Table 1

Taxonomy level querying methods implemented in libKiSAO
Method name Description
 Listing
getAllAlgorithms() Lists simulation algorithms stored in KiSAO
getAllCharacteristics() Lists simulation algorithm characteristics stored in KiSAO
getAllParameters() Lists simulation algorithm parameters stored in KiSAO
getType(entry) Returns type (algorithm, characteristic or parameter) of the
specified entry
isAlgorithm(entry) Checks if the specified entry represents simulation algorithm
in KiSAO
isCharacteristic(entry) Checks if the specified entry represents simulation algorithm
characteristic in KiSAO
isParameter(entry) Checks if the specified entry represents simulation algorithm
parameter in KiSAO
 Search
searchById(id) Looks for the entry with the specified identifier or miriam urn
searchByName(name) Looks for the entries with the specified name or synonym
 Retrieving Element Information
getName(entry) Returns name of the specified entry
getAllSynonyms(entry) Returns synonyms of the specified entry
getSynonyms(entry, type) Returns synonyms of the specified type (exact, related,
broad or narrow)
getDefinition(entry) Returns definition of the specified entry
getLinks(entry) Returns links to articles/books that describe the specified entry
getId(iri) Returns id (e.g. kisao:0000001) of the specified entry
getMiriamURN(entry) Returns MIRIAM URN (e.g. urn: miriam: biomodels.kisao:
KISAO_0000001) of the specified entry
getIdentifiersOrgURL(entry) Returns identifiers.org URL of the specified entry
isDeprecated(entry) Checks whether the specified entry is deprecated
 Querying Hierarchy
getAncestors(entry, direct) Returns ancestors of the specified entry
getDescendants(entry, direct) Returns descendants of the specified entry
isA(descendantCandidate, ancestorCandidate) Checks if a descendantCandidate entry is a descendant
(concerning rdf:subClassOf relationship) of the
ancestorCandidate entry in KiSAO

The table lists the methods implemented in libKiSAO which enable querying the taxonomy level of KiSAO.

Zhukova et al.

Zhukova et al. BMC Research Notes 2012 5:520   doi:10.1186/1756-0500-5-520

Open Data