The Chronious Ontology Suite: Methodology and Design Principles 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 ICBO 2011, Buffalo, July 28-30, 2011

Contents 1)Purpose 2)Technical details 3)Methodological principles 4)Design principles 5)Conclusion 2

1) Purpose 3

4  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).

1) Purpose 5  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.)

2) Technical details 6

7  Modular structure  MLOCC: 476 classes  COPD: 964 classes  CKD: 972 classes  Development in OWL-DL

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

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

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

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

12 Excerpt from the COPD Ontology: The branch Realizable Entity

3) Methodological principles 13  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.

3) Methodological principles 14  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.

3) Methodological principles 15  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.

4a) General design principles (1) 16  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.

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

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

5) Conclusion & next steps 19  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).

Downloads 20   

Acknowledgments 21 Research leading up to the present article has been supported by the ICT 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).