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SED-ML / KiSAO

Ontology of algorithms for analyzing biological models, their parameters, and their outputs
Artistic License 2.0
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combine computational-biology mathematical-modeling modeling ontology sed-ml simulation systems-biology

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KiSAO

The Kinetic Simulation Algorithm Ontology (KiSAO: http://co.mbine.org/standards/kisao) is an ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs.

Overview of KiSAO

Browsing KiSAO

KiSAO can be browsed through BioPortal and OLS.

Browsing the substitutability of algorithms catalogued by KiSAO

A matrix of the substitutability of algorithms catalogued by KiSAO is available here. Rules for generating this matrix are encoded into KiSAO Python package (see below) and described in its documentation.

Obtaining KiSAO in other formats

KiSAO is developed in the OWL format. The current release of KiSAO is available in OWL format here. KiSAO is available in CSV and RDF/XML formats from BioPortal.

Working with KiSAO in code

A package is available for working with KiSAO in Python: https://github.com/SED-ML/KiSAO/tree/dev/libkisao/python.

A older package is available for working with KiSAO in Java: https://co.mbine.org/standards/kisao/libkisao.

Obtaining older versions of KiSAO

The current release of KiSAO is available in the OWL format here. The current development version is available here. Older versions of KiSAO are available here. All versions are available in OWL format. Versions 1.0 is also available in OBO format.

Requesting new terms and relationships, requesting changes to existing terms and relationships, and reporting bugs

Please use GitHub issues to submit requests for new terms and relationships, request modifications to existing terms and relationships, and report bugs.

Contributing multiple changes to KiSAO

If you plan to request a significant number of terms, relationships, or changes, please submit your request as a pull request with the intended modifications to KiSAO. Please see the Guide to Contributing.

Releasing new versions

Please see the Guide to Contributing.

License

KiSAO is released under Artistic License 2.0.