disease.schemas

Contains data models for representing VICC normalized disease records.

class disease.schemas.DataLicenseAttributes(**data)

Define constraints for data license attributes.

attribution: Annotated[bool]

non_commercial: Annotated[bool]

share_alike: Annotated[bool]

class disease.schemas.Disease(**data)

Define disease record.

aliases: list[Annotated[str]]

associated_with: list[Annotated[str]]

concept_id: Annotated[str]

label: Annotated[str]

oncologic_disease: Optional[bool]

pediatric_disease: Optional[bool]

xrefs: list[Annotated[str]]

class disease.schemas.MatchType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Define string constraints for use in Match Type attributes.

ALIAS = 60

ASSOCIATED_WITH = 60

CONCEPT_ID = 100

FUZZY_MATCH = 20

LABEL = 80

NO_MATCH = 0

XREF = 60

class disease.schemas.NamespacePrefix(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Define string constraints for how concept ID namespace prefixes are stored.

DO = 'DOID'

DOID = 'DOID'

EFO = 'efo'

GARD = 'gard'

ICD10 = 'icd10'

ICD10CM = 'icd10.cm'

ICD10WHO = 'icd10'

ICD9CM = 'icd9.cm'

ICDO = 'icdo'

IMDRF = 'imdrf'

KEGG = 'kegg.disease'

MEDDRA = 'meddra'

MEDGEN = 'medgen'

MESH = 'mesh'

MONDO = 'mondo'

NCIT = 'ncit'

OMIM = 'MIM'

ONCOTREE = 'oncotree'

ORPHANET = 'orphanet'

UMLS = 'umls'

class disease.schemas.NormalizationService(**data)

Response containing one or more merged records and source data.

disease: Optional[MappableConcept]

match_type: MatchType

query: Annotated[str]

service_meta_: ServiceMeta

source_meta_: Optional[dict[SourceName, SourceMeta]]

warnings: Optional[dict]

class disease.schemas.RecordType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Record item types.

IDENTITY = 'identity'

MERGER = 'merger'

class disease.schemas.RefType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Reference item types.

ALIASES = 'alias'

ASSOCIATED_WITH = 'associated_with'

LABEL = 'label'

XREFS = 'xref'

class disease.schemas.SearchService(**data)

Core response schema containing matches for each source

query: Annotated[str]

service_meta_: ServiceMeta

source_matches: dict[SourceName, SourceSearchMatches]

warnings: Optional[dict]

class disease.schemas.ServiceEnvironment(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Define current runtime environment.

DEV = 'dev'

PROD = 'prod'

STAGING = 'staging'

TEST = 'test'

class disease.schemas.ServiceInfo(**data)

Define response structure for GA4GH /service_info endpoint.

contactUrl: Literal['Alex.Wagner@nationwidechildrens.org']

createdAt: Literal['2021-01-01T00:00:00+00:00']

description: Literal['Resolve ambiguous references and descriptions of human diseases to consistently-structured, normalized terms']

documentationUrl: Literal['https://disease-normalizer.readthedocs.io/']

environment: ServiceEnvironment

id: Literal['org.genomicmedlab.disease_normalizer']

name: Literal['disease_normalizer']

organization: ServiceOrganization

type: ServiceType

updatedAt: Literal['2021-01-01T00:00:00+00:00']

version: Literal['0.11.3']

class disease.schemas.ServiceMeta(**data)

Metadata regarding the disease-normalization service.

name: Literal['disease-normalizer']

response_datetime: datetime

url: Literal['https://github.com/cancervariants/disease-normalization']

version: Annotated[str]

class disease.schemas.ServiceOrganization(**data)

Define service_info response for organization field

name: Literal["Genomic Medicine Lab at Nationwide Children's Hospital"]

url: Literal['https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab']

class disease.schemas.ServiceType(**data)

Define service_info response for type field

artifact: Literal['Disease Normalizer API']

group: Literal['org.genomicmedlab']

version: Literal['0.11.3']

class disease.schemas.SourceIDAfterNamespace(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Define string constraints after namespace.

DO = ''

MONDO = ''

NCIT = 'C'

OMIM = ''

ONCOTREE = ''

class disease.schemas.SourceMeta(**data)

Metadata for a given source to return in response object.

data_license: Annotated[str]

data_license_attributes: DataLicenseAttributes

data_license_url: Annotated[str]

data_url: Optional[Annotated[str]]

rdp_url: Optional[Annotated[str]]

version: Annotated[str]

class disease.schemas.SourceName(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Define string constraints to ensure consistent capitalization.

DO = 'DO'

MONDO = 'Mondo'

NCIT = 'NCIt'

OMIM = 'OMIM'

ONCOTREE = 'OncoTree'

class disease.schemas.SourcePriority(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Define priorities for sources in building merged concepts.

DO = 5

MONDO = 2

NCIT = 1

OMIM = 3

ONCOTREE = 4

class disease.schemas.SourceSearchMatches(**data)

Container for matching information from an individual source.

match_type: MatchType

records: list[Disease]

source_meta_: SourceMeta

disease.schemas.get_coding_object(concept_id)

Get coding object for CURIE identifier

system will use system prefix URL, OBO Foundry persistent URL (PURL), or source homepage, in that order of preference.

Parameters:

concept_id (str) – A lowercase concept identifier represented as a curie

Raises:

ValueError – If source of concept ID is not a valid NamespacePrefix

Return type:

Coding

Returns:

Coding object for identifier

disease.schemas.get_concept_mapping(concept_id, relation=Relation.RELATED_MATCH)

Get concept mapping for CURIE identifier

Parameters:

• concept_id (str) – A lowercase concept identifier represented as a curie

• relation (Relation) – SKOS mapping relationship, default is relatedMatch

Return type:

ConceptMapping

Returns:

Concept mapping for identifier