Index

A C F G I L M O P R S T
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

addPrefix(String) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Add a prefix mapping as a single string "foo: http://example.com#".

addPrefix(String, String) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Add a prefix mapping to the current JSON-LD context, as a prefix string and target string.

C

contains(String) - Method in class org.geneontology.obographs.owlapi.SynonymVocabulary

createIRI(String) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Given a term string, use the current prefixes to create an IRI.

F

FromOwl - Class in org.geneontology.obographs.owlapi

Implements OWL to OG translation ===

FromOwl() - Constructor for class org.geneontology.obographs.owlapi.FromOwl

G

generateGraph(OWLOntology) - Method in class org.geneontology.obographs.owlapi.FromOwl

generateGraphDocument(OWLOntology) - Method in class org.geneontology.obographs.owlapi.FromOwl

get(String) - Method in class org.geneontology.obographs.owlapi.SynonymVocabulary

getContext() - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Get a copy of the current context.

getContextString() - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Return the current prefixes as a JSON-LD string.

getDefaultContext() - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Get a copy of the default context.

getIriToScopeMap() - Method in class org.geneontology.obographs.owlapi.SynonymVocabulary

getKey() - Method in class org.geneontology.obographs.owlapi.OboGraphJsonDocumentFormat

getPrefixes() - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Get a copy of the current prefix map.

getPrefixManager() - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Get a prefix manager with the current prefixes.

guessCatalogFile(File) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Try to guess the location of the catalog.xml file.

I

INVERSE_OF - Static variable in class org.geneontology.obographs.owlapi.FromOwl

isDefinitionProperty(IRI) - Method in class org.geneontology.obographs.owlapi.FromOwl

isHasSynonymTypeProperty(IRI) - Method in class org.geneontology.obographs.owlapi.FromOwl

isHasXrefProperty(IRI) - Method in class org.geneontology.obographs.owlapi.FromOwl

isInSubsetProperty(IRI) - Method in class org.geneontology.obographs.owlapi.FromOwl

isOboInOwlIdProperty(IRI) - Method in class org.geneontology.obographs.owlapi.FromOwl

L

loadOWL(File) - Method in class org.geneontology.obographs.owlapi.RunEngine

loadOWL(IRI) - Method in class org.geneontology.obographs.owlapi.RunEngine

M

main(String...) - Static method in class org.geneontology.obographs.owlapi.RunEngine

makePrefixManager(Map<String, String>) - Static method in class org.geneontology.obographs.owlapi.PrefixHelper

Make an OWLAPI DefaultPrefixManager from a map of prefixes.

O

OboGraphJsonDocumentFormat - Class in org.geneontology.obographs.owlapi

OboGraphJsonDocumentFormat() - Constructor for class org.geneontology.obographs.owlapi.OboGraphJsonDocumentFormat

org.geneontology.obographs.owlapi - package org.geneontology.obographs.owlapi

Mapping OGs to OWL and back Currently only one direction implemented
See Spec

P

parseContext(String) - Static method in class org.geneontology.obographs.owlapi.PrefixHelper

Load a map of prefixes from the "@context" of a JSON-LD string.

PrefixHelper - Class in org.geneontology.obographs.owlapi

Provides convenience methods for working with JSON LD contexts and prefixes Taken from ROBOT

PrefixHelper() - Constructor for class org.geneontology.obographs.owlapi.PrefixHelper

Create a new IOHelper with the default prefixes.

PrefixHelper(boolean) - Constructor for class org.geneontology.obographs.owlapi.PrefixHelper

Create a new IOHelper with or without the default prefixes.

PrefixHelper(File) - Constructor for class org.geneontology.obographs.owlapi.PrefixHelper

Create a new IOHelper with prefixes from a file.

PrefixHelper(String) - Constructor for class org.geneontology.obographs.owlapi.PrefixHelper

Create a new IOHelper with prefixes from a file path.

PrefixHelper(Map<String, Object>) - Constructor for class org.geneontology.obographs.owlapi.PrefixHelper

Create a new IOHelper with the specified prefixes.

R

run() - Method in class org.geneontology.obographs.owlapi.RunEngine

RunEngine - Class in org.geneontology.obographs.owlapi

RunEngine() - Constructor for class org.geneontology.obographs.owlapi.RunEngine

S

saveContext(File) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Write the current context as a JSON-LD file.

saveContext(String) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Write the current context as a JSON-LD file.

set(String, AbstractSynonymPropertyValue.SCOPES) - Method in class org.geneontology.obographs.owlapi.SynonymVocabulary

setContext() - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Set an empty context.

setContext(Context) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Set the current JSON-LD context to the given context.

setContext(String) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Set the current JSON-LD context to the given context.

setContext(Map<String, Object>) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Set the current JSON-LD context to the given map.

setDefaults() - Method in class org.geneontology.obographs.owlapi.SynonymVocabulary

setPrefixes(Map<String, Object>) - Method in class org.geneontology.obographs.owlapi.PrefixHelper

Set the current prefix map.

SUBCLASS_OF - Static variable in class org.geneontology.obographs.owlapi.FromOwl

SUBPROPERTY_OF - Static variable in class org.geneontology.obographs.owlapi.FromOwl

SYNONYM_TYPE - Static variable in class org.geneontology.obographs.owlapi.SynonymVocabulary

SynonymVocabulary - Class in org.geneontology.obographs.owlapi

SynonymVocabulary() - Constructor for class org.geneontology.obographs.owlapi.SynonymVocabulary

T

TYPE - Static variable in class org.geneontology.obographs.owlapi.FromOwl

A C F G I L M O P R S T
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form