Web Semantics: Science, Services and Agents on the World Wide Web

abstract Ontologymappingseekstofindsemanticcorrespondencesbetweensimilarelementsofdifferentontolo-gies. It is a key challenge to achieve semantic interoperability in building the Semantic Web. This paperproposes a new generic and adaptive ontology mapping approach, called the PRIOR+, based on propa-gation theory, information retrieval techniques and artificial intelligence. The approach consists of threemajormodules,i.e.,theIR-basedsimilaritygenerator,theadaptivesimilarityfilterandweightedsimilar-ity aggregator, and the neural network based constraint satisfaction solver. The approach first measuresboth linguistic and structural similarity of ontologies in a vector space model, and then aggregates themusing an adaptive method based on their harmonies, which is defined as an estimator of performanceof similarity. Finally to improve mapping accuracy the interactive activation and competition neuralnetwork is activated, if necessary, to search for a solution that can satisfy ontology constraints. Theexperimental results show that harmony is a good estimator of f-measure; the harmony based adaptiveaggregation outperforms other aggregation methods; neural network approach significantly boosts theperformance in most cases. Our approach is competitive with top-ranked systems on benchmark testsat OAEI campaign 2007, and performs the best on real cases in OAEI benchmark tests.© 2009 Elsevier B.V. All rights reserved.

[1]  Edward A. Fox,et al.  Combination of Multiple Searches , 1993, TREC.

[2]  Ming Mao,et al.  A Profile Propagation and Information Retrieval Based Ontology Mapping Approach , 2007 .

[3]  Heiner Stuckenschmidt,et al.  Results of the Ontology Alignment Evaluation Initiative , 2007 .

[4]  Frank van Harmelen,et al.  Information Sharing on the Semantic Web , 2004, Advanced Information and Knowledge Processing.

[5]  Michael B. Spring,et al.  A Harmony based Adaptive Ontology Mapping Approach , 2008, SWWS.

[6]  Ralph Kimball,et al.  The Data Warehouse ETL Toolkit: Practical Techniques for Extracting, Cleaning, Conforming, and Delivering Data , 2004 .

[7]  David S. Wishart,et al.  DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs , 2010, Nucleic Acids Res..

[8]  Diego Calvanese,et al.  Ontology of Integration and Integration of Ontologies , 2001, Description Logics.

[9]  Terrence S. Furey,et al.  The UCSC Genome Browser Database , 2003, Nucleic Acids Res..

[10]  Erhard Rahm,et al.  COMA - A System for Flexible Combination of Schema Matching Approaches , 2002, VLDB.

[11]  Heiner Stuckenschmidt,et al.  Analyzing Mapping Extraction Approaches , 2007, OM.

[12]  Jie Yao,et al.  Searching online journals for fluorescence microscope images depicting protein subcellular location patterns , 2001, Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001).

[13]  M. Scott Marshall,et al.  Tutorial: Query Federation with SWObjects , 2011 .

[14]  Marcel Worring,et al.  Genre-based search through biomedical images , 2002, Object recognition supported by user interaction for service robots.

[15]  Marc Ehrig,et al.  Ontology Alignment: Bridging the Semantic Gap , 2006 .

[16]  William W. Cohen,et al.  Extracting information from text and images for location proteomics , 2003, BIOKDD.

[17]  Ming Mao,et al.  Ontology Mapping: An Information Retrieval and Interactive Activation Network Based Approach , 2007, ISWC/ASWC.

[18]  Pedro M. Domingos,et al.  Learning to match ontologies on the Semantic Web , 2003, The VLDB Journal.

[19]  Stefan Schlobach,et al.  Deriving Concept Mappings through Instance Mappings , 2008, ASWC.

[20]  Wei Ma,et al.  RxNorm: prescription for electronic drug information exchange , 2005, IT Professional.

[21]  Ryutaro Ichise,et al.  Machine Learning Approach for Ontology Mapping Using Multiple Concept Similarity Measures , 2008, Seventh IEEE/ACIS International Conference on Computer and Information Science (icis 2008).

[22]  Olaf Hartig,et al.  Publishing and Consuming Provenance Metadata on the Web of Linked Data , 2010, IPAW.

[23]  Mark A. Musen,et al.  A System for Ontology-Based Annotation of Biomedical Data , 2008, DILS.

[24]  Daniel P. Huttenlocher,et al.  Efficient Belief Propagation for Early Vision , 2004, Proceedings of the 2004 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2004. CVPR 2004..

[25]  Christian Becker,et al.  Extending SMW+ with a Linked Data Integration Framework , 2010, ISWC Posters&Demos.

[26]  James L. McClelland,et al.  An interactive activation model of context effects in letter perception: I. An account of basic findings. , 1981 .

[27]  David M. Shotton,et al.  OpenFlyData: The Way to Go for Biological Data Integration , 2009, DILS.

[28]  Shih-Fu Chang,et al.  Exploring Text and Image Features to Classify Images in Bioscience Literature , 2006, BioNLP@NAACL-HLT.

[29]  C. J. Date.  SQL and Relational Theory - How to Write Accurate SQL Code, Second Edition , 2012, Theory in practice.

[30]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[31]  Piotr Indyk,et al.  Enhanced hypertext categorization using hyperlinks , 1998, SIGMOD '98.

[32]  Renée J. Miller,et al.  Linking Semistructured Data on the Web , 2011, WebDB.

[33]  Kei-Hoi Cheung,et al.  Linking Open Drug Data , 2009, I-SEMANTICS.

[34]  Mansur R. Kabuka,et al.  ASMOV Results for OAEI 2007 , 2007, OM.

[35]  Egon L. Willighagen,et al.  Linking the Resource Description Framework to cheminformatics and proteochemometrics , 2011, J. Biomed. Semant..

[36]  William W. Cohen,et al.  A Stacked Graphical Model for Associating Sub-Images with Sub-Captions , 2007, Pacific Symposium on Biocomputing.

[37]  Michael B. Spring,et al.  Ontology Mapping: As a Binary Classification Problem , 2008, 2008 Fourth International Conference on Semantics, Knowledge and Grid.

[38]  Marti A. Hearst,et al.  Exploring the Efficacy of Caption Search for Bioscience Journal Search Interfaces , 2007, BioNLP@ACL.

[39]  Eduard Hovy,et al.  Combining and standardizing large- scale, practical ontologies for machine tranlation and other uses , 1998, LREC.

[40]  Yannis Kalfoglou,et al.  Ontology mapping: the state of the art , 2003, The Knowledge Engineering Review.

[41]  Wendy A. Warr,et al.  ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI) , 2009, J. Comput. Aided Mol. Des..

[42]  Natalya F. Noy,et al.  Semantic integration: a survey of ontology-based approaches , 2004, SGMD.

[43]  Frank van Harmelen,et al.  Exploring large document repositories with RDF technology: the DOPE project , 2004, IEEE Intelligent Systems.

[44]  Robert Stevens,et al.  Developing a kidney and urinary pathway knowledge base , 2011, J. Biomed. Semant..

[45]  Marek Hatala,et al.  Ontology mappings to improve learning resource search , 2006, Br. J. Educ. Technol..

[46]  Jens Lehmann,et al.  DBpedia - A crystallization point for the Web of Data , 2009, J. Web Semant..

[47]  Erhard Rahm,et al.  Similarity flooding: a versatile graph matching algorithm and its application to schema matching , 2002, Proceedings 18th International Conference on Data Engineering.

[48]  Holger Knublauch,et al.  The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications , 2004, SEMWEB.

[49]  Vipul Kashyap,et al.  The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench , 2010 .

[50]  Carole A. Goble,et al.  BioCatalogue: a universal catalogue of web services for the life sciences , 2010, Nucleic Acids Res..

[51]  P. Cochat,et al.  Et al , 2008, Archives de pediatrie : organe officiel de la Societe francaise de pediatrie.

[52]  Eric P. Xing,et al.  Structured correspondence topic models for mining captioned figures in biological literature , 2009, KDD.

[53]  Mark A. Musen,et al.  The PROMPT suite: interactive tools for ontology merging and mapping , 2003, Int. J. Hum. Comput. Stud..

[54]  Peishen Qi,et al.  Ontology Translation on the Semantic Web , 2003, OTM.

[55]  Edward P. K. Tsang,et al.  Foundations of constraint satisfaction , 1993, Computation in cognitive science.

[56]  Stefanos D. Kollias,et al.  A String Metric for Ontology Alignment , 2005, SEMWEB.

[57]  Gio Wiederhold,et al.  Mediators in the architecture of future information systems , 1992, Computer.

[58]  Andrew McCallum,et al.  Toward Optimal Active Learning through Sampling Estimation of Error Reduction , 2001, ICML.

[59]  Kate Byrne.  Having Triplets – Holding Cultural Data as RDF , 2008 .

[60]  Ralph Kimball,et al.  The Data Warehouse Toolkit: The Complete Guide to Dimensional Modeling , 1996 .

[61]  Steffen Staab,et al.  QOM - Quick Ontology Mapping , 2004, GI Jahrestagung.

[62]  Marc Ehrig.  Ontology Alignment: Bridging the Semantic Gap (Semantic Web and Beyond) , 2006 .

[63]  Lluís Padró,et al.  A Hybrid Environment for Syntax-Semantic Tagging , 1998, ArXiv.

[64]  Dieter Fensel,et al.  Ontologies: A silver bullet for knowledge management and electronic commerce , 2002 .

[65]  Hagit Shatkay,et al.  Integrating image data into biomedical text categorization , 2006, ISMB.

[66]  James A. Hendler,et al.  The Semantic Web" in Scientific American , 2001 .

[67]  Robert F. Murphy,et al.  EXTRACTING AND STRUCTURING SUBCELLULAR LOCATION INFORMATION FROM ON-LINE JOURNAL ARTICLES: THE SUBCELLULAR LOCATION IMAGE FINDER , 2004 .

[68]  William W. Cohen,et al.  High-recall protein entity recognition using a dictionary , 2005, ISMB.

[69]  Baowen Xu,et al.  LILY: the Results for the Ontology Alignment Contest OAEI 2007 , 2007, OM.

[70]  David S. Wishart,et al.  DrugBank: a comprehensive resource for in silico drug discovery and exploration , 2005, Nucleic Acids Res..

[71]  William W. Cohen,et al.  Understanding captions in biomedical publications , 2003, KDD '03.

[72]  Steven W. Zucker,et al.  On the Foundations of Relaxation Labeling Processes , 1983, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[73]  Yuzhong Qu,et al.  Constructing virtual documents for ontology matching , 2006, WWW '06.

[74]  Ross Wilkinson,et al.  Using the cosine measure in a neural network for document retrieval , 1991, SIGIR '91.

[75]  Natalya F. Noy,et al.  BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse , 2009 .

[76]  Michel Dumontier,et al.  Integrating findings of traditional medicine with modern pharmaceutical research: the potential role of linked open data , 2010, Chinese medicine.

[77]  Ming Mao,et al.  Integrating the IAC neural network in ontology mapping , 2008, WWW.

[78]  Nicole Tourigny,et al.  Bio2RDF: Towards a mashup to build bioinformatics knowledge systems , 2008, J. Biomed. Informatics.

[79]  Heiner Stuckenschmidt,et al.  Results of the Ontology Alignment Evaluation Initiative 2007 , 2006, OM.

[80]  Marc Ehrig,et al.  State of the art on ontology alignment , 2013 .

[81]  Ming Mao,et al.  Neural Network based Constraint Satisfaction in Ontology Mapping , 2008, AAAI.