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) Purpose2) Technical details3) Methodological principles4) Design principles5) Conclusion

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1) Purpose

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1) Purpose

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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

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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

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2) Technical details

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Modular structure MLOCC: 476 classes COPD: 964 classes CKD: 972 classes

Development in OWL-DL

2) Technical details

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Why OWL-DL? Ontologies are also intended for other, more

reasoning-intensive uses. Decidability allows for efficient consistency

checking.

3) Methodological principles

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Realism Re-use of BFO as Upper Ontology Modularity & re-use Methods of class extraction

3) Methodological principles

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Realism Representation of reality independent of

use-case restrictions, end user’s perspective, etc.

Fosters re-usability Accommodates multiple perspectives

3) Methodological principles

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BFO as Upper Ontology Upper Ontologies foster harmonization,

modularization and re-use. Most widely used among OBO Foundry

ontologies Ensures reality-oriented semantics

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Excerpt from the COPD Ontology:The branch Realizable Entity

3) Methodological principles

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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

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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

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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)

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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)

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Primitive sibling classes should be disjoint.

UnknownX as well as other catch-all classes for remaining cases should be avoided.

4b) Specific design principles

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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

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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

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http://www.ifomis.org/chronious/mlocc http://www.ifomis.org/chronious/copd http://www.ifomis.org/chronious/ckd

Acknowledgments

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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).