Toward principles for the design of ontologies used for knowledge sharing
International Journal of Human-Computer Studies - Special issue: the role of formal ontology in the information technology
Part-Whole Reasoning: A Case Study in Medical Ontology Engineering
IEEE Intelligent Systems
A reference ontology for biomedical informatics: the foundational model of anatomy
Journal of Biomedical Informatics - Special issue: Unified medical language system
Integrity and change in modular ontologies
IJCAI'03 Proceedings of the 18th international joint conference on Artificial intelligence
Journal of Biomedical Informatics - Special issue: Biomedical ontologies
A prototype symbolic model of canonical functional neuroanatomy of the motor system
Journal of Biomedical Informatics
Fuzzy spatial relation ontology for image interpretation
Fuzzy Sets and Systems
Proceedings of the 2009 ACM symposium on Applied Computing
Using a lightweight ontology of heart electrophysiology in an interactive web application
Companion Proceedings of the XIV Brazilian Symposium on Multimedia and the Web
Using an ECG reference ontology for semantic interoperability of ECG data
Journal of Biomedical Informatics
Desiderata for ontologies to be used in semantic annotation of biomedical documents
Journal of Biomedical Informatics
Measuring expressivity between ontology models
AIKED'12 Proceedings of the 11th WSEAS international conference on Artificial Intelligence, Knowledge Engineering and Data Bases
A reference profile ontology for communities of practice
International Journal of Metadata, Semantics and Ontologies
Ontologies and terminologies: Continuum or dichotomy?
Applied Ontology - Ontologies and Terminologies: Continuum or Dichotomy?
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Domain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain. An example of reference ontology in biomedical informatics is the Foundational Model of Anatomy (FMA), an ontology of anatomy that covers the entire range of macroscopic, microscopic, and subcellular anatomy. The purpose of this paper is to explore how two domain reference ontologies--the FMA and the Chemical Entities of Biological Interest (ChEBI) ontology, can be used (i) to align existing terminologies, (ii) to infer new knowledge in ontologies of more complex entities, and (iii) to manage and help reasoning about individual data. We analyze those kinds of usages of these two domain reference ontologies and suggest desiderata for reference ontologies in biomedicine. While a number of groups and communities have investigated general requirements for ontology design and desiderata for controlled medical vocabularies, we are focusing on application purposes. We suggest five desirable characteristics for reference ontologies: good lexical coverage, good coverage in terms of relations, compatibility with standards, modularity, and ability to represent variation in reality.