- id - Variable in class org.obolibrary.oboformat.model.Frame
-
The id.
- ID2IRI(String) - Static method in enum org.coode.owlapi.obo12.parser.OBOVocabulary
-
Converts OBO Ids to IRIs.
- ID2IRI(String, IDSpaceManager) - Static method in enum org.coode.owlapi.obo12.parser.OBOVocabulary
-
Converts OBO Ids to IRIs.
- idSpace - Variable in class org.obolibrary.oboformat.parser.XrefExpander.Rule
-
id space
- idSpaceMap - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl
-
The id space map.
- idSpaceMap - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo
-
- IdTranslator - Class in org.obolibrary.obo2owl
-
This class will eventually replace the id to uri translation in Owl2Obo and
OboO2Owl
It is currently in-progress.
- IdTranslator() - Constructor for class org.obolibrary.obo2owl.IdTranslator
-
- importedOBODocs - Variable in class org.obolibrary.oboformat.model.OBODoc
-
The imported obo docs.
- IN_COMMENT - Static variable in interface org.coode.owlapi.obo12.parser.OBOParserConstants
-
Lexical state.
- IN_QUOTED_STRING - Static variable in interface org.coode.owlapi.obo12.parser.OBOParserConstants
-
Lexical state.
- IN_STANZA_HEADER - Static variable in interface org.coode.owlapi.obo12.parser.OBOParserConstants
-
Lexical state.
- IN_TAG_VALUE - Static variable in interface org.coode.owlapi.obo12.parser.OBOParserConstants
-
Lexical state.
- IN_TAG_VALUE_PAIR - Static variable in interface org.coode.owlapi.obo12.parser.OBOParserConstants
-
Lexical state.
- indexOf(char) - Method in class org.obolibrary.oboformat.parser.OBOFormatParser.MyStream
-
- init(OWLOntologyManager) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl
-
Init
- init() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo
-
- init() - Method in class org.obolibrary.oboformat.model.Frame
-
Init clauses.
- initAnnotationPropertyMap() - Static method in class org.obolibrary.obo2owl.OWLAPIObo2Owl
-
Table 5.8 Translation of Annotation Vocabulary.
- initAnnotationPropertyMap() - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo
-
- inputOntology - Variable in class org.obolibrary.macro.MacroExpansionGCIVisitor
-
- instanceFrameMap - Variable in class org.obolibrary.oboformat.model.OBODoc
-
The instance frame map.
- InvalidXrefMapException - Exception in org.obolibrary.oboformat.parser
-
The Class InvalidXrefMapException.
- InvalidXrefMapException() - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException
-
Instantiates a new invalid xref map exception.
- InvalidXrefMapException(String, Throwable) - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException
-
Instantiates a new invalid xref map exception.
- InvalidXrefMapException(String) - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException
-
Instantiates a new invalid xref map exception.
- InvalidXrefMapException(Throwable) - Constructor for exception org.obolibrary.oboformat.parser.InvalidXrefMapException
-
Instantiates a new invalid xref map exception.
- IRI2ID(IRI) - Static method in enum org.coode.owlapi.obo12.parser.OBOVocabulary
-
- IRI_IAO_0000227 - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants
-
IRI for the 'terms merged' individual
- IRI_IAO_0000231 - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants
-
IRI for the 'has obsolescence reason' annotation property
- IRI_PROP_ISREVERSIBLEPROPERTYCHAIN - Static variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl
-
The Constant IRI_PROP_isReversiblePropertyChain.
- iriShortFormProvider - Variable in class org.obolibrary.macro.ManchesterSyntaxTool
-
- IsaExpansion() - Constructor for class org.obolibrary.oboformat.parser.XrefExpander.IsaExpansion
-
- isCheckStructure() - Method in class org.obolibrary.oboformat.writer.OBOFormatWriter
-
Checks if is check structure.
- isDiscardUntranslatable() - Method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo
-
- isOBOIRI(IRI) - Static method in enum org.coode.owlapi.obo12.parser.OBOVocabulary
-
- isTreatXrefsAsEquivalent(String) - Static method in class org.obolibrary.oboformat.model.OBODoc
-
- isURI(String) - Static method in class org.obolibrary.obo2owl.IdTranslator
-
True if id starts with a standard URI prefix (http, ftp, https) followed
by a ":".
- OBO12DocumentFormat - Class in org.coode.owlapi.obo12.parser
-
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007
- OBO12DocumentFormat() - Constructor for class org.coode.owlapi.obo12.parser.OBO12DocumentFormat
-
- OBO12ParserFactory - Class in org.coode.owlapi.obo12.parser
-
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007
- OBO12ParserFactory() - Constructor for class org.coode.owlapi.obo12.parser.OBO12ParserFactory
-
- Obo2OWLConstants - Class in org.obolibrary.obo2owl
-
- Obo2OWLConstants() - Constructor for class org.obolibrary.obo2owl.Obo2OWLConstants
-
- Obo2OWLConstants.Obo2OWLVocabulary - Enum in org.obolibrary.obo2owl
-
obo to owl vocabulary
- OBO_ID_PATTERN - Static variable in enum org.coode.owlapi.obo12.parser.OBOVocabulary
-
The pattern for OBO IDs.
- OBO_IRI_BASE - Static variable in enum org.coode.owlapi.obo12.parser.OBOVocabulary
-
- OBO_IRI_PATTERN - Static variable in enum org.coode.owlapi.obo12.parser.OBOVocabulary
-
- obodoc - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl
-
The obodoc.
- obodoc - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo
-
- OBODoc - Class in org.obolibrary.oboformat.model
-
An OBODoc is a container for a header frame and zero or more entity frames.
- OBODoc() - Constructor for class org.obolibrary.oboformat.model.OBODoc
-
default constructor.
- OBODocDiffer - Class in org.obolibrary.oboformat.diff
-
Diffs two OBO Documents.
- OBODocDiffer() - Constructor for class org.obolibrary.oboformat.diff.OBODocDiffer
-
- OBODocNameProvider(OBODoc) - Constructor for class org.obolibrary.oboformat.writer.OBOFormatWriter.OBODocNameProvider
-
Instantiates a new OBO doc name provider.
- OBOFormatConstants - Class in org.obolibrary.oboformat.parser
-
oboformat constants
- OBOFormatConstants() - Constructor for class org.obolibrary.oboformat.parser.OBOFormatConstants
-
- OBOFormatConstants.OboFormatTag - Enum in org.obolibrary.oboformat.parser
-
oboformat tags
- OBOFormatDanglingReferenceException - Exception in org.obolibrary.oboformat.parser
-
The Class OBOFormatDanglingReferenceException.
- OBOFormatDanglingReferenceException() - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException
-
Instantiates a new oBO format dangling reference exception.
- OBOFormatDanglingReferenceException(String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException
-
Instantiates a new oBO format dangling reference exception.
- OBOFormatDanglingReferenceException(Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException
-
Instantiates a new oBO format dangling reference exception.
- OBOFormatDanglingReferenceException(String, Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatDanglingReferenceException
-
Instantiates a new oBO format dangling reference exception.
- OBOFormatException - Exception in org.obolibrary.oboformat.parser
-
The Class OBOFormatException.
- OBOFormatException() - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException
-
Instantiates a new oBO format exception.
- OBOFormatException(String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException
-
Instantiates a new oBO format exception.
- OBOFormatException(Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException
-
Instantiates a new oBO format exception.
- OBOFormatException(String, Throwable) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatException
-
Instantiates a new oBO format exception.
- OBOFormatOWLAPIParser - Class in org.semanticweb.owlapi.oboformat
-
oboformat parser
- OBOFormatOWLAPIParser() - Constructor for class org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser
-
- OBOFormatOWLAPIParserFactory - Class in org.semanticweb.owlapi.oboformat
-
- OBOFormatOWLAPIParserFactory() - Constructor for class org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParserFactory
-
- OBOFormatParser - Class in org.obolibrary.oboformat.parser
-
implements the OBO Format 1.4 specification.
- OBOFormatParser() - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser
-
- OBOFormatParser(OBOFormatParser.MyStream) - Constructor for class org.obolibrary.oboformat.parser.OBOFormatParser
-
- OBOFormatParser.MyStream - Class in org.obolibrary.oboformat.parser
-
- OBOFormatParserException - Exception in org.obolibrary.oboformat.parser
-
The Class OBOFormatParserException.
- OBOFormatParserException(String, Throwable, int, String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatParserException
-
- OBOFormatParserException(String, int, String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatParserException
-
- OBOFormatParserException(Throwable, int, String) - Constructor for exception org.obolibrary.oboformat.parser.OBOFormatParserException
-
- OBOFormatRenderer - Class in org.semanticweb.owlapi.oboformat
-
renderer for obo
- OBOFormatRenderer() - Constructor for class org.semanticweb.owlapi.oboformat.OBOFormatRenderer
-
- OBOFormatStorer - Class in org.semanticweb.owlapi.oboformat
-
- OBOFormatStorer() - Constructor for class org.semanticweb.owlapi.oboformat.OBOFormatStorer
-
- OBOFormatWriter - Class in org.obolibrary.oboformat.writer
-
The Class OBOFormatWriter.
- OBOFormatWriter() - Constructor for class org.obolibrary.oboformat.writer.OBOFormatWriter
-
- OBOFormatWriter.NameProvider - Interface in org.obolibrary.oboformat.writer
-
Provide names for given OBO identifiers.
- OBOFormatWriter.OBODocNameProvider - Class in org.obolibrary.oboformat.writer
-
- OBOFormatWriter.OWLOntologyNameProvider - Class in org.obolibrary.oboformat.writer
-
Alternative implementation to lookup labels in an OWLOntology.
This implementation might be a bit slower as it involves additional id
conversion back into OWL.
- oboIdToIRI(String) - Method in class org.obolibrary.obo2owl.OWLAPIObo2Owl
-
Obo id to iri.
- OboInOwlCardinalityTools - Class in org.obolibrary.obo2owl
-
Tools for checking and fixing cardinality constrains for OBO ontologies in
OWL.
- OboInOwlCardinalityTools.AnnotationCardinalityConfictHandler - Interface in org.obolibrary.obo2owl
-
Functor for resolving conflicts for an annotation property and its
cardinality constraint.
- OboInOwlCardinalityTools.AnnotationCardinalityException - Exception in org.obolibrary.obo2owl
-
Exception indication a non-resolvable conflict for an annotation property
and its cardinality constraint.
- OboInOwlCardinalityTools.AnnotationCardinalityReporter - Interface in org.obolibrary.obo2owl
-
Functor for reporting conflicts for an annotation property and its
cardinality constraint.
- OBOParserConstants - Interface in org.coode.owlapi.obo12.parser
-
Token literal values and constants.
- OBOParserHandler - Interface in org.coode.owlapi.obo12.parser
-
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007
- OBOPrefix - Enum in org.coode.owlapi.obo12.parser
-
Author: Matthew Horridge
Stanford University
Bio-Medical Informatics Research Group
Date: 18/04/2012
- OBOVocabulary - Enum in org.coode.owlapi.obo12.parser
-
Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007
- OIO_ISEXPANSION - Variable in class org.obolibrary.macro.AbstractMacroExpansionVisitor
-
- OIOVOCAB_IRI_PREFIX - Static variable in class org.obolibrary.obo2owl.Obo2OWLConstants
-
OIO vocabulary prefix
- ONTOLOGY_URI_BASE - Static variable in enum org.coode.owlapi.obo12.parser.OBOVocabulary
-
- ontologyId - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo
-
- OPEN_SQUARE_BRACKET - Static variable in interface org.coode.owlapi.obo12.parser.OBOParserConstants
-
RegularExpression Id.
- org.coode.owlapi.obo12.parser - package org.coode.owlapi.obo12.parser
-
- org.obolibrary.macro - package org.obolibrary.macro
-
- org.obolibrary.obo2owl - package org.obolibrary.obo2owl
-
- org.obolibrary.oboformat.diff - package org.obolibrary.oboformat.diff
-
- org.obolibrary.oboformat.model - package org.obolibrary.oboformat.model
-
- org.obolibrary.oboformat.parser - package org.obolibrary.oboformat.parser
-
- org.obolibrary.oboformat.writer - package org.obolibrary.oboformat.writer
-
- org.obolibrary.owl - package org.obolibrary.owl
-
- org.semanticweb.owlapi.formats - package org.semanticweb.owlapi.formats
-
- org.semanticweb.owlapi.oboformat - package org.semanticweb.owlapi.oboformat
-
- outputManager - Variable in class org.obolibrary.macro.MacroExpansionGCIVisitor
-
- outputOntology - Variable in class org.obolibrary.macro.MacroExpansionGCIVisitor
-
- OWLAPIObo2Owl - Class in org.obolibrary.obo2owl
-
The Class OWLAPIObo2Owl.
- OWLAPIObo2Owl(OWLOntologyManager) - Constructor for class org.obolibrary.obo2owl.OWLAPIObo2Owl
-
Instantiates a new oWLAPI obo2 owl.
- OWLAPIOwl2Obo - Class in org.obolibrary.obo2owl
-
owlapi version of Owl2Obo
- OWLAPIOwl2Obo(OWLOntologyManager) - Constructor for class org.obolibrary.obo2owl.OWLAPIOwl2Obo
-
- OWLAPIOwl2Obo.UntranslatableAxiomException - Exception in org.obolibrary.obo2owl
-
untranslatable axiom exception
- owlObjectToTag(OWLObject) - Static method in class org.obolibrary.obo2owl.OWLAPIOwl2Obo
-
- owlOntology - Variable in class org.obolibrary.obo2owl.OWLAPIObo2Owl
-
The owl ontology.
- owlOntology - Variable in class org.obolibrary.obo2owl.OWLAPIOwl2Obo
-
- OWLOntologyNameProvider(OWLOntology, String) - Constructor for class org.obolibrary.oboformat.writer.OBOFormatWriter.OWLOntologyNameProvider
-
- OwlStringException(Throwable) - Constructor for exception org.obolibrary.obo2owl.OwlStringTools.OwlStringException
-
- OwlStringTools - Class in org.obolibrary.obo2owl
-
Tools to read and write a set of owl axioms to/from a string.
- OwlStringTools() - Constructor for class org.obolibrary.obo2owl.OwlStringTools
-
- OwlStringTools.OwlStringException - Exception in org.obolibrary.obo2owl
-
Exception indicating an un-recoverable error during the handling of axiom
strings.