KiSAO

KiSAO

Content
Description	An ontology providing support in unambiguously referring to simulation algorithms when describing a simulation experiment.
Data types captured	simulation algorithms, their characteristics and parameters
Contact
Research center	EMBL-EBI
Primary citation	PMID 22027554
Access
Standards	MIRIAM
Data format	OWL
Website	KiSAO home page, KiSAO at BioPortal
Download URL	KiSAO home page
Tools
Standalone	libKiSAO, a java library to query KiSAO
Miscellaneous
License	Artistic Licence
Version	2.3.5 (April 2014)
Curation policy	yes (manual)
Bookmarkable entities	yes

The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. KiSAO is part of the BioModels.net project and of the COMBINE initiative.^[1]

Structure

KiSAO consists of three main branches:

• simulation algorithm,
• simulation algorithm characteristic,
• simulation algorithm parameter.

The elements of each algorithm branch are linked to characteristic and parameter branches using has characteristic and has parameter relationships accordingly.The algorithm branch itself is hierarchically structured using subClassOf relationships, which denote that the descendant algorithms were derived from, or specify, more general ancestors.

See also

• COMBINE
• SED-ML
• MIRIAM
• SBO
• TEDDY

References

1. Courtot, M.; Juty, N.; Knupfer, C.; Waltemath, D.; Zhukova, A.; Drager, 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 Novere, N. (2014). "Controlled vocabularies and semantics in systems biology". Molecular Systems Biology 7: 543. doi:10.1038/msb.2011.77. PMC 3261705. PMID 22027554.