Table 1 Taxonomy level querying methods implemented in libKiSAO

 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