Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X _ __init__() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) (gene.etl.base.Base method) (gene.etl.merge.Merge method) (gene.etl.ncbi.NCBI method) (gene.query.QueryHandler method) A AbstractDatabase (class in gene.database.database) add_merged_record() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) add_record() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) add_source_metadata() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) ALIAS (gene.schemas.MatchType attribute), [1] aliases (gene.schemas.BaseGene attribute) ALIASES (gene.schemas.RefType attribute) ALT_LOC (gene.schemas.Annotation attribute) Annotation (class in gene.schemas) APPROVED (gene.schemas.SymbolStatus attribute) associated_with (gene.schemas.BaseGene attribute) ASSOCIATED_WITH (gene.schemas.MatchType attribute), [1] (gene.schemas.RefType attribute) attribution (gene.schemas.DataLicenseAttributes attribute) AwsEnvName (class in gene.database.database) B Base (class in gene.etl.base) BaseGene (class in gene.schemas) BaseNormalizationService (class in gene.schemas) C CCDS (gene.schemas.NamespacePrefix attribute) CD (gene.schemas.NamespacePrefix attribute) check_schema_initialized() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) check_tables_populated() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) Chromosome (class in gene.schemas) close_connection() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) complete_write_transaction() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) concept_id (gene.schemas.BaseGene attribute) CONCEPT_ID (gene.schemas.MatchType attribute), [1] confirm_aws_db_use() (in module gene.database.database) COSMIC (gene.schemas.NamespacePrefix attribute) create_db() (in module gene.database.database) create_merged_concepts() (gene.etl.merge.Merge method) D data_license (gene.schemas.SourceMeta attribute) data_license_attributes (gene.schemas.SourceMeta attribute) data_license_url (gene.schemas.SourceMeta attribute) data_url (gene.schemas.SourceMeta attribute) DatabaseException DatabaseInitializationException DatabaseReadException DatabaseWriteException DataLicenseAttributes (class in gene.schemas) delete_normalized_concepts() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) delete_source() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) description (gene.schemas.GeneGroup attribute) DEVELOPMENT (gene.database.database.AwsEnvName attribute) DISCONTINUED (gene.schemas.SymbolStatus attribute) drop_db() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) DynamoDbDatabase (class in gene.database.dynamodb) E ENA (gene.schemas.NamespacePrefix attribute) end (gene.schemas.GeneSequenceLocation attribute) Ensembl (class in gene.etl.ensembl) ENSEMBL (gene.schemas.GeneTypeFieldName attribute) (gene.schemas.NamespacePrefix attribute) (gene.schemas.SourceIDAfterNamespace attribute) (gene.schemas.SourceName attribute) (gene.schemas.SourcePriority attribute) ENTREZ (gene.schemas.NamespacePrefix attribute) export_db() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) F FORWARD (gene.schemas.Strand attribute) FUZZY_MATCH (gene.schemas.MatchType attribute), [1] G Gene (class in gene.schemas) gene (gene.schemas.NormalizeService attribute) gene.database.database module gene.database.dynamodb module gene.database.postgresql module gene.etl.base module gene.etl.ensembl module gene.etl.exceptions module gene.etl.hgnc module gene.etl.merge module gene.etl.ncbi module gene.query module gene.schemas module gene_type (gene.schemas.BaseGene attribute) GeneFileVersionError GeneGroup (class in gene.schemas) GeneNormalizerEtlError genes (gene.schemas.GeneGroup attribute) GeneSequenceLocation (class in gene.schemas) GeneSourceFetchError GeneTypeFieldName (class in gene.schemas) genome_assemblies (gene.schemas.SourceMeta attribute) get_all_concept_ids() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) get_all_records() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) get_record_by_id() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) get_refs_by_type() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) get_seqrepo() (gene.etl.base.Base method) get_source_metadata() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) H HGNC (class in gene.etl.hgnc) (gene.schemas.GeneTypeFieldName attribute) (gene.schemas.NamespacePrefix attribute) (gene.schemas.SourceIDAfterNamespace attribute) (gene.schemas.SourceName attribute) (gene.schemas.SourcePriority attribute) HOMEODB (gene.schemas.NamespacePrefix attribute) HORDE (gene.schemas.NamespacePrefix attribute) I IDENTITY (gene.schemas.RecordType attribute) IMGT (gene.schemas.NamespacePrefix attribute) IMGT_GENE_DB (gene.schemas.NamespacePrefix attribute) initialize_db() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) InvalidParameterException IUPHAR (gene.schemas.NamespacePrefix attribute) K KZNF (gene.schemas.NamespacePrefix attribute) L label (gene.schemas.BaseGene attribute) list_tables() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) LNCRNADB (gene.schemas.NamespacePrefix attribute) load_from_remote() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) location_annotations (gene.schemas.BaseGene attribute) locations (gene.schemas.BaseGene attribute) M MAMIT (gene.schemas.NamespacePrefix attribute) match_type (gene.schemas.BaseNormalizationService attribute) (gene.schemas.Gene attribute) MatchesNormalized (class in gene.schemas) MatchType (class in gene.schemas), [1] Merge (class in gene.etl.merge) MERGER (gene.schemas.RecordType attribute) MEROPS (gene.schemas.NamespacePrefix attribute) MIRBASE (gene.schemas.NamespacePrefix attribute) MITOCHONDRIA (gene.schemas.Chromosome attribute) model_computed_fields (gene.schemas.BaseGene attribute) (gene.schemas.BaseNormalizationService attribute) (gene.schemas.DataLicenseAttributes attribute) (gene.schemas.Gene attribute) (gene.schemas.GeneGroup attribute) (gene.schemas.GeneSequenceLocation attribute) (gene.schemas.MatchesNormalized attribute) (gene.schemas.NormalizeService attribute) (gene.schemas.SearchService attribute) (gene.schemas.ServiceMeta attribute) (gene.schemas.SourceMeta attribute) (gene.schemas.SourceSearchMatches attribute) (gene.schemas.UnmergedNormalizationService attribute) module gene.database.database gene.database.dynamodb gene.database.postgresql gene.etl.base gene.etl.ensembl gene.etl.exceptions gene.etl.hgnc gene.etl.merge gene.etl.ncbi gene.query gene.schemas N name (gene.schemas.ServiceMeta attribute) NamespacePrefix (class in gene.schemas) NCBI (class in gene.etl.ncbi) (gene.schemas.GeneTypeFieldName attribute) (gene.schemas.NamespacePrefix attribute) (gene.schemas.SourceIDAfterNamespace attribute) (gene.schemas.SourceName attribute) (gene.schemas.SourcePriority attribute) NO_MATCH (gene.schemas.MatchType attribute), [1] non_commercial (gene.schemas.DataLicenseAttributes attribute) normalize() (gene.query.QueryHandler method) normalize_unmerged() (gene.query.QueryHandler method) normalized_concept_id (gene.schemas.UnmergedNormalizationService attribute) normalized_id (gene.schemas.NormalizeService attribute) NormalizeService (class in gene.schemas) NOT_FOUND_ON_REFERENCE (gene.schemas.Annotation attribute) O OMIM (gene.schemas.NamespacePrefix attribute) ORPHANET (gene.schemas.NamespacePrefix attribute) P perform_etl() (gene.etl.base.Base method) PostgresDatabase (class in gene.database.postgresql) PREV_SYMBOL (gene.schemas.MatchType attribute), [1] previous_symbols (gene.schemas.BaseGene attribute) PREVIOUS_SYMBOLS (gene.schemas.RefType attribute) PRODUCTION (gene.database.database.AwsEnvName attribute) PSEUDOGENE (gene.schemas.NamespacePrefix attribute) PUBMED (gene.schemas.NamespacePrefix attribute) Q query (gene.schemas.BaseNormalizationService attribute) (gene.schemas.SearchService attribute) QueryHandler (class in gene.query) R rdp_url (gene.schemas.SourceMeta attribute) records (gene.schemas.MatchesNormalized attribute) (gene.schemas.SourceSearchMatches attribute) RecordType (class in gene.schemas) REFSEQ (gene.schemas.NamespacePrefix attribute) RefType (class in gene.schemas) RESERVED (gene.schemas.Annotation attribute) response_datetime (gene.schemas.ServiceMeta attribute) REVERSE (gene.schemas.Strand attribute) RFAM (gene.schemas.NamespacePrefix attribute) S search() (gene.query.QueryHandler method) SearchService (class in gene.schemas) sequence_id (gene.schemas.GeneSequenceLocation attribute) service_meta_ (gene.schemas.BaseNormalizationService attribute) (gene.schemas.SearchService attribute) ServiceMeta (class in gene.schemas) share_alike (gene.schemas.DataLicenseAttributes attribute) SNORNABASE (gene.schemas.NamespacePrefix attribute) source_matches (gene.schemas.SearchService attribute) (gene.schemas.UnmergedNormalizationService attribute) source_meta_ (gene.schemas.MatchesNormalized attribute) (gene.schemas.NormalizeService attribute) (gene.schemas.SourceSearchMatches attribute) SourceIDAfterNamespace (class in gene.schemas) SourceMeta (class in gene.schemas) SourceName (class in gene.schemas) SourcePriority (class in gene.schemas) SourceSearchMatches (class in gene.schemas) STAGING (gene.database.database.AwsEnvName attribute) start (gene.schemas.GeneSequenceLocation attribute) Strand (class in gene.schemas) strand (gene.schemas.BaseGene attribute) symbol (gene.schemas.BaseGene attribute) SYMBOL (gene.schemas.MatchType attribute), [1] (gene.schemas.RefType attribute) symbol_status (gene.schemas.BaseGene attribute) SymbolStatus (class in gene.schemas) T type (gene.schemas.GeneSequenceLocation attribute) type_identifier (gene.schemas.GeneGroup attribute) U UCSC (gene.schemas.NamespacePrefix attribute) UNIPROT (gene.schemas.NamespacePrefix attribute) UnmergedNormalizationService (class in gene.schemas) UNPLACED (gene.schemas.Annotation attribute) update_merge_ref() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) url (gene.schemas.ServiceMeta attribute) V VEGA (gene.schemas.NamespacePrefix attribute) version (gene.schemas.ServiceMeta attribute) (gene.schemas.SourceMeta attribute) W warnings (gene.schemas.BaseNormalizationService attribute) (gene.schemas.SearchService attribute) WITHDRAWN (gene.schemas.SymbolStatus attribute) X XREF (gene.schemas.MatchType attribute), [1] xrefs (gene.schemas.BaseGene attribute) XREFS (gene.schemas.RefType attribute)