The Journal of Physiological Sciences
Online ISSN : 1880-6562
Print ISSN : 1880-6546
ISSN-L : 1880-6546
Regular Papers
Specifications of insilicoML 1.0: A Multilevel Biophysical Model Description Language
Yoshiyuki AsaiYasuyuki SuzukiYoshiyuki KidoHideki OkaEric HeienMasao NakanishiTakahito UraiKenichi HagiharaYoshihisa KurachiTaishin Nomura
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2008 Volume 58 Issue 7 Pages 447-458

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Abstract

An extensible markup language format, insilicoML (ISML), version 0.1, describing multilevel biophysical models has been developed and is available in the public domain. ISML is fully compatible with CellML 1.0, a model description standard developed by the IUPS Physiome Project, for enhancing knowledge integration and model sharing. This article illustrates the new specifications of ISML 1.0 that largely extend the capability of ISML 0.1. ISML 1.0 can describe various types of mathematical models, including ordinary/partial differential/difference equations representing the dynamics of physiological functions and the geometry of living organisms underlying the functions. ISML 1.0 describes a model using a set of functional elements (modules), each of which can specify mathematical expressions of the module functions. Structural and logical relationships between any two modules are specified by edges, which allow modular, hierarchical, and/or network representations of the model. The role of edge relationships is enriched by key words in order for use in constructing a physiological ontology. The ontology is further improved by the traceability of history of the model’s development and by linking between different ISML models stored in the model’s database using meta-information. ISML 1.0 is designed to operate with a model database and integrated environments for model development and simulations for knowledge integration and discovery.

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© 2008 by The Physiological Society of Japan
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