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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 4, Issue 3

Issues

Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models

Allyson L. Lister
  • Centre for Integrated Systems Biology of Ageing and Nutrition (http://www.cisban.ac.uk), United Kingdom of Great Britain and Northern Ireland
  • School of Computing Science (http://www.cs.ncl.ac.uk), Newcastle University (http://www.ncl.ac.uk), United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Matthew Pocock
  • School of Computing Science (http://www.cs.ncl.ac.uk), Newcastle University (http://www.ncl.ac.uk), United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Anil Wipat
  • Corresponding author
  • Centre for Integrated Systems Biology of Ageing and Nutrition (http://www.cisban.ac.uk), United Kingdom of Great Britain and Northern Ireland
  • School of Computing Science (http://www.cs.ncl.ac.uk), Newcastle University (http://www.ncl.ac.uk), United Kingdom of Great Britain and Northern Ireland
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2007-80

Abstract

The creation of quantitative, simulatable, Systems Biology Markup Language (SBML) models that accurately simulate the system under study is a time-intensive manual process that requires careful checking. Currently, the rules and constraints of model creation, curation, and annotation are distributed over at least three separate documents: the SBML schema document (XSD), the Systems Biology Ontology (SBO), and the “Structures and Facilities for Model Definition” document. The latter document contains the richest set of constraints on models, and yet it is not amenable to computational processing. We have developed a Web Ontology Language (OWL) knowledge base that integrates these three structure documents, and that contains a representative sample of the information contained within them. This Model Format OWL (MFO) performs both structural and constraint integration and can be reasoned over and validated. SBML Models are represented as individuals of OWL classes, resulting in a single computationally amenable resource for model checking. Knowledge that was only accessible to humans is now explicitly and directly available for computational approaches. The integration of all structural knowledge for SBML models into a single resource creates a new style of model development and checking.

About the article

Published Online: 2016-10-18

Published in Print: 2007-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 4, Issue 3, Pages 252–263, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2007-80.

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© 2007 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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