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feat!: use preferred formats for MappableConcept.mappings #215

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Dec 31, 2024
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feat!: use preferred formats for MappableConcept.mappings #215

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6d4531b
feat!: use preferred formats for `MappableConcept.mappings`
korikuzma Dec 27, 2024
7e1ec5a
update schema example
korikuzma Dec 27, 2024
be907bc
use obo foundry purl or homepage
korikuzma Dec 30, 2024
5406200
revert
korikuzma Dec 30, 2024
6b059e8
add few more urls
korikuzma Dec 30, 2024
b72f3a3
trailing slash
korikuzma Dec 31, 2024
fb70350
fix meddra
korikuzma Dec 31, 2024
7750db3
use curie for concept mapping code
korikuzma Dec 31, 2024
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66 changes: 46 additions & 20 deletions src/disease/query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,11 @@
from disease import NAMESPACE_LOOKUP, PREFIX_LOOKUP, SOURCES_LOWER_LOOKUP, __version__
from disease.database.database import AbstractDatabase
from disease.schemas import (
NAMESPACE_TO_SYSTEM_URI,
SYSTEM_URI_TO_NAMESPACE,
Disease,
MatchType,
NamespacePrefix,
NormalizationService,
RefType,
SearchService,
Expand Down Expand Up @@ -299,19 +302,20 @@ def _add_merged_meta(self, response: dict) -> dict:
"""
sources_meta = {}
disease = response["disease"]
sources = [response["normalized_id"].split(":")[0]]
if disease.mappings:
sources += [m.coding.system for m in disease.mappings]

sources = []
concept_id_source = response["normalized_id"].split(":")[0]
if concept_id_source in PREFIX_LOOKUP:
sources.append(PREFIX_LOOKUP[concept_id_source])

for m in disease.mappings or []:
ns = SYSTEM_URI_TO_NAMESPACE.get(m.coding.system, "").lower()
if ns in PREFIX_LOOKUP:
sources.append(PREFIX_LOOKUP[ns])

for src in sources:
try:
src_name = PREFIX_LOOKUP[src]
except KeyError:
# not an imported source
continue
else:
if src_name not in sources_meta:
sources_meta[src_name] = self.db.get_source_metadata(src_name)
if src not in sources_meta:
sources_meta[src] = self.db.get_source_metadata(src)
response["source_meta_"] = sources_meta
return response

Expand All @@ -325,6 +329,36 @@ def _add_disease(
:param match_type: type of match achieved
:return: completed normalized response object ready to return to user
"""

def _create_concept_mapping(
concept_id: str, relation: Relation = Relation.RELATED_MATCH
) -> ConceptMapping:
"""Create concept mapping for identifier

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

:param concept_id: Concept identifier represented as a curie
:param relation: SKOS mapping relationship, default is relatedMatch
:return: Concept mapping for identifier
"""
source = concept_id.split(":")[0]

try:
source = NamespacePrefix(source)
except ValueError:
try:
source = NamespacePrefix(source.upper())
except ValueError as e:
err_msg = f"Namespace prefix not supported: {source}"
raise ValueError(err_msg) from e

system = NAMESPACE_TO_SYSTEM_URI.get(source, source)

return ConceptMapping(
coding=Coding(code=code(concept_id), system=system), relation=relation
)

disease_obj = MappableConcept(
id=f"normalize.disease.{record['concept_id']}",
conceptType="Disease",
Expand All @@ -333,15 +367,7 @@ def _add_disease(
)

source_ids = record.get("xrefs", []) + record.get("associated_with", [])
mappings = []
for source_id in source_ids:
system, source_code = source_id.split(":")
mappings.append(
ConceptMapping(
coding=Coding(code=code(source_code), system=system.lower()),
relation=Relation.RELATED_MATCH,
)
)
mappings = [_create_concept_mapping(source_id) for source_id in source_ids]
if mappings:
disease_obj.mappings = mappings

Expand Down
69 changes: 58 additions & 11 deletions src/disease/schemas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,41 @@ class NamespacePrefix(Enum):
WIKIDATA = "wikidata"


# Source to URI. Will use OBO Foundry persistent URL (PURL) or source homepage
NAMESPACE_TO_SYSTEM_URI: dict[NamespacePrefix, str] = {
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NamespacePrefix.NCIT: "http://purl.obolibrary.org/obo/ncit.owl",
NamespacePrefix.MONDO: "http://purl.obolibrary.org/obo/mondo.owl",
NamespacePrefix.DO: "http://purl.obolibrary.org/obo/doid.owl",
NamespacePrefix.DOID: "http://purl.obolibrary.org/obo/doid.owl",
NamespacePrefix.OMIM: "https://www.omim.org",
NamespacePrefix.ONCOTREE: "https://oncotree.mskcc.org",
NamespacePrefix.COHD: "https://cohd.io",
NamespacePrefix.DECIPHER: "https://www.deciphergenomics.org",
NamespacePrefix.EFO: "https://www.ebi.ac.uk/efo/",
NamespacePrefix.GARD: "https://rarediseases.info.nih.gov",
NamespacePrefix.HP: "http://purl.obolibrary.org/obo/hp.owl",
NamespacePrefix.HPO: "http://purl.obolibrary.org/obo/hp.owl",
NamespacePrefix.ICD11: "https://icd.who.int/en/",
NamespacePrefix.ICDO: "https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology/",
NamespacePrefix.KEGG: "https://www.genome.jp/kegg/disease/",
NamespacePrefix.MEDDRA: "https://www.meddra.org",
NamespacePrefix.MEDGEN: "https://www.ncbi.nlm.nih.gov/medgen/",
NamespacePrefix.MESH: "https://id.nlm.nih.gov/mesh/",
NamespacePrefix.MP: "http://purl.obolibrary.org/obo/mp.owl",
NamespacePrefix.OBI: "http://purl.obolibrary.org/obo/obi.owl",
NamespacePrefix.ORPHANET: "https://www.orpha.net",
NamespacePrefix.PATO: "http://purl.obolibrary.org/obo/pato.owl",
NamespacePrefix.UMLS: "https://www.nlm.nih.gov/research/umls/index.html",
NamespacePrefix.WIKIPEDIA: "https://en.wikipedia.org",
NamespacePrefix.WIKIDATA: "https://www.wikidata.org",
}

# URI to source
SYSTEM_URI_TO_NAMESPACE = {
system_uri: ns.value for ns, system_uri in NAMESPACE_TO_SYSTEM_URI.items()
}


class SourcePriority(IntEnum):
"""Define priorities for sources in building merged concepts."""

Expand Down Expand Up @@ -275,30 +310,42 @@ class NormalizationService(BaseModel):
"normalized_id": "ncit:C4989",
"disease": {
"id": "normalize.disease.ncit:C4989",
"type": "Disease",
"conceptType": "Disease",
"label": "Childhood Leukemia",
"aliases": [
"childhood leukemia (disease)",
"leukemia",
"pediatric leukemia (disease)",
"Leukemia",
"leukemia (disease) of childhood",
],
"mappings": [
{
"coding": {"code": "0004355", "system": "mondo"},
"coding": {
"code": "mondo:0004355",
"system": "http://purl.obolibrary.org/obo/mondo.owl",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "7757", "system": "doid"},
"coding": {
"code": "DOID:7757",
"system": "http://purl.obolibrary.org/obo/doid.owl",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "C1332977", "system": "umls"},
"coding": {
"code": "umls:C1332977",
"system": "https://www.nlm.nih.gov/research/umls/index.html",
},
"relation": "relatedMatch",
},
],
"extensions": [
{
"name": "aliases",
"value": [
"childhood leukemia (disease)",
"leukemia",
"pediatric leukemia (disease)",
"Leukemia",
"leukemia (disease) of childhood",
],
},
{
"name": "pediatric_disease",
"value": True,
Expand Down
72 changes: 57 additions & 15 deletions tests/unit/test_query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,47 +24,80 @@ def neuroblastoma():
label="Neuroblastoma",
mappings=[
{
"coding": {"code": "0005072", "system": "mondo"},
"coding": {
"code": "mondo:0005072",
"system": "http://purl.obolibrary.org/obo/mondo.owl",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "NBL", "system": "oncotree"},
"coding": {
"code": "oncotree:NBL",
"system": "https://oncotree.mskcc.org",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "769", "system": "doid"},
"coding": {
"code": "DOID:769",
"system": "http://purl.obolibrary.org/obo/doid.owl",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "C0027819", "system": "umls"},
"coding": {
"code": "umls:C0027819",
"system": "https://www.nlm.nih.gov/research/umls/index.html",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "9500/3", "system": "icdo"},
"coding": {
"code": "icdo:9500/3",
"system": "https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology/",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "0000621", "system": "efo"},
"coding": {
"code": "efo:0000621",
"system": "https://www.ebi.ac.uk/efo/",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "7185", "system": "gard"},
"coding": {
"code": "gard:7185",
"system": "https://rarediseases.info.nih.gov",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "D009447", "system": "mesh"},
"coding": {
"code": "mesh:D009447",
"system": "https://id.nlm.nih.gov/mesh/",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "635", "system": "orphanet"},
"coding": {
"code": "orphanet:635",
"system": "https://www.orpha.net",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "C2751421", "system": "umls"},
"coding": {
"code": "umls:C2751421",
"system": "https://www.nlm.nih.gov/research/umls/index.html",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "18012", "system": "medgen"},
"coding": {
"code": "medgen:18012",
"system": "https://www.ncbi.nlm.nih.gov/medgen/",
},
"relation": "relatedMatch",
},
],
Expand Down Expand Up @@ -112,19 +145,28 @@ def mafd2():
label="major affective disorder 2",
mappings=[
{
"coding": {"code": "309200", "system": "mim"},
"coding": {"code": "MIM:309200", "system": "https://www.omim.org"},
"relation": "relatedMatch",
},
{
"coding": {"code": "C564108", "system": "mesh"},
"coding": {
"code": "mesh:C564108",
"system": "https://id.nlm.nih.gov/mesh/",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "326975", "system": "medgen"},
"coding": {
"code": "medgen:326975",
"system": "https://www.ncbi.nlm.nih.gov/medgen/",
},
"relation": "relatedMatch",
},
{
"coding": {"code": "C1839839", "system": "umls"},
"coding": {
"code": "umls:C1839839",
"system": "https://www.nlm.nih.gov/research/umls/index.html",
},
"relation": "relatedMatch",
},
],
Expand Down
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