Kinetic Simulation Algorithm Ontology (KiSAO)
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 conjunction with simulation descriptions, such as SED-ML, will allow simulation software to automatically choose the best algorithm available to perform a simulation and unambiguously refer to it.
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...or from the KiSAO project at BioPortal
The latest KiSAO release is encoded in OWL 2 and consists of two parts:
- kisao.owl: the core version containing all but deprecated terms.
- kisao_full.owl: the full version which imports core KiSAO and also contains deprecated terms.
For more information about different versions of KiSAO check the release notes
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CITE
To reference KiSAO, please cite:
Courtot M., Juty N., Knüpfer C., Waltemath D., Zhukova A., Dräger A., Dumontier M., Finney A., Golebiewski M., Hastings J., Hoops S., Keating S., Kell D.B., Kerrien S., Lawson J., Lister A., Lu J., Machne R., Mendes P., Pocock M., Rodriguez N., Villeger A., Wilkinson D.J., Wimalaratne S., Laibe C., Hucka M., Le Novère N. (2011) Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7:543. doi:10.1038/msb.2011.77