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]

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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]

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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.

COHD = 'cohd'

DECIPHER = 'decipher'

DO = 'DOID'

DOID = 'DOID'

EFO = 'efo'

GARD = 'gard'

HP = 'HP'

HPO = 'HP'

ICD10 = 'icd10'

ICD10CM = 'icd10.cm'

ICD10WHO = 'icd10'

ICD11 = 'icd11'

ICD9 = 'icd9'

ICD9CM = 'icd9.cm'

ICDO = 'icdo'

IDO = 'ido'

IMDRF = 'imdrf'

KEGG = 'kegg.disease'

MEDDRA = 'meddra'

MEDGEN = 'medgen'

MESH = 'mesh'

MF = 'mf'

MONDO = 'mondo'

MP = 'MP'

MPATH = 'mpath'

NCIT = 'ncit'

NIFSTD = 'nifstd'

OBI = 'obi'

OGMS = 'ogms'

OMIM = 'omim'

OMIMPS = 'omimps'

ONCOTREE = 'oncotree'

ORPHANET = 'orphanet'

PATO = 'pato'

SCDO = 'scdo'

UMLS = 'umls'

WIKIDATA = 'wikidata'

WIKIPEDIA = 'wikipedia.en'

class disease.schemas.NormalizationService(**data)

Response containing one or more merged records and source data.

disease: Optional[Disease]

match_type: MatchType

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

normalized_id: Optional[str]

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

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

query: Annotated[str]

service_meta_: ServiceMeta

source_matches: Dict[SourceName, SourceSearchMatches]

warnings: Optional[Dict]

class disease.schemas.ServiceMeta(**data)

Metadata regarding the disease-normalization service.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

name: Literal['disease-normalizer']

response_datetime: datetime

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

version: Annotated[str]

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]]

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

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

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

records: List[Disease]

source_meta_: SourceMeta