Index

Symbols

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

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

_

__init__() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method) (disease.etl.base.Base method) (disease.etl.base.DiseaseNormalizerEtlError 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_note() (disease.etl.base.DiseaseNormalizerEtlError 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) args (disease.etl.base.DiseaseNormalizerEtlError attribute) artifact (disease.schemas.ServiceType 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)

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) contactUrl (disease.schemas.ServiceInfo attribute) create_db() (in module disease.database.database) create_merged_concepts() (disease.etl.merge.Merge method) createdAt (disease.schemas.ServiceInfo attribute)

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) delete_normalized() (in module disease.etl.update) 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) (in module disease.etl.update) description (disease.schemas.ServiceInfo attribute) DEV (disease.schemas.ServiceEnvironment attribute) DEVELOPMENT (disease.database.database.AwsEnvName attribute) Disease (class in disease.schemas) disease (disease.schemas.NormalizationService attribute) disease-normalizer command line option --version disease-normalizer-check-db command line option --db_url --silent disease-normalizer-dump-database command line option --db_url --output_directory --silent -o disease-normalizer-update command line option --all --aws_instance --db_url --normalize --silent --use_existing SOURCES disease-normalizer-update-from-remote command line option --data_url --db_url --silent

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.etl.update module disease.query module disease.schemas module DiseaseNormalizerEtlError DO (class in disease.etl.do) (disease.schemas.NamespacePrefix attribute) (disease.schemas.SourceIDAfterNamespace attribute) (disease.schemas.SourceName attribute) (disease.schemas.SourcePriority attribute) documentationUrl (disease.schemas.ServiceInfo 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) environment (disease.schemas.ServiceInfo 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_coding_object() (in module disease.schemas) get_concept_mapping() (in module disease.schemas)

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) group (disease.schemas.ServiceType attribute)

I

ICD10 (disease.schemas.NamespacePrefix attribute) ICD10CM (disease.schemas.NamespacePrefix attribute) ICD10WHO (disease.schemas.NamespacePrefix attribute) ICD9CM (disease.schemas.NamespacePrefix attribute) ICDO (disease.schemas.NamespacePrefix attribute) id (disease.schemas.ServiceInfo attribute)

IDENTITY (disease.schemas.RecordType 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) load_source() (in module disease.etl.update)

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) 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.etl.update 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)

N

name (disease.schemas.ServiceInfo attribute) (disease.schemas.ServiceMeta attribute) (disease.schemas.ServiceOrganization 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)

NO_MATCH (disease.schemas.MatchType attribute) non_commercial (disease.schemas.DataLicenseAttributes attribute) NormalizationService (class in disease.schemas) normalize() (disease.query.QueryHandler method)

O

OMIM (class in disease.etl.omim) (disease.schemas.NamespacePrefix attribute) (disease.schemas.SourceIDAfterNamespace attribute) (disease.schemas.SourceName attribute) (disease.schemas.SourcePriority attribute) oncologic_disease (disease.schemas.Disease attribute) OncoTree (class in disease.etl.oncotree)

ONCOTREE (disease.schemas.NamespacePrefix attribute) (disease.schemas.SourceIDAfterNamespace attribute) (disease.schemas.SourceName attribute) (disease.schemas.SourcePriority attribute) organization (disease.schemas.ServiceInfo attribute) ORPHANET (disease.schemas.NamespacePrefix attribute) OWLBase (class in disease.etl.base)

P

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) PROD (disease.schemas.ServiceEnvironment attribute) 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

search() (disease.query.QueryHandler method) SearchService (class in disease.schemas) service_meta_ (disease.schemas.NormalizationService attribute) (disease.schemas.SearchService attribute) ServiceEnvironment (class in disease.schemas) ServiceInfo (class in disease.schemas) ServiceMeta (class in disease.schemas) ServiceOrganization (class in disease.schemas) ServiceType (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) SOURCES disease-normalizer-update command line option SourceSearchMatches (class in disease.schemas) STAGING (disease.database.database.AwsEnvName attribute) (disease.schemas.ServiceEnvironment attribute)

T

TEST (disease.schemas.ServiceEnvironment attribute)

type (disease.schemas.ServiceInfo attribute)

U

UMLS (disease.schemas.NamespacePrefix attribute) update_all_and_normalize() (in module disease.etl.update) update_all_sources() (in module disease.etl.update) update_merge_ref() (disease.database.database.AbstractDatabase method) (disease.database.dynamodb.DynamoDbDatabase method) (disease.database.postgresql.PostgresDatabase method)

update_normalized() (in module disease.etl.update) update_source() (in module disease.etl.update) updatedAt (disease.schemas.ServiceInfo attribute) url (disease.schemas.ServiceMeta attribute) (disease.schemas.ServiceOrganization attribute)

V

version (disease.schemas.ServiceInfo attribute) (disease.schemas.ServiceMeta attribute) (disease.schemas.ServiceType attribute) (disease.schemas.SourceMeta attribute)

W

warnings (disease.schemas.NormalizationService attribute) (disease.schemas.SearchService attribute)

with_traceback() (disease.etl.base.DiseaseNormalizerEtlError method)

X

XREF (disease.schemas.MatchType attribute)

xrefs (disease.schemas.Disease attribute) XREFS (disease.schemas.RefType attribute)