processor The StreamMapster query translator is an extension of the ODEMapster processor. It consists of the following compoents: • •

• • • •

SPARQLSTR parser. Parses incoming queries written in SPARQLSTR (see [CC09] for details) and transforms into an abstract syntax tree. It is based on the ARQ 3 extensions for the Streaming SPARQL language [BGJ08]. Query rewriter: Generates a conjunctive query based on the incoming parsed SPARQLSTR query. Query rewriting algorithms for this task include [CDL+05, PHM09]. For phase 1 the query rewriting algorithm is does not take into account the ontology taxonomy to add new atoms to the resulting conjunctive query. S2O reader. Reads the S2O mapping document. Query translator: Using the S2O document transforms the conjunctive query into a query over the sources specified by the S2O mapping. Query serializer: produces a string query according to a specific implementation, in this case the only implementation is for the SNEEql language. Streaming data adapter. Launches a query against a streaming data system, in this case the out-of-network SNEE version, and receives the incoming tagged tuples.

For sample queries and mapping definitions see Section 3.

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http://jena.sourceforge.net/ARQ/


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2 Source Code The source code of the StreamMapster ontology-based streaming data access component was delivered and is available in the project source code repository.

2.1 StreamMapster This component was implemented as an extension to the ODEMapster [BG06] processor, capable of providing ontology-based data access to relational databases. It was implemented in Java in the es.upm.fi.dia.oeg.* package. The SPARQLSTR parser is implemented based on the ARQ SPARQL parser, and the additions made for Streaming SPARQL [BGJ08]. The StreamMapster processor basically reads a SPARQLSTR query, and using a S2O file produces a SNEEql query string. It is possible to execute this query with the out-of-network SNEE engine, by changing a configuration parameter. In this case the query results are retrieved by StreamMapster. The following folder directory structure shows the StreamMapster source code organisation: • • • •

src: Source code (java files) are placed in this folder. lib: Java library dependencies (jar files) are included in this folder. bin: Compiled java files are placed in this folder. input: Input files (S2O document, queries) are placed in this folder.

When executing the SNEEql queries with the out-of-network SNEE processor [GGF+09a], the following folders are also needed: • • •

var: Required working directory. ext: Stream schemas are stored here. output: Query compiler and other output files are placed here.


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2.1.1 Dependencies The StreamMapster component depends on the following Java libraries, included in the lib directory: • • • • • • • • • • • • • • • • •

snee.jar streamschema.jar jena.jar arq-jena-sparql.jar cayenne.jar commons-digester.jar icu4j_3_4.jar iri.jar jakarta-regexp-1.3.jar jep-2.3.1.jar junit-4.5.jar log4j-1.2.12.jar lucene-core-2.3.1.jar slf4j-api-1.5.6.jar slf4j-log4j12-1.5.6.jar xercesImpl.jar antlr-2.7.5.jar

Notice that the out-of-network SNEE engine has a dependency on Haskell. Please refer to [GGF+09b] for details.


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3 Input Files The StreamMapster requires a S2O mapping file that is specified through a configuration parameter. The queries to be translated are also specified through configuration (See Section 4.2). The sample S2O file used for this prototype defines streams like the following (the presented examples are simplifications of the XML original definitions): Streamschema‐desc name="sensor" has‐stream name="windsamples" keycol‐desc name="ts" timestamp‐desc name="ts" nonkeycol‐desc name="speed" nonkeycol‐desc name="temperature" nonkeycol‐desc name="direction"

The keycol‐desc and timestamp‐desc fields are not used for the moment. They are meant to specify the stream key fields and timestamp field respectively. It defines the following kinds of mappings: • • •

Class definition mappings Datatype property mappings Object property mappings

The following definition shows how to specify a Class mapping. The virtualStream indicates the IRI that can be used in a SPARQLSTR query to specify a stream. Windows can be applied to this stream. conceptmap‐def name="http://ssg4env.eu#WindSpeedMeasurement" virtualStream="http:/ssg4env/mes.srdf" uri‐as operation oper‐id="concat" has‐value http://www.ssg4env.eu#WindSpeedMeasurement has‐column windsamples.id has‐value _ has‐column windsamples.ts


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Datatype property mapping definitions can be specified as follows: attributemap‐def name="http://ssg4env.eu#hasSpeed" selector aftertransform operation oper‐id="constant" arg‐restriction on‐param="const‐val" has‐column windsamples.speed

Object property mapping definitions can be specified as follows: dbrelationmap‐def name="http://ssg4env.eu#isProducedBy" toConcept="http://ssg4env.eu#Sensor" joins‐via condition oper‐id="equals" arg‐restriction on‐param="value1" has‐column sensors.sensorid arg‐restriction on‐param="value2" has‐column windsamples.id

The sample input queries features include: • • • •

Variable binding queries. Streams and window specification. Simple Filter operations over variables Simple graph matching (type matching, object and datatype property matching)

Here is a sample SPARQLSTR query: PREFIX fire: PREFIX rdf: SELECT ?speed ?direction ?sid ?name FROM STREAM [RANGE NOW ‐ 10 HOUR STEP 1 MINUTE] WHERE { ?WindSpeed a fire:WindSpeedMeasurement; fire:hasSpeed ?speed; fire:isProducedBy ?Sensor. ?WindDirection a fire:WindDirectionMeasurement; fire:hasDirection ?direction. ?Sensor a fire:Sensor; fire:hasName ?name; fire:hasSensorid ?sid.


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FILTER ( ?speed > 4 ) FILTER ( ?speed 4 and windsamples.speed < 10 and windsamples.direction = 3;


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4 Installation and Execution In this chapter we describe how to compile, configure and run StreamMapster.

4.1 Build The StreamMapster package is a compressed zip file that includes the folders described in Section 2.1. This file must be unpackaged and placed in some working folder. In the directory root, a build.xml file can be found. This is an Ant 4 build file that can be used to build and execute StreamMapster. Ant can be downloaded freely from its web page. In order to build the project, you must execute Ant in the StreamMapster root directory: >ant

In the build.xml file, the default build target is “build”, and will generate the executable .class files for the source code in the bin directory.

4.2 Configuration All input parameters are configured in a properties file in the input directory: props.conf. The following parameters are the most important ones for the StreamMapster execution: • • •

r2o.file.path: The full file path of the S2O file. r2o.sparql.streaming.query.file.path: the full path of the SPARQLSTR query. r2o.model.execute: true if SNEE is to be invoked, false otherwise.

SNEE configuration files and parameters specification can be found in [GGF+09b].

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4.3 Execution To execute StreamMapster execute the MapsterConnector target of the build.xml file using Ant: >ant MapsterConnector

If the r2o.model.execute parameter is set to true, then the SNEE engine will be invoked and the produced SNEEql query executed. StreamMapster will display the results using the SPARQL Query Results XML Format 5 : 2 9 1260648604734 ...

The tick variable has been artificially added only to display the data timestamp retrieved from SNEE. If SNEE is not invoked, then the SNEEql query is displayed in the output: SELECT windsamples.speed, sensors.sensorname, sensors.sensorid, windsamples.direction

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FROM sensors,windsamples[FROM NOW - 10 HOUR TO NOW - 0 HOUR ] WHERE sensors.sensorid = windsamples.id and windsamples.speed > 4 and windsamples.speed < 10 and windsamples.direction = 3;


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5 Bibliography [Bar06]

Jesús Barrasa. Modelo para la definición automática de correspondencias semánticas entre ontologías y modelos relacionales. PhD Thesis. Departamento de Inteligencia Artificial. Facultad de Informática. UPM. December 2006.

[BBC+09]

Davide Francesco Barbieri, Daniele Braga, Stefano Ceri, Emanuele Della Valle, Michael Grossniklaus. C-SPARQL: SPARQL for Continuous Querying. In Proceedings of the 18th international conference on World wide web, pages 10611062, 2009.

[BCG05]

Jesús Barrasa, Óscar Corcho, Asunción Gómez-Pérez. R2O, an Extensible and Semantically Based Database-to-ontology Mapping Language. In: Bussler, C., Tannen, V., Fundulaki, I. (eds.) SWDB 2004 LNCS, vol. 3372, 2005. Springer.

[BG06]

Jesús Barrasa, Asunción Gómez-Pérez. Upgrading Relational Legacy Data to the Semantic Web. In Proceedings of the 15th international conference on World Wide Web, pages 1069 – 1070, 2006.

[BGF+08]

Christian Y.A. Brenninkmeijer, Ixent Galpin,Alvaro A.A. Fernandes, and Norman W. Paton A Semantics for a Query Language over Sensors, Streams and Relations. In Proceedings of the 25th British national conference on Databases: Sharing Data, Information and Knowledge, pages 87 – 99, Cardiff, Wales, UK. 2008. Springer-Verlag.

[BGJ08]

Andre Bolles, Marco Grawunder and Jonas Jacobi. Streaming SPARQL Extending SPARQL to process data streams. The Semantic Web: Research and Applications, pages 448-462, 2008.

[CCG09]

Jean-Paul Calbimonte, Oscar Corcho and Alasdair J G Gray. Design of the SemSorGrid4Env ontology-based data integration model. Deliverable. D4.1, SemSorGrid4Env, August 2009.

[CC09]

Jean-Paul Calbimonte and Oscar Corcho. Enabling Ontology-based Access to Streaming Data Sources. Technical Report. Ontology Engineering Group, Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid. December 2009.

[CDL+05]

Diego Calvanese, Giuseppe De Giacomo, Domenico Lembo, Maurizio Lenzerini, Riccardo Rosati. DL-Lite: Tractable description logics for ontologies. In:


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Proceedings of the Twentieth National Conference on Artificial Intelligence (AAAI 2005), pages 602-607. 2005. [GBJ+08]

Ixent Galpin, Christian Y.A. Brenninkmeijer, Farhana Jabeen, Alvaro A.A. Fernandes, Norman W. Paton. An Architecture for Query Optimization in Sensor Networks. In Proceedings of the 2008 IEEE 24th International Conference on Data Engineering, pages 1439-1441, Cancún, México, April 2008. IEEE.

[GBJ+09]

Ixent Galpin, Christian Y.A. Brenninkmeijer, Farhana Jabeen, Alvaro A.A. Fernandes, and Norman W. Paton Comprehensive Optimization of Declarative Sensor Network Queries. In Proceedings of the 21st International Conference on Scientific and Statistical Database Management, pages 339 – 360, New Orleans, LA, USA, June 2009. Springer.

[GGF+09]

Alasdair J. G. Gray, Ixent Galpin, Alvaro A. A. Fernandes, Norman W. Paton, Kevin Page, Jason Sadler, Manolis Koubarakis, Kostis Kyzirakos, Jean-Paul Calbimonte, Oscar Corcho, Raúl Garcia, Víctor Manuel Díaz, and Israel Liebana. SemSorGrid4Env architecture phase I. Deliverable. D1.3v1, SemSorGrid4Env, August 2009.

[GGF+09a]

Ixent Galpin, Alasdair J G Gray, Alvaro A A Fernandes, Norman W. Paton, Alexis Kotsifakos, Dimitris Kotsakos, and Dimitrios Gunopulos. Data Requirements, Data Management and Analysis Issues, and Query-Based Functionalities. Deliverable D2.1, SemSorGrid4Env, August 2009.

[GGF+09b]

Alasdair J G Gray, Ixent Galpin, Alvaro A A Fernandes, Norman W. Paton, Alexis Kotsifakos, Dimitris Kotsakos, and Dimitrios Gunopulos. Implementation and Deployment of Data Management and Analysis and the Query Processing Components – Phase 1. Deliverable D2.2v1. SemSorGrid4Env, December 2009.

[GGFP09]

Alasdair J. G. Gray, Ixent Galpin, Alvaro A. A. Fernandes, and Norman W. Paton. Web services data access and integration - the data stream realisation (WSDAIStreaming) specification. Technical report, University of Manchester, August 2009.

[PHM09]

Hector Pérez-Urbina, Ian Horrocks and Boris Motik. Efficient query answering form OWL 2. In Proceedings of the 8th International Semantic Web Conference 2009, pages 489-504, October 2009.

[PS08]

Eric Prud'hommeaux and Andy Seaborne (eds). SPARQL query language for RDF. Recommendation, W3C, 15 January 2008. http://www.w3.org/TR/rdfsparql-query/.


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