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Open Source models, methods, tools and applications
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 GALEN Common Reference Model
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Computer-based clinical terminology for representing medical concepts |
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| keywords |
clinical domains |
| Clinical coding and classification, medical terminologies,
controlled vocabulary,
nomenclature, compositional representations, intermediate representations,
open source, ontologies,
Common Reference Model for medical terminologies,
open source, description logics, ontologies |
multiple |
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| developed by |
GALEN project, GALEN-IN-USE project and OpenGALEN |
| released |
Seven versions have been released between 1999 and 2005. |
| status |
Available for download and use under the GALEN Open source License.
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| download |
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| description |
The GALEN Common Reference Model (CRM) offers a way to represent a clinical terminology, an underlying framework of medical knowledge describing what things are and how they are organised. It does not describe medical knowledge.
The CRM is a computer-based clinical terminology for representing medical concepts (a reference model is a
model that contain references to other models).
It is designed to support mappings to other coding systems and languages, data analysis, sharing information between applications and re-use.
(Reference models are
models that contain references to other models.)
The GALEN CRM forms part of the wide range of medical terminology models, methods, architectures and tools
developed by GALEN and successor pojects.
The CRM "source files are in GRAIL notation (an early description logic syntax and formalism).
A fully open source knowledge management environment exists (OpenKNoMe)
to read and edit these.
No suitable open source compliant description logic engine currently exists."
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| references |
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Rector AL, Rogers JE, Zanstra PE, Van Der Haring E.
OpenGALEN: Open Source Medical Terminology and Tools.
Proc AMIA Symp. 2003; : 982.
[PubMed]
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Abstract
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The GALEN programme of research into medical terminology began in 1991. In 1999 OpenGALEN was formed to provide an open source route both for disseminating the results of that programme and as a framework for its future development. Currently available open source resources include a sophisticated ontology development environment and a large open source description logic-based ontology for the medical domain.
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Rogers J, Roberts A, Solomon D, van der Haring E, Wroe C, Zanstra P, Rector A.
GALEN ten years on: tasks and supporting tools.
Medinfo. 2001; 10(Pt 1): 256-60.
[PubMed]
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Abstract
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The GALEN technology has matured over more than a decade of use. We describe a set of software tools and associated methodologies that together are supporting ontological engineering in a production, rather than a research setting.
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Rector AL. Clinical Terminology: Why is it so hard? Methods of Information in Medicine 1999;38:239-252.
[PubMed]
[]
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Abstract
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Despite years of work, no re-usable clinical terminology has yet been demonstrated in widespread use. This paper puts forward ten reasons why developing such terminologies is hard. All stem from underestimating the change entailed in using terminology in software for 'patient centred' systems rather than for its traditional functions of statistical and financial reporting. Firstly, the increase in scale and complexity are enormous. Secondly, the resulting scale exceeds what can be managed manually with the rigour required by software, but building appropriate rigorous representations on the necessary scale is, in itself, a hard problem. Thirdly, 'clinical pragmatics'--practical data entry, presentation and retrieval for clinical tasks--must be taken into account, so that the intrinsic differences between the needs of users and the needs of software are addressed. This implies that validation of clinical terminologies must include validation in use as implemented in software.
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Rogers JE, Solomon WD, Rector AL, Pole P, Zanstra P, van der Haring E.
Rubrics to dissections to GRAIL to classifications.
Stud Health Technol Inform. 1997;43 Pt A:241-5.
[PubMed]
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This paper summarises the process in the GALEN-IN-USE project by which rubrics from traditional medical coding schemes are analysed into an intermediate, relatively informal conceptual representation which is then automatically translated into the GRAIL formalism and its Common Reference Model.
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Rector AL, Zanstra PE, Solomon WD et al.
Reconciling users' needs and formal requirements: issues in developing a reusable ontology for medicine.
IEEE Trans Inf Technol Biomed. 1998 Dec;2(4):229-42.
[PubMed]
[]
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"
A common language, or terminology, for representing what clinicians have said and done is an important requirement for individual clinical systems, and it is a pre-requisite for integrating disparate applications in a distributed telematic healthcare environment. Formal representations based on description logics or closely related formalisms are increasingly used for representing medical terminologies. GALEN's experience in using one such formalism raises two major issues, as follows: how to make ontologies based on description logics easy to use and understand for both clinicians and applications developers; what features are required of the ontology and description logic if they are to achieve their aims. Based on our experience we put forward four contentions: two relating to each of these two issues, as follows: that natural language generation is essential to make a description logic based ontology accessible to users; that the description logic based ontology should be treated as an "assembly language" and accessed via "intermediate representations" oriented to users and "perspectives" adapting it to specific applications; that independence and reuse are best supported by partitioning the subsumption hierarchy of elementary concepts into orthogonal taxonomies, each of which forms a pure tree in which the branches at each level are disjoint but nonexhaustive subconcepts of the parent concept; that the expressivity of the description logic must include support for transitive relations despite the computational cost, and that this computational cost is acceptable in practice. The authors argue that these features will be necessary, though by no means sufficient, for the development of any large reusable ontology for medicine.
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| acknowledgements |
| Pieter Zanstra, Radboud University Nijmegen |
| page history |
Entry on OpenClinical: 12 July 2003 (under separate topic area)
Last main updates: 5 February 2004, 24 October 2006
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Common Reference Model Tutorial