Specifications of insilicoML 1.0: A Multilevel Biophysical Model Description Language
Specifications of insilicoML 1.0: A Multilevel Biophysical Model Description Language
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DOI：
10.2170/physiolsci.rp013308
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发表时间：
2008-12-01
影响因子：
2.3
通讯作者：
Nomura, Taishin
中科院分区：
文献类型：
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作者：
Asai, Yoshiyuki;Suzuki, Yasuyuki;Nomura, Taishin
描述多级生物物理模型的可扩展标记语言格式insiloML(ISML)0.1版已经开发出来，并且在公共领域中可用。ISML完全兼容由UPS Physiome Project开发的模型描述标准CeIIML 1.0，以加强知识集成和模型共享。本文说明了ISML 1.0的新规范，这些规范极大地扩展了ISML 0.1的功能。ISML 1.0可以描述各种类型的数学模型，包括表示生理功能的动力学和作为功能基础的活体的几何形状的常/偏微分/差分方程式。ISML 1.0使用一组功能元素(模块)来描述模型，每个功能元素都可以指定模块函数的数学表达式。任意两个模块之间的结构和逻辑关系由边指定，这允许模型的模块化、层次化和/或网络表示。边缘关系的作用被关键词丰富，以便用于构建生理本体。通过模型开发历史的可跟踪性以及通过使用元信息在模型数据库中存储的不同ISML模型之间进行链接，进一步改进了本体。ISML 1.0旨在与模型数据库和集成环境一起运行，用于模型开发和模拟，以进行知识集成和发现。
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 CeIIML 1.0, a model description standard developed by the UPS 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.