Table 2 Mappings between OntoCAT's interface and the underlying resources respective functionalities.

QueryServiceLocator().getOntologyQuery()

http://rest.bioontology.org/bioportal/

OWLOntology

ontology methods

getOntologies()

.getOntologyNames()

Δ

eager fetching with .getOntology()

./ontologies

?email=email_address

.getOntologyID()

Δ

getOntology()

.getOntologyNames()

.getOntologyLoadDate()

.getVersion()

./virtual/ontology/ontologyAccession ?email=email_address

getOntologies().get(0)

term methods

searchAll()

.getPrefixedTermsByName(query, false)

Δ

./search/

?query=url-encoded_query

&sexactmatch=[1/0]

&includeproperties=[1/0]

&maxnumhits = 10000000

&email=email_address

.getClassesInSignature()

OWLClass.getAnnotations()

searchOntology()

depending on the search options a combination of:

1) .getTermsByExactName(query, ontolo-gyAccession)

2) .getTermsByName(query, ontologyAcces-sion, false)

3) .getTermsByAnnotationData(ontologyAccession, annotationType, query, fromDblValue, toDblValue), .getAnnotationStringValue()

Δ

./search/

?query = url-encoded query

&isexactmatch=[1/0]

&includeproperties=[1/0]

&maxnumhits = 10000000

&email=email_address

&ontologyids=ontologyAccession

searchAll()

there is only one ontology

getTerm()

Δ

.getTermById(termAccession, ontologyAccession)

./virtual/ontology/ontologyAccession

?conceptid=url-encoded termAccession

&email=email_address

.getClassesInSignature()

Δ

if termAccession was not found:

./search/?query=url-encoded _termAccession

&isexactmatch = 1

&includeproperties = 1 &maxnumhits = 10000000

&email=email_address

&ontologyids=ontologyAccession

getAllTerms()

no native support, slow

getRootTerms()

getAllChildren()

./virtual/ontology/ontologyAccession/all ?pagesize = 300

&pagenum=pagenum

&email=email_address

.getClassesInSignature()

Δ

getAnnotations()

.getTermMetadata(termAccession, ontologyAccession)

getTerm()

OWLClass.getAnnotations() OWLAnnotation.getProperty().getIRI().toURI()

OWLAnnotation.getValue().getLiteral()

getSynonyms()

getAnnotations()

Δ

getTerm()

Δ

getAnnotations()

Δ

getDefinitions()

getAnnotations()

Δ

getTerm()

Δ

getAnnotations()

Δ

hierarchy methods

getRootTerms()

.getRootTerms(ontologyAccession)

eager fetching with getTerm()

./virtual/ontology/ontologyAccession

?conceptid = root &email=email_address

getChildren()

.getClassesInSignature()

OWLClass.getSuperClasses()

getAnnotations()

getTermPath()

non-recursive traversal of the path to root with getParents()

Δ

./virtual/rootpath/ontologyAccession/url-encoded termAccession &email=email_address

Δ

non-recursive traversal of the path to root with getParents()

Δ

eager fetching with getTerm()

getChildren()

.getTermChildren(termAccession, ontologyAccession, 1, null)

getTerm()

Δ

OWLClass.getSubClasses()

getParents()

.getTermParents(termAccession, ontologyAccession)

getTerm()

Δ

OWLClass.getSuperClasses()

getAllChildren()

getChildren() called non-recursively

getAllParents()

getParents() called non-recursively

getRelations()

.getTermXrefs(termAccession, ontology-Accession).

getTermRelations(termAccession, ontolo-gyAccession)

not implemented in OntoCAT

not implemented in OntoCAT