[SED-ML-discuss] Announcing libKiSAO

[Anna Z. <zhu...@eb...>]

Dear KiSAO/SED-ML users,

We would like to announce libKiSAO -- a new Java library for querying 
Kinetic Simulation Algorithm Ontology (KiSAO 
http://www.biomodels.net/kisao) from within your Java programs. It 
supports new, recently redesigned, OWL version of KiSA Ontology 
(http://www.biomodels.net/kisao/#kisao2.0) and provides easy methods for 
retrieving information about simulation algorithms, their 
characteristics, parameters and interrelationships, stored in KiSAO.

With libKiSAO you can:

    * Get a collection of simulation algorithms stored in KiSAO.          

      |            Collection<IRI> algorithms = kisaoQuery.getAllAlgorithms();|

    * Get descendants and ancestors of a given simulation algorithm.

      |            boolean directOnly = true;
                  Collection<IRI> descendants = kisaoQuery.getDescendants(algorithmIRI, directOnly);|

    * Find a simulation algorithm by its name, synonym, MIRIAM urn or id.

      |            IRI iriByName = kisaoQuery.getIRIByName("tau-leaping method");
                  IRI iriByMiriamUrn = kisaoQuery.getIRIbyURN("urn:miriam:biomodels.kisao:KISAO_0000039");|

    * Get information about a simulation algorithm.         

      |            String name = kisaoQuery.getName(algorithmIRI);
                  Collection<String> synonyms = kisaoQuery.getAllSynonyms(algorithmIRI);
                  String definition = kisaoQuery.getDefinition(algorithmIRI);
      |

    * Get characteristics and parameters, used by a given simulation
      algorithm.          

      |            boolean hasCharacteristic = true;
                  Collection<String> algorithmCharacteristics = kisaoQuery.getCharacteristics(algorithmIRI, hasCharacteristic);
                  Collection<String> algorithmParameters = kisaoQuery.getParameters(algorithmIRI);|

    * Get algorithms with the specified characteristics (e.g. discrete
      stochastic).          

      |            boolean hasCharacteristic = true;
                  Collection<IRI> discreteStochasticAlgorithms = kisaoQuery.getAlgorithmsByCharacteristic(hasCharacteristic,
                  	KiSAOIRI.DISCRETE_VARIABLE_CHARACTERISTIC_IRI, KiSAOIRI.STOCHASTIC_SYSTEM_BEHAVIOUR_CHARACTERISTIC_IRI);|

    * And much more...

libKiSAO 1.0.1 release candidate version can be *downloaded* from 
SourceForge 
(https://sourceforge.net/projects/kisao/files/libKiSAO-1.0.1-rc1.zip/download).

More information and examples are available on the libKiSAO web page 
(http://www.biomodels.net/kisao/libkisao.html).

Any feedback, use cases, feature requests, questions, bugs or 
suggestions are very welcome.

Thank you for your attention and co-operation,

Sincerely,

Anna Zhukova

BioModels.net Team