Towards Reusing Model Components in Systems Biology

by: Adelinde M Uhrmacher, Daniela Degenring, Jens Lemcke, Mario Krahmer

Computational Methods in Systems Biology (2005), pp. 192-206.

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Abstract

For reusing model components, it is crucial to understand what information is needed and how it should be presented. The centrality of abstraction being inherent in the modelling process distinguishes model components from software components and makes their reuse even more difficult. Objectives and assumptions which are often difficult to explicitate become an important aspect in describing model components. Following the argumentation line of the Web Service ontology OWL-S, we propose a set of metadata which is structured into profile, process model, and grounding to describe model components. On the basis of the specific model component Tryptophan Synthase, its metadata is refined in XML. The reuse of the described model component is illustrated by integrating it into a model of the Tryptophan operon.

@incollection{citeulike:1596240, abstract = {For reusing model components, it is crucial to understand what information is needed and how it should be presented. The centrality of abstraction being inherent in the modelling process distinguishes model components from software components and makes their reuse even more difficult. Objectives and assumptions which are often difficult to explicitate become an important aspect in describing model components. Following the argumentation line of the Web Service ontology OWL-S, we propose a set of metadata which is structured into profile, process model, and grounding to describe model components. On the basis of the specific model component Tryptophan Synthase, its metadata is refined in XML. The reuse of the described model component is illustrated by integrating it into a model of the Tryptophan operon.}, author = {Uhrmacher, Adelinde M. and Degenring, Daniela and Lemcke, Jens and Krahmer, Mario }, citeulike-article-id = {1596240}, journal = {Computational Methods in Systems Biology}, keywords = {composition, systems\_biology, xml}, pages = {192--206}, posted-at = {2007-08-27 13:44:43}, priority = {0}, title = {Towards Reusing Model Components in Systems Biology}, url = {http://www.springerlink.com/content/rueq504ak0cf6wwk }, year = {2005} }

RIS record

TY - CHAP ID - citeulike:1596240 L3 - citeulike-article-id:1596240 TI - Towards Reusing Model Components in Systems Biology JF - Computational Methods in Systems Biology SP - 192 EP - 206 N2 - For reusing model components, it is crucial to understand what information is needed and how it should be presented. The centrality of abstraction being inherent in the modelling process distinguishes model components from software components and makes their reuse even more difficult. Objectives and assumptions which are often difficult to explicitate become an important aspect in describing model components. Following the argumentation line of the Web Service ontology OWL-S, we propose a set of metadata which is structured into profile, process model, and grounding to describe model components. On the basis of the specific model component Tryptophan Synthase, its metadata is refined in XML. The reuse of the described model component is illustrated by integrating it into a model of the Tryptophan operon. KW - composition KW - systems_biology KW - xml AU - Uhrmacher, Adelinde AU - Degenring, Daniela AU - Lemcke, Jens AU - Krahmer, Mario PY - 2005/// UR - http://www.springerlink.com/content/rueq504ak0cf6wwk ER -

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