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The Chronious Ontology Suite: Methodology and Design Principles

The Chronious Ontology Suite: Methodology and Design Principles. ICBO 2011, Buffalo, July 28-30, 2011. Luc Schneider[1], Mathias Brochhausen[1,2] [1] Institute for Formal Ontology and Medical Information Science, Saarland University, Saarbrücken, Germany

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The Chronious Ontology Suite: Methodology and Design Principles

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  1. The Chronious Ontology Suite: Methodology and Design Principles ICBO 2011, Buffalo, July 28-30, 2011 Luc Schneider[1], Mathias Brochhausen[1,2] [1] Institute for Formal Ontology and Medical Information Science, Saarland University, Saarbrücken, Germany [2] University of Arkansas of Medical Sciences, Little Rock, USA

  2. Contents • Purpose • Technical details • Methodological principles • Design principles • Conclusion 2

  3. 1) Purpose 3

  4. 1) Purpose • CHRONIOUS aims to provide an integrated telemedicine platform to monitor the general health status of chronic disease patients. • For demonstrative purposes CHRONIOUS focuses on COPD and CKD (including Renal Insufficiency). 4

  5. 1) Purpose • The CHRONIOUS Ontology Suite • Part of literature search tool • Used alongside MeSH annotations • Adds clinical experts knowledge • Provides topic-neutral representation (objects, processes, qualities, etc.) 5

  6. 2) Technical details 6

  7. 2) Technical details • Modular structure • MLOCC: 476 classes • COPD: 964 classes • CKD: 972 classes • Development in OWL-DL 7

  8. 2) Technical details • Why OWL-DL? • Ontologies are also intended for other, more reasoning-intensive uses. • Decidability allows for efficient consistency checking. 8

  9. 3) Methodological principles • Realism • Re-use of BFO as Upper Ontology • Modularity & re-use • Methods of class extraction 9

  10. 3) Methodological principles • Realism • Representation of reality independent of use-case restrictions, end user’s perspective, etc. • Fosters re-usability • Accommodates multiple perspectives 10

  11. 3) Methodological principles • BFO as Upper Ontology • Upper Ontologies foster harmonization, modularization and re-use. • Most widely used among OBO Foundry ontologies • Ensures reality-oriented semantics 11

  12. Excerpt from the COPD Ontology: The branch Realizable Entity 12

  13. 3) Methodological principles • Modularity & re-use • CHRONIOUS resources are built in a modular fashion to enable representing multiple prespectives. • CHRONIOUS ontology development is done re-using pre-existing resources. 13

  14. 3) Methodological principles • Methods of class extraction (1) • Create glossary of candidate classes; let domain experts evaluate domain coverage. • Assign classes to different ontological categories from BFO. • Assign classes either to middle layer (MLOCC) or to one of the domain ontologies. • Order classes in subsumption hierarchy. 14

  15. 3) Methodological principles • Methods of class extraction (2) • Identify non-taxonomic relations and represent those as object properties. • Constitute a class dictionary. • Specify inverse relations and mathematical properties of object properties. • State formal axioms. 15

  16. 4a) General design principles (1) • Domain Ontologies should only contain types, not instances or tokens • Taxonomies are exclusively based on formal subsumption. • Immediate subclasses of a given class should ideally be exhaustive. 16

  17. 4a) General design principles (2) • Primitive sibling classes should be disjoint. • UnknownX as well as other catch-all classes for remaining cases should be avoided. 17

  18. 4b) Specific design principles • Occurents do not participate in other occurents. • Realizable entities do not participate in occurents. • Realizable entities, except roles, only characterize independent continuants. 18

  19. 5) Conclusion & next steps • The CHRONIOUS Ontology Suite (COS) provides a usable ontological resource to a medical knowledge management platform maintaining the realist point of view and sticking to proofed best practice in ontology development. • Each module of the COS can be re-used. • Reconciliation with OGMS & IAO (includes optimization of MLOCC). 19

  20. Downloads • http://www.ifomis.org/chronious/mlocc • http://www.ifomis.org/chronious/copd • http://www.ifomis.org/chronious/ckd 20

  21. Acknowledgments Research leading up to the present article has been supported by the ICT-2007-1-216461 grant within the Seventh Framework Programme of the EU, as well as by a post-doc grant from the National Research Fund, Luxembourg (cofunded under the Marie Curie Actions of the European Commission [FP7-COFUND]), and has been carried out under subcontract to the Fraunhofer Institute for Biomedical Engineering, St. Ingbert (Germany). 21

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