Reconciliation of Dynamic Medical Knowledge Organizing Systems (DynaMO)

Context

Information systems exploiting semantic technologies are numerous nowadays. The medical and biomedical domains do not escape this revolution. Actually, institutions like hospitals or biobanks which make available biospecimen for researchers requires such technologies to associate biospecimen with digital data in order to make the semantic of the data explicit to promote data sharing and data exchange. However, medical and biomedical domains are highly dynamic and the knowledge of these domains are constantly evolving over time. In consequence, models for representing this knowledge like ontologies, thesauri, terminologies or more generally speaking knowledge organizing systems (KOS) that are the heart of information systems need to smoothly follow as faithfully as possible the evolution of the underlying domain otherwise, information systems will not be exploitable anymore.

Moreover, by virtue of the size of the medical domain several knowledge organizing systems are necessary to obtain the largest coverage possible. This is why mappings between the existing termino-ontological resources are defined. However, evolution of one of the knowledge organizing systems can impact directly on existing mappings therefore, new techniques and tools are required to ensure consistency between the aligned knowledge organizing systems. This maintenance of mappings must take into account all specificities of the underlying domain as well as the structure and format of the involved knowledge organizing systems.

Research Issues

In this context, the DynaMO project aims at investigating open research issues dealing with medical knowledge organizing systems evolution. As depicted in the picture below, the following issues will be studied:

  • Understanding the evolution of medical knowledge organizing systems to be able to characterize the various aspects of the evolution process as well as to conceptualize and formalize the identified components of evolution.
  • Understanding the impact of evolution on the dependent artifacts (i.e. mappings, data …) in order to propose a mechanism for maintaining the mappings.

More particularly, the objectives of the project consist in the definition of a formal framework to:

  • Support medical knowledge organizing systems evolution in a consistent way,
  • Support the maintenance of mappings directly impacted by knowledge organizing systems local evolution,
  • Guarantee the consistency of the underlying data and information systems exploiting knowledge organizing systems elements after evolution.

The development of a tool supporting the overall approach is also foreseen.

Duration

May 2011 - May 2015

Contact

For any additional information please contact Cédric Pruski.

Consortium

This project is developed in collaboration with the IASI team of the LRI, CNRS and Paris-Sud 11 University.

The DynaMO project is entirely supported by the National Research Fund, Luxembourg

Publications

J. C. Dos Reis, C. Pruski, M. Da Silveira, C. Reynaud-Delaître, DyKOSMap: A framework for mapping adaptation between biomedical knowledge organization systems, Journal of Biomedical Informatics, 55, 153-173, (doi:10.1016/j.jbi.2015.04.001), 2015

J. C. Dos Reis, D. Dinh, M. Da Silveira, C. Pruski, C. Reynaud-Delaître, Recognizing lexical and semantic change patterns in evolving life science ontologies to inform mapping adaptation, Artificial Intelligence in Medicine, 63(3), 153-170, (DOI: http://dx.doi.org/10.1016/j.artmed.2014.11.002), 2015

J. C. Dos Reis, C. Pruski, C. Reynaud-Delaître, Heuristiques pour l'adaptation des mappings entre ontologies dynamiques, 15th Conference on Knowledge Extraction and Management (EGC), Luxembourg, 2015 (PDF)

J. C. Dos Reis, C. Pruski, C. Reynaud-Delaître, State-of-the-art on mapping maintenance and challenges towards a fully automatic approach, Expert Systems with Applications, 42(3), 1465-1478, (DOI: 10.1016/j.eswa.2014.08.047), 2015

D. Dinh, J.C. Dos Reis, C. Pruski, M. Da Silveira, C. Reynaud-Delaître, On the identification of Conceptual Information for Supporting Mapping Maintenance under Evolving Life Science Ontologies, Journal of Web Semantics, (to appear) (DOI: 10.1016/j.websem.2014.05.002)

J.C. Dos Reis, D. Dinh, C. Pruski, M. Da Silveira, C. Reynaud-Delaître, The influence of similarity between concepts in evolving biomedical ontologies for mapping adaptation, European Mediacal Informatics Conference (MIE), 31/08 - 03/09, Istanbul, Turquie, 2014

J.C. Dos Reis, D. Dinh, C. Pruski, M. Da Silveira and C. Reynaud-Delaître, Identifying change patterns of concept attributes in ontology evolution, Proc. of the 11th ESWC, Anissaras, Crete, (Greece), 2014.

J.C. Dos Reis, M. Da Silveira, D. Dinh, C. Pruski, C. Reynaud-Delaître, Requirements for Implementing Mappings Adaptation Systems, Web2Touch 2014 Modelling The Collaborative Web Knowledge, Conference Track@ the 23rd WETICE Conference, June, 23rd-25th, University Campus, Parma, Italy, 2014

J. C. Dos Reis, C. Pruski, M. Da Silveira, C. Reynaud-Delaître, Understanding semantic mapping evolution by observing changes in biomedical ontologies, Journal of Biomedical Informatics, 47, 71-82, 2014.

J.C. Dos Reis, C. Pruski, M. Da Silveira, C. Reynaud-Delaître, Characterizing Semantic Mappings Adaptation via Biomedical KOS Evolution: A Case Study Investigating SNOMED CT and ICD, AMIA 2013 Annual Symposium, Washington DC (USA), 2013

J.C. Dos Reis, D. Dinh, C. Pruski, M. Da Silveira, C. Reynaud-Delaître, Mapping Adaptation Actions for the Automatic Reconciliation of Dynamic Ontologies, ACM International Conference on Information and Knowledge Management (CIKM 2013), San Francisco, CA (USA), 2013

D. Dinh, J.C. Dos Reis, M. Da Silveira, C. Pruski, C. Reynaud-Delaître, Identification des informations conceptuelles définissant un alignement entre ontologies médicales, 2e édition du Symposium sur l'Ingénierie de l'Information Médicale (SIIM 2013), Lille (France), 2013 (PDF)

A. Gross, J.C. Dos Reis, M. Hartung, C. Pruski, E. Rahm, Semi-Automatic Adaptation of Mappings between Life Science Ontologies, Proceedings of the Data Integration in the Life Sciences conference (DILS), Montreal (Canada), 2013

J.C. Dos Reis, Maintaining Mappings Valid between Dynamic KOS, PhD Symposium of the 10th Extended Semantic Web Conference (ESWC'13), Montpellier (France), 2013

J.C. Dos Reis, C. Pruski, M. Da Silveira, C. Reynaud-Delaître, Analyzing the Evolution of Semantic Correspondences between SNOMED CT and ICD-9-CM, Med-e-tel, Luxembourg, 2013

J.C. Dos Reis, C. Pruski, M. Da Silveira, C. Reynaud-Delaître, Vers une approche automatique pour la maintenance des mappings entre ressources termino-ontologiques du domaine de la santé. Proceedings of the french workshop on IC pour l'Interopérabilté Sémantique dans les applications en e-Santé, Paris (France), 2012 (PDF)

J. C. Dos Reis, C. Pruski, M. Da Silveira, C. Reynaud-Delaître, Analyzing and Supporting the Mapping Maintenance Problem in Biomedical Knowledge Organization Systems. Proceedings of the Workshop on Semantic Interoperability in Medical Informatics (SIMI2012), Heraklion (Greece), 2012 (PDF)

PhD Thesis

J. C. Dos Reis, Mapping Adaptation between Biomedical Knowledge Organization Systems. PhD Thesis - University of Paris-Sud, October 2014 (PDF)

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