Biophysical annotation and representation of CellML models
Open accessAbstract
Motivation: CellML is an implementation-independent model description language for specifying and exchanging biological processes. The focus of CellML is the representation of mathematical formulations of biological processes. The language captures the mathematical and model building constructs well, but does not lend itself to capturing the biology these models represent. Results: This article describes the development of an ontological framework for annotating CellML models with biophysical concepts. We demonstrate that, by using these ontological mappings, in combination with a set of graph reduction rules, it is possible to represent the underlying biological process described in a CellML model. Contact: sarala.dissanayake@auckland.ac.nz Supplementary information: Supplementary data are available at Bioinformatics online.
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Both SBML and CellML support annotation with SBO terms.
“Both SBML and CellML support annotation with SBO terms. SBML elements contain an optional sboTerm attribute [25, 29, 31].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [25]
The Introduction says SBO can be used to annotate physical concepts modeled in CellML, and the Discussion describes mapping CellML-related ontology classes to SBO terms. The passages do not establish that SBML supports SBO annotation or that SBML elements have an optional sboTerm attribute. (LLM, conf=0.86)
Experimental — accuracy not yet measuredCellML models do not encode biological information explicitly, but instead consist of mathematical formulations of biological processes.
“CellML models do not encode biological information explicitly in the model, but instead consist of mathematical formulations of biological processes [25].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [25]
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- Authors
- Wimalaratne, S. M., Halstead, M. D. B., Lloyd, C. M., Crampin, E. J., & Nielsen, P. F.
- Affiliations
- University of Auckland (NZ)
- Corresponding author
- Wimalaratne, S. M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-06-29
- Volume
- 25
- Issue
- 17
- Pages
- 2263-2270
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2139383813
- Cited by
- 19
- References
- 15
- Citations by year
- 2024: 1 · 2023: 2 · 2022: 1 · 2019: 1 · 2018: 1 · 2015: 4 · 2013: 1 · 2012: 1
- FWCI
- 1.07
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- CellML, ontological framework, model description language, biological modelling
- MeSH terms
- Models, Biological, Programming Languages, Software, Computational Biology, Internet, Biophysical Phenomena
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