Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | U | V | W | X _ __init__() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) (disease.etl.base.Base method) (disease.etl.base.OWLBase method) (disease.etl.do.DO method) (disease.etl.merge.Merge method) (disease.etl.mondo.Mondo method) (disease.etl.ncit.NCIt method) (disease.etl.omim.OMIM method) (disease.etl.oncotree.OncoTree method) (disease.query.QueryHandler method) A AbstractDatabase (class in disease.database.database) add_merged_record() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) add_record() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) add_source_metadata() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) ALIAS (disease.schemas.MatchType attribute) aliases (disease.schemas.Disease attribute) ALIASES (disease.schemas.RefType attribute) associated_with (disease.schemas.Disease attribute) ASSOCIATED_WITH (disease.schemas.MatchType attribute) (disease.schemas.RefType attribute) attribution (disease.schemas.DataLicenseAttributes attribute) AwsEnvName (class in disease.database.database) B Base (class in disease.etl.base) C check_schema_initialized() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) check_tables_populated() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) close_connection() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) COHD (disease.schemas.NamespacePrefix attribute) complete_write_transaction() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) concept_id (disease.schemas.Disease attribute) CONCEPT_ID (disease.schemas.MatchType attribute) confirm_aws_db_use() (in module disease.database.database) create_db() (in module disease.database.database) create_merged_concepts() (disease.etl.merge.Merge method) D data_license (disease.schemas.SourceMeta attribute) data_license_attributes (disease.schemas.SourceMeta attribute) data_license_url (disease.schemas.SourceMeta attribute) data_url (disease.schemas.SourceMeta attribute) DatabaseException DatabaseInitializationException DatabaseReadException DatabaseWriteException DataLicenseAttributes (class in disease.schemas) DECIPHER (disease.schemas.NamespacePrefix attribute) delete_normalized_concepts() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) delete_source() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) DEVELOPMENT (disease.database.database.AwsEnvName attribute) Disease (class in disease.schemas) disease (disease.schemas.NormalizationService attribute) disease.database.database module disease.database.dynamodb module disease.database.postgresql module disease.etl.base module disease.etl.do module disease.etl.merge module disease.etl.mondo module disease.etl.ncit module disease.etl.omim module disease.etl.oncotree module disease.query module disease.schemas module DO (class in disease.etl.do) (disease.schemas.NamespacePrefix attribute) (disease.schemas.SourceIDAfterNamespace attribute) (disease.schemas.SourceName attribute) (disease.schemas.SourcePriority attribute) DOID (disease.schemas.NamespacePrefix attribute) drop_db() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) DynamoDbDatabase (class in disease.database.dynamodb) E EFO (disease.schemas.NamespacePrefix attribute) export_db() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) F FUZZY_MATCH (disease.schemas.MatchType attribute) G GARD (disease.schemas.NamespacePrefix attribute) get_all_concept_ids() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) get_all_records() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) get_record_by_id() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) get_refs_by_type() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) get_source_metadata() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) H HP (disease.schemas.NamespacePrefix attribute) HPO (disease.schemas.NamespacePrefix attribute) I ICD10 (disease.schemas.NamespacePrefix attribute) ICD10CM (disease.schemas.NamespacePrefix attribute) ICD10WHO (disease.schemas.NamespacePrefix attribute) ICD11 (disease.schemas.NamespacePrefix attribute) ICD9 (disease.schemas.NamespacePrefix attribute) ICD9CM (disease.schemas.NamespacePrefix attribute) ICDO (disease.schemas.NamespacePrefix attribute) IDENTITY (disease.schemas.RecordType attribute) IDO (disease.schemas.NamespacePrefix attribute) IMDRF (disease.schemas.NamespacePrefix attribute) initialize_db() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) InvalidParameterException K KEGG (disease.schemas.NamespacePrefix attribute) L label (disease.schemas.Disease attribute) LABEL (disease.schemas.MatchType attribute) (disease.schemas.RefType attribute) list_tables() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) load_from_remote() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) M match_type (disease.schemas.NormalizationService attribute) (disease.schemas.SourceSearchMatches attribute) MatchType (class in disease.schemas) MEDDRA (disease.schemas.NamespacePrefix attribute) MEDGEN (disease.schemas.NamespacePrefix attribute) Merge (class in disease.etl.merge) MERGER (disease.schemas.RecordType attribute) MESH (disease.schemas.NamespacePrefix attribute) MF (disease.schemas.NamespacePrefix attribute) model_computed_fields (disease.schemas.DataLicenseAttributes attribute) (disease.schemas.Disease attribute) (disease.schemas.NormalizationService attribute) (disease.schemas.SearchService attribute) (disease.schemas.ServiceMeta attribute) (disease.schemas.SourceMeta attribute) (disease.schemas.SourceSearchMatches attribute) module disease.database.database disease.database.dynamodb disease.database.postgresql disease.etl.base disease.etl.do disease.etl.merge disease.etl.mondo disease.etl.ncit disease.etl.omim disease.etl.oncotree disease.query disease.schemas Mondo (class in disease.etl.mondo) MONDO (disease.schemas.NamespacePrefix attribute) (disease.schemas.SourceIDAfterNamespace attribute) (disease.schemas.SourceName attribute) (disease.schemas.SourcePriority attribute) MP (disease.schemas.NamespacePrefix attribute) MPATH (disease.schemas.NamespacePrefix attribute) N name (disease.schemas.ServiceMeta attribute) NamespacePrefix (class in disease.schemas) NCIt (class in disease.etl.ncit) NCIT (disease.schemas.NamespacePrefix attribute) (disease.schemas.SourceIDAfterNamespace attribute) (disease.schemas.SourceName attribute) (disease.schemas.SourcePriority attribute) NIFSTD (disease.schemas.NamespacePrefix attribute) NO_MATCH (disease.schemas.MatchType attribute) non_commercial (disease.schemas.DataLicenseAttributes attribute) NormalizationService (class in disease.schemas) normalize() (disease.query.QueryHandler method) normalized_id (disease.schemas.NormalizationService attribute) O OBI (disease.schemas.NamespacePrefix attribute) OGMS (disease.schemas.NamespacePrefix attribute) OMIM (class in disease.etl.omim) (disease.schemas.NamespacePrefix attribute) (disease.schemas.SourceIDAfterNamespace attribute) (disease.schemas.SourceName attribute) (disease.schemas.SourcePriority attribute) OMIMPS (disease.schemas.NamespacePrefix attribute) OncoTree (class in disease.etl.oncotree) ONCOTREE (disease.schemas.NamespacePrefix attribute) (disease.schemas.SourceIDAfterNamespace attribute) (disease.schemas.SourceName attribute) (disease.schemas.SourcePriority attribute) ORPHANET (disease.schemas.NamespacePrefix attribute) OWLBase (class in disease.etl.base) P PATO (disease.schemas.NamespacePrefix attribute) pediatric_disease (disease.schemas.Disease attribute) perform_etl() (disease.etl.base.Base method) (disease.etl.base.OWLBase method) (disease.etl.do.DO method) (disease.etl.mondo.Mondo method) (disease.etl.ncit.NCIt method) (disease.etl.omim.OMIM method) (disease.etl.oncotree.OncoTree method) PostgresDatabase (class in disease.database.postgresql) PRODUCTION (disease.database.database.AwsEnvName attribute) Q query (disease.schemas.NormalizationService attribute) (disease.schemas.SearchService attribute) QueryHandler (class in disease.query) R rdp_url (disease.schemas.SourceMeta attribute) records (disease.schemas.SourceSearchMatches attribute) RecordType (class in disease.schemas) RefType (class in disease.schemas) response_datetime (disease.schemas.ServiceMeta attribute) S SCDO (disease.schemas.NamespacePrefix attribute) search() (disease.query.QueryHandler method) SearchService (class in disease.schemas) service_meta_ (disease.schemas.NormalizationService attribute) (disease.schemas.SearchService attribute) ServiceMeta (class in disease.schemas) share_alike (disease.schemas.DataLicenseAttributes attribute) source_matches (disease.schemas.SearchService attribute) source_meta_ (disease.schemas.NormalizationService attribute) (disease.schemas.SourceSearchMatches attribute) SourceIDAfterNamespace (class in disease.schemas) SourceMeta (class in disease.schemas) SourceName (class in disease.schemas) SourcePriority (class in disease.schemas) SourceSearchMatches (class in disease.schemas) STAGING (disease.database.database.AwsEnvName attribute) U UMLS (disease.schemas.NamespacePrefix attribute) update_merge_ref() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) url (disease.schemas.ServiceMeta attribute) V version (disease.schemas.ServiceMeta attribute) (disease.schemas.SourceMeta attribute) W warnings (disease.schemas.NormalizationService attribute) (disease.schemas.SearchService attribute) WIKIDATA (disease.schemas.NamespacePrefix attribute) WIKIPEDIA (disease.schemas.NamespacePrefix attribute) X XREF (disease.schemas.MatchType attribute) xrefs (disease.schemas.Disease attribute) XREFS (disease.schemas.RefType attribute)