gms | German Medical Science

MAINZ//2011: 56. GMDS-Jahrestagung und 6. DGEpi-Jahrestagung

Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V.
Deutsche Gesellschaft für Epidemiologie e. V.

26. - 29.09.2011 in Mainz

Study items, properties, and clinical phenotypes

Meeting Abstract

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  • Heinrich Herre - IMISE/Universität Leipzig, Leipzig
  • Silvia Gross - IMISE/Universität Leipzig, Leipzig
  • Alexandr Uciteli - University Leipzig, Leipzig

Mainz//2011. 56. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (gmds), 6. Jahrestagung der Deutschen Gesellschaft für Epidemiologie (DGEpi). Mainz, 26.-29.09.2011. Düsseldorf: German Medical Science GMS Publishing House; 2011. Doc11gmds555

DOI: 10.3205/11gmds555, URN: urn:nbn:de:0183-11gmds5554

Published: September 20, 2011

© 2011 Herre et al.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc-nd/3.0/deed.en). You are free: to Share – to copy, distribute and transmit the work, provided the original author and source are credited.


Outline

Text

Introduction and background: The precise definition and semantically correct representation of documentation features and study items has an important impact on the value and quality of clinical trials. It is an essential assumption to support the reuse of such features, to compare the data of different study projects, and to establish a common basis for the interpretation of the resulting data. We report on work in progress of a long term project, initiated in [1], which aims at the development of an ontology of study items and of clinical phenotypes. There is a close relation between the notions of study item, data element, property, and clinical phenotype.

Methods: The usage of the General Formal Ontology (GFO) [2] is a part of the method, whose basic idea consists in the ontological reconstruction and modelling of entities of the medical domain [3]. This reconstruction uses the ontology of properties, as expounded in GFO, as well as some basic constructs of the ISO-11179-standard, notably the notion of data element [4].

Results: We propose a definition of study items which are described as particular data elements in ISO-11179 [1], whose conceptual structure is ontologically reconstructed and uncovered within the GFO. Furthermore, we propose a definition of the notion of a clinical phenotype and relate it to the notion of data element and to the notion of property in GFO. We outline a formal ontological framework, based on GFO, to treat clinical phenotypes, properties and study items in a uniform manner. This framework takes up the approach in [5] and makes a further step in establishing a conceptual tool for the specification of clinical phenotypes. Furthermore, we implemented a first version of a prototype for managing study items. Study items must be captured and specified in a semantically correct way and computationally presented such that they can be efficiently retrieved and used.

Discussion and conclusion: The final aim of the presented research is the development of ontologies of clinical phenotpyes. To achieve such ontologies, a number of ontological relations must be introduced and specified, which connect phenotypes to form complex properties. These relations must include, among others, part-of, participation in a process, causality, function realization. Furthermore, a suitable process ontology must be integrated to specify physiological information.


References

1.
Uciteli A, Groß S, Herre H. An Ontologically Founded Architecture for Information Systems in Clinical and Epidemiological Research. BMC Biomedical Semantics. 2011.
2.
Herre H. General Formal Ontology (GFO): A Foundational Ontology for Conceptual Modelling. In: Poli R, Obrst L, eds. Theory and Applications of Ontology. Berlin: Springer; 2010.
3.
Herre H, Heller B. Semantic foundations of medical information systems based on top-level ontologies. Knowledge-Based Systems. 2006;19:107-15.
4.
ISO/IEC 11179 standard. Information technology –— Metadata registries (MDR) –— Part 3: Registry metamodel and basic attributes. 2010. Available from: http://jtc1sc32.org/doc/N1951-2000/32N1983Ta-Text-for-ballot-FCD_11179-3.pdf External link
5.
Hoehndorf R, Oellrich A, Rebholz-Schuhmann D. Interoperability between phenotype and anatomy ontologies. Bioinformatics. 2010;26:3112-8.