A B C D E F G H I L M N O P Q R S T U V W X
All Classes All Packages

A

ABOUT_ORGANISM_LABEL - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

ABOUT_ORGANISM_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

ABOUT_ORGANISM1 - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

ACCESS_URL - Static variable in class org.bridgedb.rdf.constants.DCatConstants

ACCESS_URL_URI - Static variable in class org.bridgedb.rdf.constants.DCatConstants

ACCRUAL_PERIODICITY - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

ACCRUAL_PERIODICITY_URI - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

add(RepositoryConnection) - Method in class org.bridgedb.rdf.UriPattern

add(RepositoryConnection, Organism) - Static method in class org.bridgedb.rdf.OrganismRdf

addAll(RepositoryConnection) - Static method in class org.bridgedb.rdf.OrganismRdf

addAll(RepositoryConnection) - Static method in class org.bridgedb.rdf.UriPattern

addComments(RDFHandler) - Method in class org.bridgedb.rdf.OrganismRdf

addXrefPrefix(String, String) - Static method in class org.bridgedb.rdf.pairs.RdfBasedCodeMapper

ALTERNATIVE - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

ALTERNATIVE_URI - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

ANY_URI - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

asCodeMapperResource(DataSource) - Static method in class org.bridgedb.rdf.BridgeDBRdfHandler

asResource(DataSource) - Static method in class org.bridgedb.rdf.BridgeDBRdfHandler

ASSERTION_METHOD - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

assumeUnknownsAreBio() - Static method in enum org.bridgedb.rdf.DataSourceMetaDataProvidor

AUTHORED_BY - Static variable in class org.bridgedb.rdf.constants.PavConstants

AUTHORED_ON - Static variable in class org.bridgedb.rdf.constants.PavConstants

B

BASE_64_BINARY - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

BIO - org.bridgedb.rdf.DataSourceMetaDataProvidor

BOOLEAN - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

BridgeDBConstants - Class in org.bridgedb.rdf.constants

BridgeDBConstants() - Constructor for class org.bridgedb.rdf.constants.BridgeDBConstants

BridgeDBRdfHandler - Class in org.bridgedb.rdf

BridgeDbRdfTools - Class in org.bridgedb.rdf

BridgeDbRdfTools() - Constructor for class org.bridgedb.rdf.BridgeDbRdfTools

BROAD_MATCH - Static variable in class org.bridgedb.rdf.constants.SkosConstants

BROADER - Static variable in class org.bridgedb.rdf.constants.SkosConstants

byCode(String) - Static method in class org.bridgedb.rdf.UriPattern

byCodeAndType(String, UriPatternType) - Static method in class org.bridgedb.rdf.UriPattern

byPattern(String) - Static method in class org.bridgedb.rdf.UriPattern

BYTE_SIZE - Static variable in class org.bridgedb.rdf.constants.DCatConstants

BYTE_SIZE_URI - Static variable in class org.bridgedb.rdf.constants.DCatConstants

C

checkRegexPatterns() - Static method in class org.bridgedb.rdf.UriPattern

CHEMICAL_ENTITY - Static variable in class org.bridgedb.rdf.constants.ChemInf

ChemInf - Class in org.bridgedb.rdf.constants

ChemInf() - Constructor for class org.bridgedb.rdf.constants.ChemInf

CITE_AS_AUTHORITY - Static variable in class org.bridgedb.rdf.constants.CitoConstants

CITE_AS_AUTHORITY_URI - Static variable in class org.bridgedb.rdf.constants.CitoConstants

CitoConstants - Class in org.bridgedb.rdf.constants

CitoConstants() - Constructor for class org.bridgedb.rdf.constants.CitoConstants

CLOSE_MATCH - Static variable in class org.bridgedb.rdf.constants.SkosConstants

CODE_MAPPER_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

CODE_MAPPER1 - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

CODE_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

codeMapperPattern - org.bridgedb.rdf.UriPatternType

compare(String, String) - Static method in enum org.bridgedb.rdf.DataSourceMetaDataProvidor

compareTo(UriPattern) - Method in class org.bridgedb.rdf.UriPattern

CONFIG_FILE_NAME - Static variable in class org.bridgedb.rdf.BridgeDBRdfHandler

convert(File, File) - Static method in class org.bridgedb.rdf.create.FormatConvertor

convert(Collection<File>, File) - Static method in class org.bridgedb.rdf.create.LinkSetCombiner

count(File) - Static method in class org.bridgedb.rdf.create.LinkSetCombiner

CREATED_BY - Static variable in class org.bridgedb.rdf.constants.PavConstants

CREATED_ON - Static variable in class org.bridgedb.rdf.constants.PavConstants

CREATED_WITH - Static variable in class org.bridgedb.rdf.constants.PavConstants

CreateRdf - Class in org.bridgedb.rdf

CreateRdf() - Constructor for class org.bridgedb.rdf.CreateRdf

D

DATA_DUMP - Static variable in class org.bridgedb.rdf.constants.VoidConstants

DATA_SOURCE_LABEL - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

DATA_SOURCE_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

DATA_SOURCE1 - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

DATABASE_CROSS_REFERENCE - Static variable in class org.bridgedb.rdf.constants.ChemInf

DATASET - Static variable in class org.bridgedb.rdf.constants.VoidConstants

DATASET_DESCRIPTION - Static variable in class org.bridgedb.rdf.constants.VoidConstants

DataSourceMetaDataProvidor - Enum in org.bridgedb.rdf

dataSourceUriPattern - org.bridgedb.rdf.UriPatternType

DATE - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

DATE_TIME - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

DCatConstants - Class in org.bridgedb.rdf.constants

DCatConstants() - Constructor for class org.bridgedb.rdf.constants.DCatConstants

DCTermsConstants - Class in org.bridgedb.rdf.constants

DCTermsConstants() - Constructor for class org.bridgedb.rdf.constants.DCTermsConstants

DECIMAL - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

DEFAULT_BASE_URI - Static variable in class org.bridgedb.rdf.create.FormatConvertor

DEFAULT_BASE_URI - Static variable in class org.bridgedb.rdf.create.LinkSetCombiner

DEFAULT_BASE_URI - Static variable in class org.bridgedb.rdf.RdfBase

DEFAULT_FILE_FORMAT - Static variable in class org.bridgedb.rdf.RdfBase

DEFAULT_FORMAT - Static variable in class org.bridgedb.rdf.BridgeDbRdfTools

DERIVED_BY - Static variable in class org.bridgedb.rdf.constants.PavConstants

DERIVED_FROM - Static variable in class org.bridgedb.rdf.constants.PavConstants

DERIVED_ON - Static variable in class org.bridgedb.rdf.constants.PavConstants

DESCRIPTION - Static variable in class org.bridgedb.rdf.constants.DCatConstants

DESCRIPTION - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

DESCRIPTION_URI - Static variable in class org.bridgedb.rdf.constants.DCatConstants

DESCRIPTION_URI - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

DISTRIBUTION - Static variable in class org.bridgedb.rdf.constants.DCatConstants

DISTRIBUTION_URI - Static variable in class org.bridgedb.rdf.constants.DCatConstants

DOUBLE - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

DOWNLOAD - Static variable in class org.bridgedb.rdf.constants.DCatConstants

DOWNLOAD_URI - Static variable in class org.bridgedb.rdf.constants.DCatConstants

DulConstants - Class in org.bridgedb.rdf.constants

DulConstants() - Constructor for class org.bridgedb.rdf.constants.DulConstants

dulns - Static variable in class org.bridgedb.rdf.constants.DulConstants

DURATION - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

E

EQUIVALENT_CLASS - Static variable in class org.bridgedb.rdf.constants.OWLConstants

EXACT_MATCH - Static variable in class org.bridgedb.rdf.constants.SkosConstants

EXAMPLE_RESOURCE - Static variable in class org.bridgedb.rdf.constants.VoidConstants

existingByPattern(String) - Static method in class org.bridgedb.rdf.UriPattern

existingByPrefixAndPostfix(String, String) - Static method in class org.bridgedb.rdf.UriPattern

EXPRESSES - Static variable in class org.bridgedb.rdf.constants.DulConstants

F

factory() - Static method in class org.bridgedb.rdf.OrganismRdf

FLOAT - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

FoafConstants - Class in org.bridgedb.rdf.constants

FoafConstants() - Constructor for class org.bridgedb.rdf.constants.FoafConstants

FormatConvertor - Class in org.bridgedb.rdf.create

FormatConvertor() - Constructor for class org.bridgedb.rdf.create.FormatConvertor

FULFILLS_LENS - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

FULL_NAME_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

fullInit() - Static method in class org.bridgedb.rdf.identifiers.org.IdentifersOrgReader

FUNCTIONAL_RNA_CODING_GENE - Static variable in class org.bridgedb.rdf.constants.ChemInf

G

G_DAY - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

G_MONTH - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

G_MONTH_DAY - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

G_YEAR - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

G_YEAR_MONTH - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

GENE - Static variable in class org.bridgedb.rdf.constants.ChemInf

getAvaiableFormats() - Static method in class org.bridgedb.rdf.BridgeDbRdfTools

getAvaiableWriters() - Static method in class org.bridgedb.rdf.BridgeDbRdfTools

getIdFromUri(String) - Method in class org.bridgedb.rdf.UriPattern

getPossibleSingletonString(RepositoryConnection, Resource, URI) - Static method in class org.bridgedb.rdf.RdfBase

getPostfix() - Method in class org.bridgedb.rdf.UriPattern

getPrefix() - Method in class org.bridgedb.rdf.UriPattern

getProvider(String) - Static method in enum org.bridgedb.rdf.DataSourceMetaDataProvidor

getRdfLabel(Organism) - Static method in class org.bridgedb.rdf.OrganismRdf

getResourceId() - Method in class org.bridgedb.rdf.UriPattern

getResourceId(Organism) - Static method in class org.bridgedb.rdf.OrganismRdf

getSingletonString(RepositoryConnection, Resource, URI) - Static method in class org.bridgedb.rdf.RdfBase

getSysCodes() - Method in class org.bridgedb.rdf.UriPattern

getType() - Method in class org.bridgedb.rdf.UriPattern

getUri(String) - Method in class org.bridgedb.rdf.UriPattern

getUriPattern() - Method in class org.bridgedb.rdf.UriPattern

getUriPatterns() - Static method in class org.bridgedb.rdf.UriPattern

getXrefPrefix(String) - Static method in class org.bridgedb.rdf.pairs.RdfBasedCodeMapper

H

HAS_DATA_SOURCE - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_DATA_TYPE_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_FUNCTIONAL_PARENT - Static variable in class org.bridgedb.rdf.constants.OboConstants

HAS_IDENTIFERS_ORG_INFO_PATTERN_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_IDENTIFERS_ORG_PATTERN_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_PART - Static variable in class org.bridgedb.rdf.constants.OboConstants

HAS_POSTFIX_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_PREFIX_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_PRIMARY_URI_PATTERN_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_REGEX_PATTERN_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_REGEX_URI_PATTERN_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_REGEX_URL_PATTERN_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

HAS_URI_PATTERN_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

hasChemAxonCanonicalisedTautomer - Static variable in class org.bridgedb.rdf.constants.ChemInf

hasComponentWithUnchargedCounterpart - Static variable in class org.bridgedb.rdf.constants.ChemInf

hasIsotopicallyUnspecifiedParent - Static variable in class org.bridgedb.rdf.constants.ChemInf

hasMajorTautomerAtpH7point4 - Static variable in class org.bridgedb.rdf.constants.ChemInf

hasOPSNormalizedCounterpart - Static variable in class org.bridgedb.rdf.constants.ChemInf

hasPostfix() - Method in class org.bridgedb.rdf.UriPattern

hasStereoundefinedParent - Static variable in class org.bridgedb.rdf.constants.ChemInf

hasUnchargedCounterpart - Static variable in class org.bridgedb.rdf.constants.ChemInf

HEX_BINARY - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

I

ID_EXAMPLE_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

IdenitifiersOrgConstants - Class in org.bridgedb.rdf.constants

IdenitifiersOrgConstants() - Constructor for class org.bridgedb.rdf.constants.IdenitifiersOrgConstants

IdentifersOrgReader - Class in org.bridgedb.rdf.identifiers.org

IdentifersOrgReader() - Constructor for class org.bridgedb.rdf.identifiers.org.IdentifersOrgReader

identifiersOrgPatternInfo - org.bridgedb.rdf.UriPatternType

identifiersOrgPatternSimple - org.bridgedb.rdf.UriPatternType

IMPORTED_BY - Static variable in class org.bridgedb.rdf.constants.PavConstants

IMPORTED_FROM - Static variable in class org.bridgedb.rdf.constants.PavConstants

IMPORTED_ON - Static variable in class org.bridgedb.rdf.constants.PavConstants

IN_DATASET - Static variable in class org.bridgedb.rdf.constants.VoidConstants

INCHI_KEY - Static variable in class org.bridgedb.rdf.constants.ChemInf

init() - Static method in class org.bridgedb.rdf.BridgeDBRdfHandler

init() - Static method in class org.bridgedb.rdf.identifiers.org.IdentifersOrgReader

INTEGER - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

IS_DEPRICATED_BY_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

IS_SYMETRIC - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

IS_TAUTOMER_OF - Static variable in class org.bridgedb.rdf.constants.OboConstants

IS_URI_PATTERN_OF - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

isChemAxonCanonicalisedTtautomerOf - Static variable in class org.bridgedb.rdf.constants.ChemInf

isComponentWithUnchargedCounterpartOf - Static variable in class org.bridgedb.rdf.constants.ChemInf

isCounterpartWithDifferentChargeOf - Static variable in class org.bridgedb.rdf.constants.ChemInf

isIsotopicallyUnspecifiedParentOf - Static variable in class org.bridgedb.rdf.constants.ChemInf

isIsotopologueOf - Static variable in class org.bridgedb.rdf.constants.ChemInf

isOPSNormalizedCounterpartOf - Static variable in class org.bridgedb.rdf.constants.ChemInf

isStereoisomerOf - Static variable in class org.bridgedb.rdf.constants.ChemInf

isStereoundefinedParentOf - Static variable in class org.bridgedb.rdf.constants.ChemInf

ISSUED - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

ISSUED_URI - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

isUnchargedCounterpartOf - Static variable in class org.bridgedb.rdf.constants.ChemInf

L

LANDING_PAGE - Static variable in class org.bridgedb.rdf.constants.DCatConstants

LANDING_PAGE_URI - Static variable in class org.bridgedb.rdf.constants.DCatConstants

LAST_REFERSHED_ON - Static variable in class org.bridgedb.rdf.constants.PavConstants

LATIN_NAME_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

LENS_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

LICENSE - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

LICENSE_URI - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

LINK_PREDICATE - Static variable in class org.bridgedb.rdf.constants.VoidConstants

LINKSET - Static variable in class org.bridgedb.rdf.constants.VoidConstants

LINKSET_JUSTIFICATION - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

LinkSetCombiner - Class in org.bridgedb.rdf.create

LinkSetCombiner() - Constructor for class org.bridgedb.rdf.create.LinkSetCombiner

LOCAL_MIRAM_REGISTRY - Static variable in class org.bridgedb.rdf.identifiers.org.IdentifersOrgReader

M

main(String[]) - Static method in class org.bridgedb.rdf.BridgeDBRdfHandler

main(String[]) - Static method in class org.bridgedb.rdf.BridgeDbRdfTools

main(String[]) - Static method in class org.bridgedb.rdf.create.FormatConvertor

main(String[]) - Static method in class org.bridgedb.rdf.create.LinkSetCombiner

main(String[]) - Static method in class org.bridgedb.rdf.CreateRdf

main(String[]) - Static method in class org.bridgedb.rdf.identifiers.org.IdentifersOrgReader

MAIN_URL_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

mainUrlPattern - org.bridgedb.rdf.UriPatternType

MAPPING_RELATION - Static variable in class org.bridgedb.rdf.constants.SkosConstants

MEDIA_TYPE - Static variable in class org.bridgedb.rdf.constants.DCatConstants

MEDIA_TYPE_URI - Static variable in class org.bridgedb.rdf.constants.DCatConstants

MIRAM_REGISTRY_URI - Static variable in class org.bridgedb.rdf.identifiers.org.IdentifersOrgReader

MIRIAM_ONLY - org.bridgedb.rdf.DataSourceMetaDataProvidor

MODIFIED_ON - Static variable in class org.bridgedb.rdf.constants.PavConstants

N

NAMESPACE - Static variable in class org.bridgedb.rdf.constants.IdenitifiersOrgConstants

NAMESPACE_URI - Static variable in class org.bridgedb.rdf.constants.IdenitifiersOrgConstants

NARROW_MATCH - Static variable in class org.bridgedb.rdf.constants.SkosConstants

NARROWER - Static variable in class org.bridgedb.rdf.constants.SkosConstants

NON_NEGATIVE_INTEGER - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

NOTATION - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

O

OBJECTS_DATATYPE - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

OBJECTS_SPECIES - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

OBJECTSTARGET - Static variable in class org.bridgedb.rdf.constants.VoidConstants

OboConstants - Class in org.bridgedb.rdf.constants

OboConstants() - Constructor for class org.bridgedb.rdf.constants.OboConstants

OLD_PREFIX - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

OLD_PREFIX_NAME - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

org.bridgedb.rdf - package org.bridgedb.rdf

org.bridgedb.rdf.constants - package org.bridgedb.rdf.constants

org.bridgedb.rdf.create - package org.bridgedb.rdf.create

org.bridgedb.rdf.identifiers.org - package org.bridgedb.rdf.identifiers.org

org.bridgedb.rdf.pairs - package org.bridgedb.rdf.pairs

ORGANISM_LABEL - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

ORGANISM_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

ORGANISM1 - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

OrganismRdf - Class in org.bridgedb.rdf

OWLConstants - Class in org.bridgedb.rdf.constants

OWLConstants() - Constructor for class org.bridgedb.rdf.constants.OWLConstants

P

PAGE - Static variable in class org.bridgedb.rdf.constants.FoafConstants

PAGE_URI - Static variable in class org.bridgedb.rdf.constants.FoafConstants

parseRdfFile(File) - Static method in class org.bridgedb.rdf.BridgeDBRdfHandler

parseRdfInputStream(InputStream) - Static method in class org.bridgedb.rdf.BridgeDBRdfHandler

PART_OF - Static variable in class org.bridgedb.rdf.constants.OboConstants

PATHWAY - Static variable in class org.bridgedb.rdf.constants.ChemInf

PavConstants - Class in org.bridgedb.rdf.constants

PavConstants() - Constructor for class org.bridgedb.rdf.constants.PavConstants

PREFIX - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

PREFIX - Static variable in class org.bridgedb.rdf.constants.OboConstants

PREFIX - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

PREFIX_NAME - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

PREFIX_NAME - Static variable in class org.bridgedb.rdf.constants.CitoConstants

PREFIX_NAME - Static variable in class org.bridgedb.rdf.constants.DCatConstants

PREFIX_NAME - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

PREFIX_NAME - Static variable in class org.bridgedb.rdf.constants.FoafConstants

PREFIX_NAME - Static variable in class org.bridgedb.rdf.constants.IdenitifiersOrgConstants

PREFIX_NAME - Static variable in class org.bridgedb.rdf.constants.VoidConstants

PREVIOUS_VERSION - Static variable in class org.bridgedb.rdf.constants.PavConstants

PRIMARY_TOPIC - Static variable in class org.bridgedb.rdf.constants.FoafConstants

PRIMARY_TOPIC_URI - Static variable in class org.bridgedb.rdf.constants.FoafConstants

PRIMARY_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

PROTEIN - Static variable in class org.bridgedb.rdf.constants.ChemInf

PROTEIN_CODING_GENE - Static variable in class org.bridgedb.rdf.constants.ChemInf

PUBLISHER - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

PUBLISHER_URI - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

Q

QNAME - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

R

RDF - org.bridgedb.rdf.DataSourceMetaDataProvidor

RdfBase - Class in org.bridgedb.rdf

RdfBase() - Constructor for class org.bridgedb.rdf.RdfBase

RdfBasedCodeMapper - Class in org.bridgedb.rdf.pairs

RdfBasedCodeMapper() - Constructor for class org.bridgedb.rdf.pairs.RdfBasedCodeMapper

RdfConstants - Class in org.bridgedb.rdf.constants

RdfConstants() - Constructor for class org.bridgedb.rdf.constants.RdfConstants

RdfSchemaConstants - Class in org.bridgedb.rdf.constants

seeAlso

RdfSchemaConstants() - Constructor for class org.bridgedb.rdf.constants.RdfSchemaConstants

readDataSource(RepositoryConnection, Resource) - Method in class org.bridgedb.rdf.BridgeDBRdfHandler

readRdf(Resource, Set<Statement>) - Static method in class org.bridgedb.rdf.OrganismRdf

readUriPattern(RepositoryConnection, Resource, String, UriPatternType) - Static method in class org.bridgedb.rdf.UriPattern

refreshUriPatterns() - Static method in class org.bridgedb.rdf.UriPattern

REGEX - Static variable in class org.bridgedb.rdf.constants.IdenitifiersOrgConstants

REGEX_URI - Static variable in class org.bridgedb.rdf.constants.IdenitifiersOrgConstants

register(String, String, UriPatternType) - Static method in class org.bridgedb.rdf.UriPattern

registerUriPatterns() - Static method in class org.bridgedb.rdf.UriPattern

RELATED - Static variable in class org.bridgedb.rdf.constants.SkosConstants

RELATED_MATCH - Static variable in class org.bridgedb.rdf.constants.SkosConstants

RETRIEVED_BY - Static variable in class org.bridgedb.rdf.constants.PavConstants

RETRIEVED_FROM - Static variable in class org.bridgedb.rdf.constants.PavConstants

RETRIEVED_ON - Static variable in class org.bridgedb.rdf.constants.PavConstants

S

SAME_AS - Static variable in class org.bridgedb.rdf.constants.OWLConstants

SAMEAS_URI - Static variable in class org.bridgedb.rdf.constants.OWLConstants

saveRegister() - Static method in class org.bridgedb.rdf.identifiers.org.IdentifersOrgReader

SEE_ALSO - Static variable in class org.bridgedb.rdf.constants.RdfSchemaConstants

setProvidor(String, DataSourceMetaDataProvidor) - Static method in enum org.bridgedb.rdf.DataSourceMetaDataProvidor

sharesOPSNormalizedParentWith - Static variable in class org.bridgedb.rdf.constants.ChemInf

SHORT_NAME_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

shutDown(Repository, RepositoryConnection) - Static method in class org.bridgedb.rdf.RdfBase

SkosConstants - Class in org.bridgedb.rdf.constants

SkosConstants() - Constructor for class org.bridgedb.rdf.constants.SkosConstants

SOURCE_ACCESSED_BY - Static variable in class org.bridgedb.rdf.constants.PavConstants

SOURCE_ACCESSED_FROM - Static variable in class org.bridgedb.rdf.constants.PavConstants

SOURCE_ACCESSED_ON - Static variable in class org.bridgedb.rdf.constants.PavConstants

SPARQL_ENDPOINT - Static variable in class org.bridgedb.rdf.constants.VoidConstants

STRING - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

SUBJECTS_DATATYPE - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

SUBJECTS_SPECIES - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

SUBJECTSTARGET - Static variable in class org.bridgedb.rdf.constants.VoidConstants

SUBSET - Static variable in class org.bridgedb.rdf.constants.VoidConstants

SYSTEM_CODE_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

T

TARGET - Static variable in class org.bridgedb.rdf.constants.ChemInf

TARGET - Static variable in class org.bridgedb.rdf.constants.VoidConstants

TEST_PREDICATE - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

THEME - Static variable in class org.bridgedb.rdf.constants.DCatConstants

THEME_URI - Static variable in class org.bridgedb.rdf.constants.DCatConstants

THING - Static variable in class org.bridgedb.rdf.constants.OWLConstants

TIME - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

TITLE - Static variable in class org.bridgedb.rdf.constants.DCatConstants

TITLE - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

TITLE_URI - Static variable in class org.bridgedb.rdf.constants.DCatConstants

TITLE_URI - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

toIdSysCodePair(Xref) - Method in class org.bridgedb.rdf.pairs.RdfBasedCodeMapper

toString() - Method in class org.bridgedb.rdf.UriPattern

toXref(IdSysCodePair) - Method in class org.bridgedb.rdf.pairs.RdfBasedCodeMapper

TRANSITIVE - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

TRANSITIVE_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

TRIPLES - Static variable in class org.bridgedb.rdf.constants.VoidConstants

TYPE_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

TYPE_URI - Static variable in class org.bridgedb.rdf.constants.RdfConstants

U

UNABLE_TO_CONNECT - Static variable in class org.bridgedb.rdf.identifiers.org.IdentifersOrgReader

UNISGNED_BYTE - Static variable in class org.bridgedb.rdf.constants.XMLSchemaConstants

URI_PATTERN_LABEL - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

URI_PATTERN_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

URI_PATTERN1 - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

URI_SPACE_SHORT - Static variable in class org.bridgedb.rdf.constants.VoidConstants

URI_SPACE_URI - Static variable in class org.bridgedb.rdf.constants.VoidConstants

UriPattern - Class in org.bridgedb.rdf

UriPatternType - Enum in org.bridgedb.rdf

URN_BASE_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

V

valueOf(String) - Static method in enum org.bridgedb.rdf.DataSourceMetaDataProvidor

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.bridgedb.rdf.UriPatternType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.bridgedb.rdf.DataSourceMetaDataProvidor

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.bridgedb.rdf.UriPatternType

Returns an array containing the constants of this enum type, in the order they are declared.

VARIOUS - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

VERSION - Static variable in class org.bridgedb.rdf.constants.PavConstants

VIA_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

VOCABULARY - Static variable in class org.bridgedb.rdf.constants.VoidConstants

VoidConstants - Class in org.bridgedb.rdf.constants

VoidConstants() - Constructor for class org.bridgedb.rdf.constants.VoidConstants

voidns - Static variable in class org.bridgedb.rdf.constants.CitoConstants

voidns - Static variable in class org.bridgedb.rdf.constants.DCatConstants

voidns - Static variable in class org.bridgedb.rdf.constants.DCTermsConstants

voidns - Static variable in class org.bridgedb.rdf.constants.FoafConstants

voidns - Static variable in class org.bridgedb.rdf.constants.IdenitifiersOrgConstants

voidns - Static variable in class org.bridgedb.rdf.constants.VoidConstants

W

writeRDF(Set<Statement>, RDFFormat) - Static method in class org.bridgedb.rdf.BridgeDbRdfTools

writeRDF(Set<Statement>, RDFFormat, Writer) - Static method in class org.bridgedb.rdf.BridgeDbRdfTools

writeRdfToFile(File) - Static method in class org.bridgedb.rdf.BridgeDBRdfHandler

writeRdfToFile(File, SortedSet<DataSource>) - Static method in class org.bridgedb.rdf.BridgeDBRdfHandler

X

XMLSchemaConstants - Class in org.bridgedb.rdf.constants

XMLSchemaConstants() - Constructor for class org.bridgedb.rdf.constants.XMLSchemaConstants

XREF_PREFIX_URI - Static variable in class org.bridgedb.rdf.constants.BridgeDBConstants

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