Infrastructure for dynamic knowledge integration - Automated biomedical ontology extension using textual resources

We present a novel ontology integration technique that explicitly takes the dynamics and data-intensiveness of e-health and biomedicine application domains into account. Changing and growing knowledge, possibly contained in unstructured natural language resources, is handled by application of cutting-edge Semantic Web technologies. In particular, semi-automatic integration of ontology learning results into a manually developed ontology is employed. This integration bases on automatic negotiation of agreed alignments, inconsistency resolution and natural language generation methods. Their novel combination alleviates the end-user effort in the incorporation of new knowledge to large extent. This allows for efficient application in many practical use cases, as we show in the paper.

[1]  R GruberThomas.  Toward principles for the design of ontologies used for knowledge sharing , 1995 .

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

[3]  Michel C. A. Klein,et al.  Ontology Evolution: Not the Same as Schema Evolution , 2004, Knowledge and Information Systems.

[4]  Siegfried Handschuh,et al.  D2.3.8v2 Report and Prototype of Dynamics in the Ontology Lifecycle , 2006 .

[5]  S. Misbah Deen,et al.  Dynamic ontology integration in a multi-agent environment , 2006, 20th International Conference on Advanced Information Networking and Applications - Volume 1 (AINA'06).

[6]  Steffen Staab,et al.  Learning Ontologies for the Semantic Web , 2001 .

[7]  Vladimir I. Levenshtein,et al.  Binary codes capable of correcting deletions, insertions, and reversals , 1965 .

[8]  Trevor J. M. Bench-Capon,et al.  Argumentation over ontology correspondences in MAS , 2007, AAMAS '07.

[9]  Jérôme Euzenat,et al.  Reaching Agreement over Ontology Alignments , 2006, International Semantic Web Conference.

[10]  A MusenMark,et al.  The PROMPT suite , 2003 .

[11]  Jeff Z. Pan,et al.  Inconsistencies, Negations and Changes in Ontologies , 2006, AAAI.

[12]  Olivier Corby,et al.  Building and using a medical ontology for knowledge management and cooperative work in a health care network , 2006, Comput. Biol. Medicine.

[13]  Michael Wooldridge,et al.  Introducing Autonomic Behaviour in Semantic Web Agents , 2005, International Semantic Web Conference.

[14]  Ian Horrocks,et al.  OWL Web Ontology Language Reference-W3C Recommen-dation , 2004 .

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

[16]  Asunción Gómez-Pérez,et al.  METHONTOLOGY: From Ontological Art Towards Ontological Engineering , 1997, AAAI 1997.

[17]  H. Sofia Pinto,et al.  A methodology for ontology integration , 2001, K-CAP '01.

[18]  Kalina Bontcheva,et al.  User-friendly ontology authoring using a controlled language , 2006, LREC.

[19]  Steffen Staab,et al.  OntoEdit: Collaborative Ontology Development for the Semantic Web , 2002, SEMWEB.

[20]  Ljiljana Stojanovic,et al.  Methods and tools for ontology evolution , 2004 .

[21]  Jérôme Euzenat,et al.  An API for Ontology Alignment , 2004, SEMWEB.

[22]  Yorick Wilks,et al.  User-Centred Ontology Learning for Knowledge Management , 2002, NLDB.

[23]  James A. Hendler,et al.  Dynamic Ontologies on the Web , 2000, AAAI/IAAI.

[24]  Tudor Groza,et al.  SemVersion: RDF-based ontology versioning system , 2006 .

[25]  Peter Haase,et al.  Eu-ist Integrated Project (ip) Ist-2003-506826 Sekt D3.1.1.b State-of-the-art on Ontology Evolution Sekt Consortium , 2004 .

[26]  Steffen Staab,et al.  Tackling the Ontology Acquisition Bottleneck: An Experiment in Ontology Re-Engineering , 2003 .

[27]  Volker Haarslev,et al.  A Hybrid Approach for Ontology Integration , 2005 .

[28]  Nicola Guarino,et al.  Formal ontology, conceptual analysis and knowledge representation , 1995, Int. J. Hum. Comput. Stud..

[29]  Steffen Staab,et al.  International Handbooks on Information Systems , 2013 .

[30]  Dan Brickley,et al.  Rdf vocabulary description language 1.0 : Rdf schema , 2004 .

[31]  Johanna Völker,et al.  Ontology Learning and Reasoning - Dealing with Uncertainty and Inconsistency , 2005, ISWC-URSW.

[32]  L. Stein,et al.  OWL Web Ontology Language - Reference , 2004 .

[33]  Johanna Völker,et al.  A Framework for Ontology Learning and Data-driven Change Discovery , 2005 .

[34]  Steffen Staab,et al.  Handbook on Ontologies (International Handbooks on Information Systems) , 2004 .

[35]  Steffen Staab,et al.  On How to Perform a Gold Standard Based Evaluation of Ontology Learning , 2006, SEMWEB.

[36]  Mariano Fernández-López,et al.  Ontological Engineering , 2003, Encyclopedia of Database Systems.

[37]  Kalina Bontcheva,et al.  RoundTrip Ontology Authoring , 2008, SEMWEB.

[38]  Asunción Gómez-Pérez,et al.  Ontology's Crossed Life Cycles , 2000, EKAW.

[39]  Diego Calvanese,et al.  A Framework for Ontology Integration , 2001, The Emerging Semantic Web.

[40]  Jérôme Euzenat,et al.  Ontology Alignment with OLA , 2004, EON.

[41]  Asunción Gómez-Pérez,et al.  The ODESeW 2.0 semantic web application framework , 2006, WWW '06.

[42]  Henrik Eriksson,et al.  The evolution of Protégé: an environment for knowledge-based systems development , 2003, Int. J. Hum. Comput. Stud..

[43]  Diego Calvanese,et al.  The Description Logic Handbook: Theory, Implementation, and Applications , 2003, Description Logic Handbook.

[44]  Steffen Staab,et al.  Ontology Learning , 2004, Encyclopedia of Machine Learning and Data Mining.