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| Nick Juty; Nicolas Le Novère; Dagmar Waltemath; Christian Knuepfer. |
| The use of computational modelling in the description and analysis of biological systems is at the heart of Systems Biology. Besides the information stored in a core model, there is increasingly a need to provide additional semantic information: to identify model components, to assist in biological interpretation of models, to define simulation conditions and to describe simulation results. This information deficit can be addressed through the use of ontologies. We describe here three ontologies created specifically to address the needs of the Systems Biology community in each sub-division, and illustrate their practical use with the 'Repressilator' model (Elowitz and Leibler, 2000). |
| Tipo: Poster |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5122/version/1 |
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| Nick Juty. |
| The Systems Biology Ontology (SBO) is composed of hierarchically arranged sets of controlled vocabularies that are commonly used in mathematical modelling, providing an additional layer of semantic information. We present recent developments in SBO, including the ontology's OBO Foundry status, its relationship to SBGN, and detail some of the restructuring work that has been undertaken. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5121/version/1 |
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| Anna Zhukova; Dagmar Waltemath; Nick Juty; Camille Laibe; Nicolas Le Novère. |
| To enable the accurate and repeatable execution of a computational simulation task, it is important to identify both the algorithm used and the initial setup. These minimum information requirements are described by the MIASE guidelines. Since the details of some algorithms are not always publicly available, and many are implemented only in a limited number of simulation tools, it is crucial to identify alternative algorithms with similar characteristics that may be used to provide comparable results in an equivalent simulation experiment. The Kinetic Simulation Algorithm Ontology (KiSAO) was developed to address this issue by describing existing algorithms and their inter-relationships through their characteristics and parameters. The use of KiSAO in... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6330/version/1 |
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| Camille Laibe; Nick Juty; Nicolas Le Novère. |
| _Background_
More than ever, the era of data integration has highlighted the key requirement to reference specific data in an unambiguous and perennial way, in order to enable community-level sharing, development, exchange and reuse of information. In the field of Systems Biology, which is concerned with creating quantitative models of biological processes, these requirements have directly led to the creation of the Minimal Information Required In the Annotation of Models (MIRIAM, "http://biomodels.net/miriam/":http://biomodels.net/miriam/). MIRIAM provides a specific set of guidelines that can be implemented within any structured modelling format.

_Objectives_
To... |
| Tipo: Poster |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5128/version/1 |
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