Law and order: Assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy

Zhang, Songmao; Bodenreider, Olivier

doi:10.1016/j.compbiomed.2005.04.007

Cited by 24 publications

(13 citation statements)

References 13 publications

(16 reference statements)

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“…Another shortcoming is we have not formally evaluated our palliative care ontology or the technical architecture developed from the ontology. Future research will involve evaluation of the ontology using formal ontology modeling principles such as those outlined by Zhang and Bodenreider (2006) and design and implementation of the technical architecture as a palliative care information system (PAL-IS).…”

Section: Discussionmentioning

confidence: 99%

Interoperable support for collaborative, mobile, and accessible health care

et al. 2011

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E-Health systems, through their use of Internet and wireless technologies, offer the possibility of near realtime data integration to support the delivery and management of health care. In practice, the wide range of choice in technologies, vendors, protocols, formats, and information representations can make even simple exchanges of information between systems problematic. Much of the focus on healthcare interoperability has been on resolving interoperability issues of system to system information exchanges. But issues around people to people interactions and people to system interactions are just as important to address from an interoperability point of view. In this paper, we identify interoperability deficiencies in collaborative care delivery and develop a methodology in two parts. In the first part, an ontology is developed to represent collaborative care delivery. In the second part, the ontology is used to design an architecture for interoperable clinical information system design. We then use a case study in palliative care to provide a proof of concept of the methodology. The case study provides an inventory of the interoperability requirements for palliative care and a perspective on the design and implementation of a people oriented clinical information system that supports collaborative health care delivery in palliative care.

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Section: Discussionmentioning

confidence: 99%

Interoperable support for collaborative, mobile, and accessible health care

et al. 2011

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“…We reported inconsistent representations to the developers of the FMA, who corrected the errors. We also formalized our consistency checking procedures into quality assurance guidelines for ontologies (Zhang & Bodenreider, 2006b). …”

Section: Discussionmentioning

confidence: 99%

Experience in Aligning AnatomicalOntologies

Zhang

Bodenreider

2007

International Journal on Semantic Web and Information Systems

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An ontology is a formal representation of a domain modeling the entities in the domain and their relations. When a domain is represented by multiple ontologies, there is need for creating mappings among these ontologies in order to facilitate the integration of data annotated with these ontologies and reasoning across ontologies. The objective of this paper is to recapitulate our experience in aligning large anatomical ontologies and to reflect on some of the issues and challenges encountered along the way. The four anatomical ontologies under investigation are the Foundational Model of Anatomy, GALEN, the Adult Mouse Anatomical Dictionary and the NCI Thesaurus. Their underlying representation formalisms are all different. Our approach to aligning concepts (directly) is automatic, rule-based, and operates at the schema level, generating mostly point-to-point mappings. It uses a combination of domain-specific lexical techniques and structural and semantic techniques (to validate the mappings suggested lexically). It also takes advantage of domain-specific knowledge (lexical knowledge from external resources such as the Unified Medical Language System, as well as knowledge augmentation and inference techniques). In addition to point-to-point mapping of concepts, we present the alignment of relationships and the mapping of concepts groupto-group. We have also successfully tested an indirect alignment through a domain-specific reference ontology. We present an evaluation of our techniques, both against a gold standard established manually and against a generic schema matching system. The advantages and limitations of our approach are analyzed and discussed throughout the paper.

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“…A taxonomy is a directed acyclic graph satisfying some conditions [7]. Our database schema allows to represent generic graphs, including directed acyclic graphs.…”

Section: Description Of the Mysql Databasementioning

confidence: 99%

“…But 3D data are not completely integrated in the ontology. Starting from FMA to embed ontology into specific computational resources seems to be relevant regarding the level of compliance with modeling principles used in FMA [7]. FMA is implemented with an open source ontology editor and knowledge-base framework called Protégé which is the only way to manage the ontology.…”

Section: Previous Workmentioning

confidence: 99%

My Corporis Fabrica: A Unified Ontological, Geometrical and Mechanical View of Human Anatomy

Palombi

Bousquet

Jospin

et al. 2009

Modelling the Physiological Human

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Abstract. A new anatomical database, My Corporis Fabrica (MyCF), is presented. It extends the reference anatomical ontology FMA (the Foundational Model of Anatomy) with the possibility to coherently integrate 3D geometrical data, as well as biomechanical parameters. The purpose of this extension is to allow the user to intuitively create a patientspecific 3D representation from a formal description of anatomical entities and also to automatically export this description to test a physical simulation. The main contribution of MyCF consists in the formalization of a comprehensive database structure implemented in MySQL, linking canonical description of anatomical entities with reality-grounded instances of such description in terms of geometrical data and physical attributes. The principle of ontology modeling inherited from FMA is maintained in order to guarantee a close consistency between the two databases. A detailed illustration is given for the knee. In this example, the canonical description of anatomical entities is developed, including the location of attachment of ligaments as well as their stiffness, using an intuitive 3D GUI. Finally, an instance of the knee based on this description is automatically augmented with the canonical part information and then exported to a physical simulator. This example shows the benefit of coupling an exhaustive description of the anatomical structures with a physical simulation to study the dynamic effect of ligaments on the stability of the knee articulation.

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Law and order: Assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy

Cited by 24 publications

References 13 publications

Interoperable support for collaborative, mobile, and accessible health care

Interoperable support for collaborative, mobile, and accessible health care

Experience in Aligning AnatomicalOntologies

My Corporis Fabrica: A Unified Ontological, Geometrical and Mechanical View of Human Anatomy

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