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Open Access Technical Note

LibKiSAO: a Java library for Querying KiSAO

Anna Zhukova1, Richard Adams2, Camille Laibe1 and Nicolas Le Novère13*

Author affiliations

1 EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom

2 SynthSys Edinburgh, University of Edinburgh, Edinburgh EH9 3JD, United Kingdom

3 Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom

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Citation and License

BMC Research Notes 2012, 5:520  doi:10.1186/1756-0500-5-520

Published: 24 September 2012

Abstract

Background

The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of Systems Biology models, their characteristics, parameters and inter-relationships. KiSAO enables the unambiguous identification of algorithms from simulation descriptions. Information about analogous methods having similar characteristics and about algorithm parameters incorporated into KiSAO is desirable for simulation tools. To retrieve this information programmatically an application programming interface (API) for KiSAO is needed.

Findings

We developed libKiSAO, a Java library to enable querying of the KiSA Ontology. It implements methods to retrieve information about simulation algorithms stored in KiSAO, their characteristics and parameters, and methods to query the algorithm hierarchy and search for similar algorithms providing comparable results for the same simulation set-up. Using libKiSAO, simulation tools can make logical inferences based on this knowledge and choose the most appropriate algorithm to perform a simulation. LibKiSAO also enables simulation tools to handle a wider range of simulation descriptions by determining which of the available methods are similar and can be used instead of the one indicated in the simulation description if that one is not implemented.

Conclusions

LibKiSAO enables Java applications to easily access information about simulation algorithms, their characteristics and parameters stored in the OWL-encoded Kinetic Simulation Algorithm Ontology. LibKiSAO can be used by simulation description editors and simulation tools to improve reproducibility of computational simulation tasks and facilitate model re-use.

Keywords:
Java library; Simulation; Algorithm search; Ontology