Index

Symbols

--all gene-normalizer-update command line option --aws_instance gene-normalizer-update command line option --data_url gene-normalizer-update-from-remote command line option --db_url gene-normalizer-check-db command line option gene-normalizer-dump-database command line option gene-normalizer-update command line option gene-normalizer-update-from-remote command line option --normalize gene-normalizer-update command line option

--output_directory gene-normalizer-dump-database command line option --silent gene-normalizer-check-db command line option gene-normalizer-dump-database command line option gene-normalizer-update command line option gene-normalizer-update-from-remote command line option --use_existing gene-normalizer-update command line option --version gene-normalizer command line option -o gene-normalizer-dump-database command line option

_

__init__() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) (gene.etl.base.Base method) (gene.etl.ensembl.Ensembl method) (gene.etl.exceptions.GeneFileVersionError method) (gene.etl.exceptions.GeneNormalizerEtlError method) (gene.etl.exceptions.GeneSourceFetchError method) (gene.etl.hgnc.HGNC 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_note() (gene.etl.exceptions.GeneFileVersionError method) (gene.etl.exceptions.GeneNormalizerEtlError method) (gene.etl.exceptions.GeneSourceFetchError 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) 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) args (gene.etl.exceptions.GeneFileVersionError attribute) (gene.etl.exceptions.GeneNormalizerEtlError attribute) (gene.etl.exceptions.GeneSourceFetchError attribute) associated_with (gene.schemas.BaseGene attribute) ASSOCIATED_WITH (gene.schemas.MatchType attribute) (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) 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() (in module gene.etl.update) 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) (in module gene.etl.update) DEV (gene.schemas.ServiceEnvironment 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)

G

Gene (class in gene.schemas) gene (gene.schemas.NormalizeService attribute) gene-normalizer command line option --version gene-normalizer-check-db command line option --db_url --silent gene-normalizer-dump-database command line option --db_url --output_directory --silent -o gene-normalizer-update command line option --all --aws_instance --db_url --normalize --silent --use_existing SOURCES gene-normalizer-update-from-remote command line option --data_url --db_url --silent 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.etl.update module gene.query module gene.schemas module gene_type (gene.schemas.BaseGene attribute) GeneFileVersionError GeneNormalizerEtlError 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) (gene.etl.ensembl.Ensembl method) (gene.etl.hgnc.HGNC method) (gene.etl.ncbi.NCBI 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)

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) load_source() (in module gene.etl.update) 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) 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) 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.etl.update 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) non_commercial (gene.schemas.DataLicenseAttributes attribute) normalize() (gene.query.QueryHandler method) normalize_unmerged() (gene.query.QueryHandler method) normalized_concept_id (gene.schemas.UnmergedNormalizationService 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) (gene.etl.ensembl.Ensembl method) (gene.etl.hgnc.HGNC method) (gene.etl.ncbi.NCBI method) PostgresDatabase (class in gene.database.postgresql) PREV_SYMBOL (gene.schemas.MatchType attribute)

previous_symbols (gene.schemas.BaseGene attribute) PREVIOUS_SYMBOLS (gene.schemas.RefType attribute) PROD (gene.schemas.ServiceEnvironment 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) ServiceEnvironment (class in gene.schemas) 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) SOURCES gene-normalizer-update command line option SourceSearchMatches (class in gene.schemas) STAGING (gene.database.database.AwsEnvName attribute) (gene.schemas.ServiceEnvironment 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) (gene.schemas.RefType attribute) symbol_status (gene.schemas.BaseGene attribute) SymbolStatus (class in gene.schemas)

T

TEST (gene.schemas.ServiceEnvironment attribute)

type (gene.schemas.GeneSequenceLocation attribute)

U

UCSC (gene.schemas.NamespacePrefix attribute) UNIPROT (gene.schemas.NamespacePrefix attribute) UnmergedNormalizationService (class in gene.schemas) UNPLACED (gene.schemas.Annotation attribute) update_all_and_normalize() (in module gene.etl.update) update_all_sources() (in module gene.etl.update)

update_merge_ref() (gene.database.database.AbstractDatabase method) (gene.database.dynamodb.DynamoDbDatabase method) (gene.database.postgresql.PostgresDatabase method) update_normalized() (in module gene.etl.update) update_source() (in module gene.etl.update) 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) with_traceback() (gene.etl.exceptions.GeneFileVersionError method) (gene.etl.exceptions.GeneNormalizerEtlError method) (gene.etl.exceptions.GeneSourceFetchError method)

WITHDRAWN (gene.schemas.SymbolStatus attribute)

X

XREF (gene.schemas.MatchType attribute)

xrefs (gene.schemas.BaseGene attribute) XREFS (gene.schemas.RefType attribute)