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Generate SSSOM for ICD11 to ICD11 codes #286

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merged 5 commits into from
Jan 10, 2025
Merged

Generate SSSOM for ICD11 to ICD11 codes #286

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8354fe6
Update icd11.py
cthoyt Jan 9, 2025
90d13c7
Update icd11.py
cthoyt Jan 9, 2025
90c97ae
Update icd11.py
cthoyt Jan 9, 2025
b1e183d
Update icd11.py
cthoyt Jan 10, 2025
9148f4c
Merge branch 'main' into add-xrefs
cthoyt Jan 10, 2025
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14 changes: 9 additions & 5 deletions src/pyobo/sources/icd11.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
logger = logging.getLogger(__name__)

PREFIX = "icd11"
CODE_PREFIX = "icd11.code"

CODE_PROP = TypeDef(reference=default_reference(PREFIX, "icd_mms_code"), is_metadata_tag=True)

Expand All @@ -49,8 +50,13 @@ def iterate_icd11() -> Iterable[Term]:
res = get_icd(ICD11_TOP_LEVEL_URL)
res_json = res.json()
version = res_json["releaseId"]
mms_directory = prefix_directory_join(PREFIX, "mms", version=version)

# Get all terms from the ICD foundation API
terms = list(iterate_icd11_helper(res_json, version))

# prepare a directory for enriching from MMS
mms_directory = prefix_directory_join(PREFIX, "mms", version=version)

# this takes a bit more than 2 hours
for term in tqdm(terms, desc="Getting MMS", unit_scale=True):
path = mms_directory.joinpath(term.identifier).with_suffix(".json")
Expand All @@ -63,12 +69,10 @@ def iterate_icd11() -> Iterable[Term]:
# writing this isn't necessary since not all terms have MMS entries
# tqdm.write(str(e))
mms_data = {}
else:
path.write_text(json.dumps(mms_data))
path.write_text(json.dumps(mms_data))

if code := mms_data.get("code"):
# TODO decide on ICD code prefix, then append this as a mapping
term.annotate_literal(CODE_PROP, code)
term.append_exact_match(Reference(prefix=CODE_PREFIX, identifier=code))

yield term

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