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schemas.py
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schemas.py
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"""Contains data models for representing VICC normalized disease records."""
import datetime
from enum import Enum, IntEnum
from typing import Dict, List, Literal, Optional
from ga4gh.core import core_models
from pydantic import BaseModel, ConfigDict, StrictBool, StrictStr
from disease.version import __version__
class MatchType(IntEnum):
"""Define string constraints for use in Match Type attributes."""
CONCEPT_ID = 100
LABEL = 80
ALIAS = 60
XREF = 60
ASSOCIATED_WITH = 60
FUZZY_MATCH = 20
NO_MATCH = 0
class SourceName(str, Enum):
"""Define string constraints to ensure consistent capitalization."""
NCIT = "NCIt"
MONDO = "Mondo"
DO = "DO"
ONCOTREE = "OncoTree"
OMIM = "OMIM"
class SourceIDAfterNamespace(Enum):
"""Define string constraints after namespace."""
NCIT = "C"
MONDO = ""
DO = "" # noqa: PIE796
ONCOTREE = "" # noqa: PIE796
OMIM = "" # noqa: PIE796
class NamespacePrefix(Enum):
"""Define string constraints for how concept ID namespace prefixes are
stored.
"""
# built-in sources
NCIT = "ncit"
MONDO = "mondo"
DOID = "DOID"
DO = DOID
OMIM = "omim"
ONCOTREE = "oncotree"
# external sources
COHD = "cohd"
DECIPHER = "decipher"
EFO = "efo"
GARD = "gard"
HP = "HP"
HPO = HP
ICD9 = "icd9"
ICD9CM = "icd9.cm"
ICD10 = "icd10"
ICD10WHO = ICD10
ICD10CM = "icd10.cm"
ICD11 = "icd11"
ICDO = "icdo"
IDO = "ido"
IMDRF = "imdrf"
KEGG = "kegg.disease"
MEDDRA = "meddra"
MEDGEN = "medgen"
MESH = "mesh"
MF = "mf"
MP = "MP"
MPATH = "mpath"
NIFSTD = "nifstd"
OBI = "obi"
OGMS = "ogms"
OMIMPS = "omimps"
ORPHANET = "orphanet"
PATO = "pato"
SCDO = "scdo"
UMLS = "umls"
WIKIPEDIA = "wikipedia.en"
WIKIDATA = "wikidata"
class SourcePriority(IntEnum):
"""Define priorities for sources in building merged concepts."""
NCIT = 1
MONDO = 2
OMIM = 3
ONCOTREE = 4
DO = 5
class Disease(BaseModel):
"""Define disease record."""
label: StrictStr
concept_id: StrictStr
aliases: List[StrictStr] = []
xrefs: List[StrictStr] = []
associated_with: List[StrictStr] = []
pediatric_disease: Optional[bool] = None
model_config = ConfigDict(
json_schema_extra={
"example": {
"label": "Von Hippel-Lindau Syndrome",
"concept_id": "ncit:C3105",
"aliases": [
"Von Hippel-Lindau Syndrome (VHL)",
"Von Hippel-Lindau Disease",
"Cerebroretinal Angiomatosis",
"von Hippel-Lindau syndrome",
"VHL syndrome",
],
"xrefs": [],
"associated_with": ["umls:C0019562"],
"pediatric_disease": None,
}
}
)
class RecordType(str, Enum):
"""Record item types."""
IDENTITY = "identity"
MERGER = "merger"
class RefType(str, Enum):
"""Reference item types."""
# Must be in descending MatchType order.
LABEL = "label"
ALIASES = "alias"
XREFS = "xref"
ASSOCIATED_WITH = "associated_with"
class DataLicenseAttributes(BaseModel):
"""Define constraints for data license attributes."""
non_commercial: StrictBool
share_alike: StrictBool
attribution: StrictBool
class SourceMeta(BaseModel):
"""Metadata for a given source to return in response object."""
data_license: StrictStr
data_license_url: StrictStr
version: StrictStr
data_url: Optional[StrictStr] = None
rdp_url: Optional[StrictStr] = None
data_license_attributes: DataLicenseAttributes
model_config = ConfigDict(
json_schema_extra={
"example": {
"data_license": "CC BY 4.0",
"data_license_url": "https://creativecommons.org/licenses/by/4.0/legalcode",
"version": "21.01d",
"data_url": "https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/archive/21.01d_Release/",
"rdp_url": "http://reusabledata.org/ncit.html",
"data_license_attributes": {
"non_commercial": False,
"attribution": True,
"share_alike": False,
},
}
}
)
class SourceSearchMatches(BaseModel):
"""Container for matching information from an individual source."""
match_type: MatchType
records: List[Disease] = []
source_meta_: SourceMeta
model_config = ConfigDict(
json_schema_extra={
"example": {
"match_type": 80,
"records": [
{
"label": "non-small cell lung carcinoma",
"concept_id": "mondo:0005233",
"aliases": [
"non-small cell lung carcinoma (disease)",
"non-small cell carcinoma of lung",
"non-small cell lung cancer",
"non-small cell cancer of lung",
"non-small cell carcinoma of the lung",
"non-small cell cancer of the lung",
"NSCLC",
"NSCLC - non-small cell lung cancer",
],
"xrefs": ["DOID:3908", "ncit:C2926", "oncotree:NSCLC"],
"associated_with": [
"mesh:D002289",
"efo:0003060",
"umls:C0007131",
],
}
],
"source_meta_": {
"data_license": "CC BY 4.0",
"data_license_url": "https://creativecommons.org/licenses/by/4.0/legalcode",
"version": "2023-07-03",
"data_url": "https://mondo.monarchinitiative.org/pages/download/",
"rdp_url": "http://reusabledata.org/monarch.html",
"data_license_attributes": {
"non_commercial": False,
"attribution": True,
"share_alike": False,
},
},
}
}
)
class ServiceMeta(BaseModel):
"""Metadata regarding the disease-normalization service."""
name: Literal["disease-normalizer"] = "disease-normalizer"
version: StrictStr
response_datetime: datetime.datetime
url: Literal[
"https://github.com/cancervariants/disease-normalization"
] = "https://github.com/cancervariants/disease-normalization"
model_config = ConfigDict(
json_schema_extra={
"example": {
"name": "disease-normalizer",
"version": __version__,
"response_datetime": "2021-04-05T16:44:15.367831",
"url": "https://github.com/cancervariants/disease-normalization",
}
}
)
class NormalizationService(BaseModel):
"""Response containing one or more merged records and source data."""
query: StrictStr
warnings: Optional[Dict] = None
match_type: MatchType
normalized_id: Optional[str] = None
disease: Optional[core_models.Disease] = None
source_meta_: Optional[Dict[SourceName, SourceMeta]] = None
service_meta_: ServiceMeta
model_config = ConfigDict(
json_schema_extra={
"example": {
"query": "childhood leukemia",
"warnings": None,
"match_type": 80,
"normalized_id": "ncit:C4989",
"disease": {
"id": "normalize.disease.ncit:C4989",
"type": "Disease",
"label": "Childhood Leukemia",
"aliases": [
"childhood leukemia (disease)",
"leukemia",
"pediatric leukemia (disease)",
"Leukemia",
"leukemia (disease) of childhood",
],
"mappings": [
{
"coding": {"code": "0004355", "system": "mondo"},
"relation": "relatedMatch",
},
{
"coding": {"code": "7757", "system": "doid"},
"relation": "relatedMatch",
},
{
"coding": {"code": "C1332977", "system": "umls"},
"relation": "relatedMatch",
},
],
"extensions": [
{
"type": "Extension",
"name": "pediatric_disease",
"value": True,
},
],
},
"source_meta_": {
"NCIt": {
"data_license": "CC BY 4.0",
"data_license_url": "https://creativecommons.org/licenses/by/4.0/legalcode",
"version": "21.01d",
"data_url": "https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/archive/21.01d_Release/",
"rdp_url": "http://reusabledata.org/ncit.html",
"data_license_attributes": {
"non_commercial": False,
"attribution": True,
"share_alike": False,
},
},
"Mondo": {
"data_license": "CC BY 4.0",
"data_license_url": "https://creativecommons.org/licenses/by/4.0/legalcode",
"version": "20210129",
"data_url": "https://mondo.monarchinitiative.org/pages/download/",
"rdp_url": "http://reusabledata.org/monarch.html",
"data_license_attributes": {
"non_commercial": False,
"attribution": True,
"share_alike": False,
},
},
"DO": {
"data_license": "CC0 1.0",
"data_license_url": "https://creativecommons.org/publicdomain/zero/1.0/legalcode",
"version": "20210305",
"data_url": "http://www.obofoundry.org/ontology/doid.html",
"rdp_url": None,
"data_license_attributes": {
"non_commercial": False,
"attribution": False,
"share_alike": False,
},
},
},
"service_meta_": {
"name": "disease-normalizer",
"version": __version__,
"response_datetime": "2021-04-05T16:44:15.367831",
"url": "https://github.com/cancervariants/disease-normalization",
},
}
}
)
class SearchService(BaseModel):
"""Core response schema containing matches for each source"""
query: StrictStr
warnings: Optional[Dict] = None
source_matches: Dict[SourceName, SourceSearchMatches]
service_meta_: ServiceMeta
model_config = ConfigDict(
json_schema_extra={
"query": "nsclc",
"source_matches": {
"OMIM": {
"records": [],
"source_meta_": {
"data_license": "custom",
"data_license_url": "https://omim.org/help/agreement",
"version": "20231030",
"data_url": "https://www.omim.org/downloads",
"rdp_url": "http://reusabledata.org/omim.html",
"data_license_attributes": {
"non_commercial": False,
"attribution": True,
"share_alike": True,
},
},
},
"DO": {
"records": [
{
"label": "lung non-small cell carcinoma",
"concept_id": "DOID:3908",
"aliases": [
"Non-small cell lung cancer",
"NSCLC",
"non-small cell lung carcinoma",
],
"xrefs": ["ncit:C2926"],
"associated_with": [
"mesh:D002289",
"kegg.disease:05223",
"efo:0003060",
"umls:C0007131",
],
"match_type": 60,
}
],
"source_meta_": {
"data_license": "CC0 1.0",
"data_license_url": "https://creativecommons.org/publicdomain/zero/1.0/legalcode",
"version": "2023-07-24",
"data_url": "http://www.obofoundry.org/ontology/doid.html",
"data_license_attributes": {
"non_commercial": False,
"attribution": False,
"share_alike": False,
},
},
},
},
"service_meta_": {
"name": "disease-normalizer",
"version": "0.4.0.dev1",
"response_datetime": "2023-10-31T10:53:30.890262",
"url": "https://github.com/cancervariants/disease-normalization",
},
}
)