Kinetic Simulation Algorithm Ontology

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, allows simulation software to choose automatically the best algorithm available to perform a simulation and unambiguously refer to it.

KiSAO is an Open Biomedical Ontologies (OBO) candidate ontology, and is free for use.

Download

Download KiSAO releases from Sourceforge ...

... or from the KiSAO project at BioPortal .

The latest KiSAO release is encoded in OWL 2 and consists in 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.

Browse

Browse KiSAO on BioPortal.

 

Search

 
Get the preferred name for a term:
Get the term full URI by its name:
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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

Software support

Support of KiSAO is helped by a Java software library, libKiSAO.

Participate

You can discuss KiSAO via the mailing list biomodels-net-discuss @ lists.sf.net

Via our ticket system, you can also suggest new terms or changes to KiSAO.