├── .github └── workflows │ └── run-bio2rdf-scripts.yml ├── .gitignore ├── .gitmodules ├── MIT-LICENSE.txt ├── README.md ├── affymetrix └── affymetrix.php ├── biomodels └── biomodels.php ├── bioportal └── bioportal.php ├── chembl ├── README.md └── chembl.php ├── clinicaltrials └── clinicaltrials.php ├── common ├── perl │ ├── add_text_index.pl │ ├── checkpoint.pl │ ├── generate_namespace_association.pl │ ├── nq2virtuoso.pl │ ├── regroup_namespace_info.pl │ ├── remove_all_information.pl │ ├── remove_information_in_release_endpoint.pl │ └── set_up_batch_free_text.pl ├── php │ ├── oboparser.php │ └── php-sql-parser.php ├── python │ └── parargs.py └── shell │ └── complete_stats.sh ├── composer.json ├── ctd ├── README.md └── ctd.php ├── dailymed └── dailymed.php ├── dbpedia ├── dbpedia-wget.sh └── dbpedia2bio2rdf.php ├── dbsnp └── dbsnp.php ├── drugbank ├── README.md └── drugbank.php ├── genage └── genage.php ├── genbank └── genbank.php ├── gendr └── gendr.php ├── goa ├── README └── goa.php ├── hgnc └── hgnc.php ├── homologene └── homologene.php ├── interpro └── interpro.php ├── ipi └── ipi.php ├── iproclass └── iproclass.php ├── irefindex └── irefindex.php ├── kegg └── kegg.php ├── linkedSPLs ├── .gitignore ├── Design │ └── Model │ │ ├── linkedSPLs_ADR_Diagram.dia │ │ ├── linkedSPLs_DDI_ER_Diagram.dia │ │ ├── linkedSPLs_Metadata_ER_Diagram.dia │ │ └── linkedSPLs_pharmgx_ER_Diagram.dia ├── LinkedSPLs-ADR │ └── README ├── LinkedSPLs-DDI │ └── dailymed_labels_and_setids.txt ├── LinkedSPLs-activeMoiety │ ├── README │ ├── createActiveMoietySubInRDF.py │ └── mergeToActiveMoiety.py ├── LinkedSPLs-clinicalDrug │ ├── README │ ├── createClinicalDrugSubInRDF.py │ └── mergeToClinicalDrug.py ├── LinkedSPLs-core │ ├── README │ └── linkedSPLs_dump_rdf_config.n3 ├── LinkedSPLs-pharmgx │ ├── README │ ├── domeo-consensus-pharmgx-annotations-in-rdf-07112014.xml │ ├── domeo-pgx-pharmgx-annotations-in-rdf-09152014.xml │ └── post-processed-pgx-consensus-oa-10072014.nt ├── LinkedSPLs-update │ ├── .gitignore │ ├── README │ ├── build.xml │ ├── data-source.properties │ ├── lib │ │ ├── mysql-connector-java-5.1.33.zip │ │ └── mysql-connector-java-5.1.33 │ │ │ ├── CHANGES │ │ │ ├── COPYING │ │ │ ├── README │ │ │ ├── README.txt │ │ │ ├── build.xml │ │ │ ├── docs │ │ │ ├── README.txt │ │ │ ├── connector-j.html │ │ │ └── connector-j.pdf │ │ │ ├── mysql-connector-java-5.1.33-bin.jar │ │ │ └── src │ │ │ ├── com │ │ │ └── mysql │ │ │ │ ├── fabric │ │ │ │ ├── FabricCommunicationException.java │ │ │ │ ├── FabricConnection.java │ │ │ │ ├── FabricStateResponse.java │ │ │ │ ├── HashShardMapping.java │ │ │ │ ├── RangeShardMapping.java │ │ │ │ ├── Response.java │ │ │ │ ├── Server.java │ │ │ │ ├── ServerGroup.java │ │ │ │ ├── ServerMode.java │ │ │ │ ├── ServerRole.java │ │ │ │ ├── ShardIndex.java │ │ │ │ ├── ShardMapping.java │ │ │ │ ├── ShardMappingFactory.java │ │ │ │ ├── ShardTable.java │ │ │ │ ├── ShardingType.java │ │ │ │ ├── hibernate │ │ │ │ │ └── FabricMultiTenantConnectionProvider.java │ │ │ │ ├── jdbc │ │ │ │ │ ├── ErrorReportingExceptionInterceptor.java │ │ │ │ │ ├── FabricMySQLConnection.java │ │ │ │ │ ├── FabricMySQLConnectionProperties.java │ │ │ │ │ ├── FabricMySQLConnectionProxy.java │ │ │ │ │ ├── FabricMySQLDataSource.java │ │ │ │ │ ├── FabricMySQLDriver.java │ │ │ │ │ ├── JDBC4FabricMySQLConnection.java │ │ │ │ │ └── JDBC4FabricMySQLConnectionProxy.java │ │ │ │ ├── proto │ │ │ │ │ └── xmlrpc │ │ │ │ │ │ ├── AuthenticatedXmlRpcMethodCaller.java │ │ │ │ │ │ ├── DigestAuthentication.java │ │ │ │ │ │ ├── InternalXmlRpcMethodCaller.java │ │ │ │ │ │ ├── ResultSetParser.java │ │ │ │ │ │ ├── XmlRpcClient.java │ │ │ │ │ │ └── XmlRpcMethodCaller.java │ │ │ │ └── xmlrpc │ │ │ │ │ ├── Client.java │ │ │ │ │ ├── base │ │ │ │ │ ├── Array.java │ │ │ │ │ ├── Data.java │ │ │ │ │ ├── Fault.java │ │ │ │ │ ├── Member.java │ │ │ │ │ ├── MethodCall.java │ │ │ │ │ ├── MethodResponse.java │ │ │ │ │ ├── Param.java │ │ │ │ │ ├── Params.java │ │ │ │ │ ├── ResponseParser.java │ │ │ │ │ ├── Struct.java │ │ │ │ │ └── Value.java │ │ │ │ │ └── exceptions │ │ │ │ │ └── MySQLFabricException.java │ │ │ │ └── jdbc │ │ │ │ ├── AbandonedConnectionCleanupThread.java │ │ │ │ ├── AssertionFailedException.java │ │ │ │ ├── AuthenticationPlugin.java │ │ │ │ ├── BalanceStrategy.java │ │ │ │ ├── BestResponseTimeBalanceStrategy.java │ │ │ │ ├── Blob.java │ │ │ │ ├── BlobFromLocator.java │ │ │ │ ├── Buffer.java │ │ │ │ ├── BufferRow.java │ │ │ │ ├── ByteArrayRow.java │ │ │ │ ├── CacheAdapter.java │ │ │ │ ├── CacheAdapterFactory.java │ │ │ │ ├── CachedResultSetMetaData.java │ │ │ │ ├── CallableStatement.java │ │ │ │ ├── CharsetMapping.java │ │ │ │ ├── Charsets.properties │ │ │ │ ├── Clob.java │ │ │ │ ├── CommunicationsException.java │ │ │ │ ├── CompressedInputStream.java │ │ │ │ ├── Connection.java │ │ │ │ ├── ConnectionFeatureNotAvailableException.java │ │ │ │ ├── ConnectionGroup.java │ │ │ │ ├── ConnectionGroupManager.java │ │ │ │ ├── ConnectionImpl.java │ │ │ │ ├── ConnectionLifecycleInterceptor.java │ │ │ │ ├── ConnectionProperties.java │ │ │ │ ├── ConnectionPropertiesImpl.java │ │ │ │ ├── ConnectionPropertiesTransform.java │ │ │ │ ├── Constants.java │ │ │ │ ├── DatabaseMetaData.java │ │ │ │ ├── DatabaseMetaDataUsingInfoSchema.java │ │ │ │ ├── DocsConnectionPropsHelper.java │ │ │ │ ├── Driver.java │ │ │ │ ├── EscapeProcessor.java │ │ │ │ ├── EscapeProcessorResult.java │ │ │ │ ├── EscapeTokenizer.java │ │ │ │ ├── ExceptionInterceptor.java │ │ │ │ ├── ExportControlled.java │ │ │ │ ├── Extension.java │ │ │ │ ├── FailoverConnectionProxy.java │ │ │ │ ├── Field.java │ │ │ │ ├── IterateBlock.java │ │ │ │ ├── JDBC4CallableStatement.java │ │ │ │ ├── JDBC4ClientInfoProvider.java │ │ │ │ ├── JDBC4ClientInfoProviderSP.java │ │ │ │ ├── JDBC4CommentClientInfoProvider.java │ │ │ │ ├── JDBC4Connection.java │ │ │ │ ├── JDBC4DatabaseMetaData.java │ │ │ │ ├── JDBC4DatabaseMetaDataUsingInfoSchema.java │ │ │ │ ├── JDBC4LoadBalancedMySQLConnection.java │ │ │ │ ├── JDBC4MySQLConnection.java │ │ │ │ ├── JDBC4MysqlSQLXML.java │ │ │ │ ├── JDBC4NClob.java │ │ │ │ ├── JDBC4PreparedStatement.java │ │ │ │ ├── JDBC4PreparedStatementHelper.java │ │ │ │ ├── JDBC4ResultSet.java │ │ │ │ ├── JDBC4ServerPreparedStatement.java │ │ │ │ ├── JDBC4UpdatableResultSet.java │ │ │ │ ├── LicenseConfiguration.java │ │ │ │ ├── LoadBalanceExceptionChecker.java │ │ │ │ ├── LoadBalancedAutoCommitInterceptor.java │ │ │ │ ├── LoadBalancedConnection.java │ │ │ │ ├── LoadBalancedMySQLConnection.java │ │ │ │ ├── LoadBalancingConnectionProxy.java │ │ │ │ ├── LocalizedErrorMessages.properties │ │ │ │ ├── Messages.java │ │ │ │ ├── MiniAdmin.java │ │ │ │ ├── MySQLConnection.java │ │ │ │ ├── MysqlDataTruncation.java │ │ │ │ ├── MysqlDefs.java │ │ │ │ ├── MysqlErrorNumbers.java │ │ │ │ ├── MysqlIO.java │ │ │ │ ├── MysqlParameterMetadata.java │ │ │ │ ├── MysqlSavepoint.java │ │ │ │ ├── NamedPipeSocketFactory.java │ │ │ │ ├── NdbLoadBalanceExceptionChecker.java │ │ │ │ ├── NetworkResources.java │ │ │ │ ├── NoSubInterceptorWrapper.java │ │ │ │ ├── NonRegisteringDriver.java │ │ │ │ ├── NonRegisteringReplicationDriver.java │ │ │ │ ├── NotImplemented.java │ │ │ │ ├── NotUpdatable.java │ │ │ │ ├── OperationNotSupportedException.java │ │ │ │ ├── OutputStreamWatcher.java │ │ │ │ ├── PacketTooBigException.java │ │ │ │ ├── ParameterBindings.java │ │ │ │ ├── PerConnectionLRUFactory.java │ │ │ │ ├── PerVmServerConfigCacheFactory.java │ │ │ │ ├── PingTarget.java │ │ │ │ ├── PreparedStatement.java │ │ │ │ ├── ProfilerEventHandlerFactory.java │ │ │ │ ├── RandomBalanceStrategy.java │ │ │ │ ├── ReflectiveStatementInterceptorAdapter.java │ │ │ │ ├── ReplicationConnection.java │ │ │ │ ├── ReplicationConnectionGroup.java │ │ │ │ ├── ReplicationConnectionGroupManager.java │ │ │ │ ├── ReplicationDriver.java │ │ │ │ ├── ResultSetImpl.java │ │ │ │ ├── ResultSetInternalMethods.java │ │ │ │ ├── ResultSetMetaData.java │ │ │ │ ├── ResultSetRow.java │ │ │ │ ├── RowData.java │ │ │ │ ├── RowDataCursor.java │ │ │ │ ├── RowDataDynamic.java │ │ │ │ ├── RowDataStatic.java │ │ │ │ ├── SQLError.java │ │ │ │ ├── Security.java │ │ │ │ ├── SequentialBalanceStrategy.java │ │ │ │ ├── ServerPreparedStatement.java │ │ │ │ ├── SingleByteCharsetConverter.java │ │ │ │ ├── SocketFactory.java │ │ │ │ ├── SocketMetadata.java │ │ │ │ ├── StandardLoadBalanceExceptionChecker.java │ │ │ │ ├── StandardSocketFactory.java │ │ │ │ ├── Statement.java │ │ │ │ ├── StatementImpl.java │ │ │ │ ├── StatementInterceptor.java │ │ │ │ ├── StatementInterceptorV2.java │ │ │ │ ├── StreamingNotifiable.java │ │ │ │ ├── StringUtils.java │ │ │ │ ├── TimeUtil.java │ │ │ │ ├── TimeZoneMapping.properties │ │ │ │ ├── UpdatableResultSet.java │ │ │ │ ├── Util.java │ │ │ │ ├── V1toV2StatementInterceptorAdapter.java │ │ │ │ ├── WatchableOutputStream.java │ │ │ │ ├── WatchableWriter.java │ │ │ │ ├── WriterWatcher.java │ │ │ │ ├── authentication │ │ │ │ ├── MysqlClearPasswordPlugin.java │ │ │ │ ├── MysqlNativePasswordPlugin.java │ │ │ │ ├── MysqlOldPasswordPlugin.java │ │ │ │ └── Sha256PasswordPlugin.java │ │ │ │ ├── configs │ │ │ │ ├── 3-0-Compat.properties │ │ │ │ ├── 5-0-Compat.properties │ │ │ │ ├── clusterBase.properties │ │ │ │ ├── coldFusion.properties │ │ │ │ ├── fullDebug.properties │ │ │ │ ├── maxPerformance.properties │ │ │ │ └── solarisMaxPerformance.properties │ │ │ │ ├── exceptions │ │ │ │ ├── DeadlockTimeoutRollbackMarker.java │ │ │ │ ├── MySQLDataException.java │ │ │ │ ├── MySQLIntegrityConstraintViolationException.java │ │ │ │ ├── MySQLInvalidAuthorizationSpecException.java │ │ │ │ ├── MySQLNonTransientConnectionException.java │ │ │ │ ├── MySQLNonTransientException.java │ │ │ │ ├── MySQLQueryInterruptedException.java │ │ │ │ ├── MySQLStatementCancelledException.java │ │ │ │ ├── MySQLSyntaxErrorException.java │ │ │ │ ├── MySQLTimeoutException.java │ │ │ │ ├── MySQLTransactionRollbackException.java │ │ │ │ ├── MySQLTransientConnectionException.java │ │ │ │ ├── MySQLTransientException.java │ │ │ │ └── jdbc4 │ │ │ │ │ ├── CommunicationsException.java │ │ │ │ │ ├── MySQLDataException.java │ │ │ │ │ ├── MySQLIntegrityConstraintViolationException.java │ │ │ │ │ ├── MySQLInvalidAuthorizationSpecException.java │ │ │ │ │ ├── MySQLNonTransientConnectionException.java │ │ │ │ │ ├── MySQLNonTransientException.java │ │ │ │ │ ├── MySQLQueryInterruptedException.java │ │ │ │ │ ├── MySQLSyntaxErrorException.java │ │ │ │ │ ├── MySQLTimeoutException.java │ │ │ │ │ ├── MySQLTransactionRollbackException.java │ │ │ │ │ ├── MySQLTransientConnectionException.java │ │ │ │ │ └── MySQLTransientException.java │ │ │ │ ├── integration │ │ │ │ ├── c3p0 │ │ │ │ │ └── MysqlConnectionTester.java │ │ │ │ └── jboss │ │ │ │ │ ├── ExtendedMysqlExceptionSorter.java │ │ │ │ │ └── MysqlValidConnectionChecker.java │ │ │ │ ├── interceptors │ │ │ │ ├── ResultSetScannerInterceptor.java │ │ │ │ ├── ServerStatusDiffInterceptor.java │ │ │ │ └── SessionAssociationInterceptor.java │ │ │ │ ├── jdbc2 │ │ │ │ └── optional │ │ │ │ │ ├── CallableStatementWrapper.java │ │ │ │ │ ├── ConnectionWrapper.java │ │ │ │ │ ├── JDBC4CallableStatementWrapper.java │ │ │ │ │ ├── JDBC4ConnectionWrapper.java │ │ │ │ │ ├── JDBC4MysqlPooledConnection.java │ │ │ │ │ ├── JDBC4MysqlXAConnection.java │ │ │ │ │ ├── JDBC4PreparedStatementWrapper.java │ │ │ │ │ ├── JDBC4StatementWrapper.java │ │ │ │ │ ├── JDBC4SuspendableXAConnection.java │ │ │ │ │ ├── MysqlConnectionPoolDataSource.java │ │ │ │ │ ├── MysqlDataSource.java │ │ │ │ │ ├── MysqlDataSourceFactory.java │ │ │ │ │ ├── MysqlPooledConnection.java │ │ │ │ │ ├── MysqlXAConnection.java │ │ │ │ │ ├── MysqlXADataSource.java │ │ │ │ │ ├── MysqlXAException.java │ │ │ │ │ ├── MysqlXid.java │ │ │ │ │ ├── PreparedStatementWrapper.java │ │ │ │ │ ├── StatementWrapper.java │ │ │ │ │ ├── SuspendableXAConnection.java │ │ │ │ │ └── WrapperBase.java │ │ │ │ ├── jmx │ │ │ │ ├── LoadBalanceConnectionGroupManager.java │ │ │ │ ├── LoadBalanceConnectionGroupManagerMBean.java │ │ │ │ ├── ReplicationGroupManager.java │ │ │ │ └── ReplicationGroupManagerMBean.java │ │ │ │ ├── log │ │ │ │ ├── Jdk14Logger.java │ │ │ │ ├── Log.java │ │ │ │ ├── LogFactory.java │ │ │ │ ├── LogUtils.java │ │ │ │ ├── NullLogger.java │ │ │ │ ├── Slf4JLogger.java │ │ │ │ └── StandardLogger.java │ │ │ │ ├── profiler │ │ │ │ ├── LoggingProfilerEventHandler.java │ │ │ │ ├── ProfilerEvent.java │ │ │ │ └── ProfilerEventHandler.java │ │ │ │ └── util │ │ │ │ ├── Base64Decoder.java │ │ │ │ ├── BaseBugReport.java │ │ │ │ ├── ErrorMappingsDocGenerator.java │ │ │ │ ├── LRUCache.java │ │ │ │ ├── PropertiesDocGenerator.java │ │ │ │ ├── ReadAheadInputStream.java │ │ │ │ ├── ResultSetUtil.java │ │ │ │ ├── ServerController.java │ │ │ │ ├── TimezoneDump.java │ │ │ │ └── VersionFSHierarchyMaker.java │ │ │ ├── demo │ │ │ └── fabric │ │ │ │ ├── Client1_Fabric.java │ │ │ │ ├── Employee.java │ │ │ │ ├── EmployeesJdbc.java │ │ │ │ ├── HibernateFabric.java │ │ │ │ └── resources │ │ │ │ └── com │ │ │ │ └── mysql │ │ │ │ └── fabric │ │ │ │ └── demo │ │ │ │ └── employee.hbm.xml │ │ │ ├── doc │ │ │ └── sources │ │ │ │ ├── connPropsToDocbook.xsl │ │ │ │ ├── errorMapToDocbook.xsl │ │ │ │ ├── placeholder.txt │ │ │ │ └── pom.xml │ │ │ ├── lib │ │ │ ├── c3p0-0.9.1-pre6.jar │ │ │ ├── c3p0-0.9.1-pre6.src.zip │ │ │ ├── jboss-common-jdbc-wrapper-src.jar │ │ │ ├── jboss-common-jdbc-wrapper.jar │ │ │ └── slf4j-api-1.6.1.jar │ │ │ ├── org │ │ │ └── gjt │ │ │ │ └── mm │ │ │ │ └── mysql │ │ │ │ └── Driver.java │ │ │ └── testsuite │ │ │ ├── BaseTestCase.java │ │ │ ├── UnreliableSocketFactory.java │ │ │ ├── fabric │ │ │ ├── BaseFabricTestCase.java │ │ │ ├── SetupFabricTestsuite.java │ │ │ ├── TestDumpCommands.java │ │ │ ├── TestResultSetParser.java │ │ │ ├── TestShardMapping.java │ │ │ ├── TestXmlRpcCore.java │ │ │ └── jdbc │ │ │ │ ├── TestBasicConnection.java │ │ │ │ ├── TestFabricMySQLConnectionSharding.java │ │ │ │ ├── TestHABasics.java │ │ │ │ ├── TestHashSharding.java │ │ │ │ └── TestRegressions.java │ │ │ ├── perf │ │ │ ├── BasePerfTest.java │ │ │ ├── LoadStorePerfTest.java │ │ │ └── RetrievalPerfTest.java │ │ │ ├── regression │ │ │ ├── BlobRegressionTest.java │ │ │ ├── CachedRowsetTest.java │ │ │ ├── CallableStatementRegressionTest.java │ │ │ ├── CharsetRegressionTest.java │ │ │ ├── ConnectionRegressionTest.java │ │ │ ├── DataSourceRegressionTest.java │ │ │ ├── EscapeProcessorRegressionTest.java │ │ │ ├── MetaDataRegressionTest.java │ │ │ ├── MicroPerformanceRegressionTest.java │ │ │ ├── NumbersRegressionTest.java │ │ │ ├── PooledConnectionRegressionTest.java │ │ │ ├── ResultSetRegressionTest.java │ │ │ ├── StatementRegressionTest.java │ │ │ ├── StressRegressionTest.java │ │ │ ├── StringRegressionTest.java │ │ │ ├── SubqueriesRegressionTest.java │ │ │ ├── SyntaxRegressionTest.java │ │ │ ├── UtilsRegressionTest.java │ │ │ └── jdbc4 │ │ │ │ ├── ExceptionSubclassesTest.java │ │ │ │ ├── MetaDataRegressionTest.java │ │ │ │ └── StatementRegressionTest.java │ │ │ ├── simple │ │ │ ├── BlobTest.java │ │ │ ├── CallableStatementTest.java │ │ │ ├── CharsetTest.java │ │ │ ├── ConnectionTest.java │ │ │ ├── DataSourceTest.java │ │ │ ├── DateTest.java │ │ │ ├── EscapeProcessingTest.java │ │ │ ├── MetadataTest.java │ │ │ ├── MiniAdminTest.java │ │ │ ├── NumbersTest.java │ │ │ ├── ReadOnlyCallableStatementTest.java │ │ │ ├── ResultSetTest.java │ │ │ ├── SSLTest.java │ │ │ ├── ServerControllerTest.java │ │ │ ├── SimpleTransformer.java │ │ │ ├── SplitDBdotNameTest.java │ │ │ ├── StatementsTest.java │ │ │ ├── StringUtilsTest.java │ │ │ ├── TestBug57662Logger.java │ │ │ ├── TestLifecycleInterceptor.java │ │ │ ├── TransactionTest.java │ │ │ ├── TraversalTest.java │ │ │ ├── UpdatabilityTest.java │ │ │ ├── XATest.java │ │ │ ├── jdbc4 │ │ │ │ └── StatementsTest.java │ │ │ └── tb2-data.txt.gz │ │ │ └── ssl-test-certs │ │ │ ├── ca-cert.pem │ │ │ ├── ca-key.pem │ │ │ ├── mykey.pem │ │ │ ├── mykey.pub │ │ │ ├── server-cert.pem │ │ │ ├── server-key.pem │ │ │ ├── server-req.pem │ │ │ └── test-cert-store │ ├── load-dailymed-spls │ │ ├── TableSchema.sql │ │ ├── dailymed_rss.py │ │ ├── get_spl_sections.py │ │ ├── loadDailymedToSql.py │ │ ├── loinc.sql │ │ ├── loinc_sections.txt │ │ └── rxnorm.py │ ├── mappings │ │ ├── ChEBI-DrugBank-bio2rdf-mapping │ │ │ ├── README │ │ │ ├── UNII-data │ │ │ │ ├── INCHI-AND-Syns-OR-Name-09162014.txt │ │ │ │ ├── INCHI-OR-Syns-OR-Name-11052014.txt │ │ │ │ ├── INCHI-OR-Syns-OR-Name-11102014.txt │ │ │ │ ├── INCHI-OR-Syns-OR-Name-11162014.txt │ │ │ │ ├── Name_Syns_UNII_DbId_0_11052014.txt │ │ │ │ ├── Name_Syns_UNII_DbId_0_11102014.txt │ │ │ │ ├── Name_Syns_UNII_DbId_0_11162014.txt │ │ │ │ ├── Name_Syns_UNII_DbId_1_09162014.txt │ │ │ │ └── README │ │ │ ├── drugbank-rxnorm-mapping │ │ │ │ ├── pt-drugbank-leftjoin-rxnorm-unconservative-mapping-01182017.tsv │ │ │ │ ├── pt-drugbank-leftjoin-rxnorm-unconservative-mapping-06252016.tsv │ │ │ │ ├── pt-drugbank-rxnorm-unconservative-mapping-01182017.tsv │ │ │ │ └── pt-drugbank-rxnorm-unconservative-mapping-06252016.tsv │ │ │ ├── scripts │ │ │ │ ├── addBio2rdf_UNII_to_DrugBank.py │ │ │ │ ├── backups │ │ │ │ │ ├── addRxTermAndRxcui.py │ │ │ │ │ ├── combineDrugBankMappings.py │ │ │ │ │ ├── combineMappings.py │ │ │ │ │ ├── parseDBIdAndChEBI.py │ │ │ │ │ ├── parseDBIdAndUNIIsByInChikey.py │ │ │ │ │ └── parseDBIdAndUNIIsByMF.py │ │ │ │ ├── parseDBIdAndChEBI.py │ │ │ │ └── parseDBIdBySynsInchiName.py │ │ │ └── validated-mapping │ │ │ │ ├── FDA_SUBSTANCE_TO_DRUGBANK_BIO2RDF-04082014.txt │ │ │ │ ├── FDA_UNII_to_ChEBI_03132014.txt │ │ │ │ ├── FDA_UNII_to_DrugBank_03132014.txt │ │ │ │ └── UNII-to-DrugBank-test-mapping-03272014-RDB-questionable-mappings-removed.xlsm │ │ ├── DrOn-to-RxNorm │ │ │ ├── DrOn-Drugbank-mapping.txt.csv │ │ │ ├── README │ │ │ ├── cleanData.py │ │ │ ├── parseDrOnFromOWLDrug.sh │ │ │ └── parseDrOnFromOWLIngredient.sh │ │ ├── FDA-pharmacogenetic-info-mapping │ │ │ ├── FDAPharmgxTable-01202017.csv │ │ │ ├── FDAPharmgxTable.csv │ │ │ ├── FDA_PGx_Table.csv │ │ │ ├── README │ │ │ ├── biomarker-to-ontology-mapping-01262017.csv │ │ │ ├── check-pharmgx-site-for-updates.cron │ │ │ ├── createFDAPharmgxDBTable.py │ │ │ ├── fda.py │ │ │ └── log.txt │ │ ├── NDFRT-to-RxNorm │ │ │ ├── #README# │ │ │ ├── README │ │ │ ├── convertNDFRTandRXNORM_UUIDsToPurls.py │ │ │ ├── converted-rxnorm-to-ndfrt-chemical-ingredient-11162014.txt │ │ │ └── rxnorm-to-ndfrt-chemical-ingredient-mapping-11162014.txt │ │ ├── PT-UNII-ChEBI-mapping │ │ │ ├── ChEBIJavaClient │ │ │ │ ├── jar │ │ │ │ │ └── ChEBIJavaClient.jar │ │ │ │ ├── libs │ │ │ │ │ └── chebiWS-client-2.2.1.jar │ │ │ │ ├── mappings │ │ │ │ │ └── config.properties │ │ │ │ └── src │ │ │ │ │ └── chebi │ │ │ │ │ └── service │ │ │ │ │ └── GetChEBIbyNames.java │ │ │ └── README │ │ ├── RxNORM-mapping │ │ │ ├── README │ │ │ ├── data │ │ │ │ ├── PS-to-Rxcui-mapping-10272014.txt │ │ │ │ ├── PS-to-Rxcui-mapping_10202014_1.txt │ │ │ │ ├── PS-to-Rxcui-mapping_10202014_2.txt │ │ │ │ ├── PS-to-Rxcui-mapping_10202014_3.txt │ │ │ │ ├── PS-to-Rxcui-mapping_10202014_4.txt │ │ │ │ └── PS-to-Rxcui-mapping_10202014_5.txt │ │ │ └── mergePT-UNII-RXCUI.py │ │ └── pharmacologic_class_indexing │ │ │ ├── README │ │ │ └── parseEPCfromXMLs.py │ └── test │ │ └── test-example-queries.py ├── README └── example-queries-bio2rdf-linkedSPLs-RDF.txt ├── lsr └── lsr.php ├── mesh └── mesh.php ├── mgi └── mgi.php ├── miriam └── miriam.php ├── ncbigene └── ncbigene.php ├── ndc └── ndc.php ├── omim └── omim.php ├── orphanet └── orphanet.php ├── pathwaycommons └── pathwaycommons.php ├── pdb ├── .gitignore ├── .project ├── .settings │ └── org.eclipse.m2e.core.prefs ├── README.md ├── pdb.php ├── pdb2rdf-cli │ ├── .classpath │ ├── .project │ ├── .settings │ │ ├── org.eclipse.jdt.core.prefs │ │ ├── org.eclipse.m2e.core.prefs │ │ └── org.maven.ide.eclipse.prefs │ ├── log4j.properties │ ├── pdb2rdf.bat │ ├── pdb2rdf.sh │ ├── pom.xml │ └── src │ │ ├── main │ │ ├── assembly │ │ │ └── assembly.xml │ │ ├── java │ │ │ └── com │ │ │ │ └── dumontierlab │ │ │ │ └── pdb2rdf │ │ │ │ ├── Pdb2Rdf.java │ │ │ │ ├── dao │ │ │ │ ├── DaoException.java │ │ │ │ ├── TripleStoreDao.java │ │ │ │ ├── VirtGraphFactory.java │ │ │ │ ├── VirtuosoDaoFactory.java │ │ │ │ └── impl │ │ │ │ │ └── VirtuosoTripleStoreDaoImpl.java │ │ │ │ ├── model │ │ │ │ └── VirtPdbRdfModel.java │ │ │ │ └── util │ │ │ │ ├── ClusterIterator.java │ │ │ │ ├── ConsoleProgressMonitorImpl.java │ │ │ │ ├── DirectoryIterator.java │ │ │ │ ├── FileCollectionIterator.java │ │ │ │ ├── FileIterator.java │ │ │ │ ├── InputInterator.java │ │ │ │ ├── Pdb2RdfInputIterator.java │ │ │ │ ├── Pdb2RdfInputIteratorAdapter.java │ │ │ │ ├── PdbsIterator.java │ │ │ │ ├── ProgressMonitor.java │ │ │ │ └── Statistics.java │ │ └── resources │ │ │ └── fastload.properties │ │ └── test │ │ └── java │ │ └── com │ │ └── dumontierlab │ │ └── pdb2rdf │ │ ├── Pdb2RdfTest.java │ │ └── util │ │ └── StatisticsTest.java ├── pdb2rdf-cluster │ ├── .classpath │ ├── .project │ ├── .settings │ │ ├── org.eclipse.jdt.core.prefs │ │ ├── org.eclipse.m2e.core.prefs │ │ └── org.maven.ide.eclipse.prefs │ ├── pom.xml │ ├── run.bat │ ├── run.sh │ └── src │ │ └── main │ │ ├── assembly │ │ └── assembly.xml │ │ ├── java │ │ └── com │ │ │ └── dumontierlab │ │ │ └── pdb2rdf │ │ │ └── cluster │ │ │ ├── ClusterServer.java │ │ │ └── servlet │ │ │ └── ClusterController.java │ │ └── resources │ │ └── log4j.properties ├── pdb2rdf-parser │ ├── .classpath │ ├── .project │ ├── .settings │ │ ├── org.eclipse.jdt.core.prefs │ │ ├── org.eclipse.m2e.core.prefs │ │ └── org.maven.ide.eclipse.prefs │ ├── pom.xml │ └── src │ │ ├── main │ │ ├── java │ │ │ ├── META-INF │ │ │ │ └── MANIFEST.MF │ │ │ └── com │ │ │ │ └── dumontierlab │ │ │ │ └── pdb2rdf │ │ │ │ ├── external │ │ │ │ └── Pdb2Rdf2Uniprot.java │ │ │ │ ├── model │ │ │ │ └── PdbRdfModel.java │ │ │ │ ├── parser │ │ │ │ ├── AbstractPdbXmlParser.java │ │ │ │ ├── AtomSiteCategoryHandler.java │ │ │ │ ├── CellCategoryHandler.java │ │ │ │ ├── ChemCompCategory.java │ │ │ │ ├── CitationAuthorCategoryHandler.java │ │ │ │ ├── CitationCategoryHandler.java │ │ │ │ ├── ContentHandlerState.java │ │ │ │ ├── DataBlockHandler.java │ │ │ │ ├── DetailLevel.java │ │ │ │ ├── EntityCategoryHandler.java │ │ │ │ ├── EntityPolyCategoryHandler.java │ │ │ │ ├── EntitySourceGeneticallyManipulatedHandler.java │ │ │ │ ├── EntitySourceNaturalCategoryHandler.java │ │ │ │ ├── ExptlCategoryHandler.java │ │ │ │ ├── NmrEnsembleCategoryHandler.java │ │ │ │ ├── NmrRefineCategoryHandler.java │ │ │ │ ├── PdbOwlOntologyGenerator.java │ │ │ │ ├── PdbXmlContentHandler.java │ │ │ │ ├── PdbXmlParser.java │ │ │ │ ├── RefineCategoryHandler.java │ │ │ │ ├── SpaceGroupCategoryHandler.java │ │ │ │ ├── StructCategoryHandler.java │ │ │ │ ├── StructConfigCategoryHandler.java │ │ │ │ ├── rna │ │ │ │ │ ├── RnaPdbXmlContentHandler.java │ │ │ │ │ ├── RnaPdbXmlParser.java │ │ │ │ │ ├── StructNucleicAcidBasePairCategoryHandler.java │ │ │ │ │ └── vocabulary │ │ │ │ │ │ ├── LeontisWesthofClassification.java │ │ │ │ │ │ ├── RnaKbOwlVocabulary.java │ │ │ │ │ │ ├── SangerClassification.java │ │ │ │ │ │ └── uri │ │ │ │ │ │ └── RnaKbUriPattern.java │ │ │ │ └── vocabulary │ │ │ │ │ ├── AbsortCorrectionTypes.java │ │ │ │ │ ├── ExperimentalMethods.java │ │ │ │ │ ├── PdbOwlVocabulary.java │ │ │ │ │ ├── PdbXmlVocabulary.java │ │ │ │ │ ├── PeriodicTable.java │ │ │ │ │ ├── SecondaryStructures.java │ │ │ │ │ ├── Vectors.java │ │ │ │ │ └── uri │ │ │ │ │ ├── Bio2RdfPdbUriPattern.java │ │ │ │ │ ├── UriBuilder.java │ │ │ │ │ └── UriPattern.java │ │ │ │ └── util │ │ │ │ ├── PdbHttpClient.java │ │ │ │ └── UriUtil.java │ │ └── resources │ │ │ └── pdb.owl │ │ └── test │ │ ├── java │ │ └── com │ │ │ └── dumontierlab │ │ │ └── pdb2rdf │ │ │ ├── external │ │ │ └── Pdb2Rdf2UniprotTest.java │ │ │ └── parser │ │ │ ├── AbstractPdbXmlParserTest.java │ │ │ ├── AtomSiteCategoryHandlerTest.java │ │ │ ├── JenaExample.java │ │ │ └── RefineCategoryHandlerTest.java │ │ └── resources │ │ ├── 1Y26_atomSiteCategory.xml │ │ └── 1Y26_refineCategory.xml └── pom.xml ├── pharmgkb └── pharmgkb.php ├── pubchem ├── README.md └── pubchem.php ├── pubmed ├── README ├── fetch.php └── pubmed.php ├── refseq └── refseq.php ├── runparser.php ├── sabiork └── sabiork.php ├── sgd └── sgd.php ├── sider └── sider.php ├── statistics ├── bio2rdf-individual-page.php ├── bio2rdf-release-page.php ├── endpoint-statistics.php └── statistics-unit-test.nt ├── taxonomy └── taxonomy.php ├── toxkb ├── .gitignore ├── Gemfile ├── README.md ├── cebs │ ├── cebs2rdf.rb │ └── siftv2parser.rb ├── dsstox │ ├── dsstoxCPDBAS2RDF.rb │ └── dsstoxGEO2RDF.rb ├── ontology │ └── toxkb.owl ├── outdated_gems │ └── rdfextraction │ │ ├── Gemfile │ │ ├── lib │ │ ├── concept.rb │ │ ├── graph.rb │ │ ├── initparam.rb │ │ ├── literal.rb │ │ ├── mysqladaptor.rb │ │ ├── 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