title: LibKiSAO: a Java library for Querying KiSAO.
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.
  
  
  RESULTS
  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.
authors.affiliation: EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom.
authors.forename: Anna
authors.initials: A
authors.lastname: Zhukova
authors.forename: Richard
authors.initials: R
authors.lastname: Adams
authors.forename: Camille
authors.initials: C
authors.lastname: Laibe
authors.forename: Nicolas
authors.initials: N
authors.lastname: Le Novère
mesh_terms: D000465:Algorithms; D011381:Programming Languages; D049490:Systems Biology