The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment.

Prefix

biomodels.kisao

Preferred Prefix

biomodels.kisao

Alternative Prefixes

biomodels.kisao kisao

Keywords

algorithm bioinformatics computer science kinetic model modeling and simulation obo ontology

Version

2.34

License

Artistic License 2.0

Links

Homepage Repository OWL

Contact

Jonathan Karr   0000-0002-2605-5080   jonrkarr

Pattern for Local Unique Identifiers

Local identifiers in Kinetic Simulation Algorithm Ontology should match this regular expression:
^\d+$

Example Local Unique Identifier

0000057   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Kinetic Simulation Algorithm Ontology should match this regular expression:
^biomodels\.kisao:\d+$

Example CURIE

biomodels.kisao:0000057

MIRIAM Namespace Embedded in LUI

The legacy MIRIAM standard for generating CURIEs with this resource annotates the namespaceEmbeddedInLUI as true. This means that you may see local unique identifiers that include a redundant prefix and delimiter (also known as a banana) and therefore look like a CURIE. For Kinetic Simulation Algorithm Ontology, the banana looks like KISAO_. Therefore, you may see local unique identifiers for this resource that look like KISAO_0000057 (instead of the canonical form 0000057) and CURIEs for this resource that look like biomodels.kisao:KISAO_0000057 (instead of the canonical form biomodels.kisao:0000057). The Bioregistry will automatically strip off the banana when standardizing local unique identifiers and CURIEs.

Publications

2011 Controlled vocabularies and semantics in systems biology

The metaregistry provides mappings between the Bioregistry and other registries. There are 10 mappings to external registries for this resource with 3 unique external prefixes.

When using this resource in RDF, the following URI format should be used:

http://purl.obolibrary.org/obo/KISAO_$1

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier 0000057 is used to demonstrate the providers available for Kinetic Simulation Algorithm Ontology. A guide for curating additional providers can be found here.

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.