Specifications of insilicoML 1.0: A Multilevel Biophysical Model Description Language

• Asai Yoshiyuki

  The Center for Advanced Medical Engineering and Informatics, Osaka University

• Suzuki Yasuyuki

  Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University

• Kido Yoshiyuki

  The Center for Advanced Medical Engineering and Informatics, Osaka University

• Oka Hideki

  Fujitsu Limited

• Heien Eric

  Department of Computer Science, Graduate School of Information Science and Technology, Osaka University

• Nakanishi Masao

  Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University

• Urai Takahito

  Intasect Communications

• Hagihara Kenichi

  The Center for Advanced Medical Engineering and Informatics, Osaka University Department of Computer Science, Graduate School of Information Science and Technology, Osaka University

• Kurachi Yoshihisa

  The Center for Advanced Medical Engineering and Informatics, Osaka University Department of Pharmacology, Graduate School of Medicine, Osaka University

• Nomura Taishin

  The Center for Advanced Medical Engineering and Informatics, Osaka University Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University

抄録

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.<br>

収録刊行物

• The Journal of Physiological Sciences

  The Journal of Physiological Sciences 58 (7), 447-458, 2008

  一般社団法人　日本生理学会

キーワード

• model descriptive language
• multiscale modeling
• model sharing
• physiome

詳細情報

• CRID: 1390282680230701056
• NII論文ID: 10027710778
• NII書誌ID: AA12129145
• DOI: 10.2170/physiolsci.rp013308
• COI: 1:STN:280:DC%2BD1M%2FitValuw%3D%3D
• ISSN: 18806562
• ISSN: 18806546
• NDL書誌ID: 9752827
• PubMed: 18983726
• Web Site: https://ndlsearch.ndl.go.jp/books/R000000004-I9752827
• Web Site: https://search.jamas.or.jp/link/ui/2009144995
• 本文言語コード: en
• データソース種別:
  • JaLC
  • NDL
  • Crossref
  • PubMed
  • CiNii Articles
  • KAKEN
• 抄録ライセンスフラグ: 使用不可