Skip to content

fix: curate ICD10CM to Bioregistry's icd10data URI format #80

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
kevinschaper wants to merge 3 commits into
base: main
Choose a base branch
from
Open

fix: curate ICD10CM to Bioregistry's icd10data URI format #80

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
a296506
fix: curate ICD10CM to Bioregistry's icd10data URI format
kevinschaper Nov 6, 2026
a0b4868
Merge branch 'main' into fix/icd10cm-prefix
kevinschaper Nov 6, 2026
4d91321
Merge branch 'main' into fix/icd10cm-prefix
kevinschaper Nov 6, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions src/prefixmaps/data/linked_data.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ linkml,biolink,https://w3id.org/biolink/vocab/,canonical
linkml,dcmitype,http://purl.org/dc/dcmitype/,canonical
linkml,dcterms,http://purl.org/dc/terms/,canonical
linkml,foaf,http://xmlns.com/foaf/0.1/,canonical
linkml,ICD10CM,https://www.icd10data.com/search?s=,canonical
linkml,linkml,https://w3id.org/linkml/,canonical
linkml,NANDO,http://identifiers.org/NANDO:,canonical
linkml,NCIThesaurus,http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#,canonical
Expand Down
3 changes: 3 additions & 0 deletions src/prefixmaps/data/linked_data.curated.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,3 +33,6 @@ prefixes:
dcmitype: http://purl.org/dc/dcmitype/
wgs: http://www.w3.org/2003/01/geo/wgs84_pos#
xml: http://www.w3.org/XML/1998/namespace
# Bioregistry's URI format for ICD-10-CM. Its icd.codes provider, which older bioregistry
# releases made canonical, has been dead since 2025-07 and is marked "gone" upstream.
ICD10CM: https://www.icd10data.com/search?s=
3 changes: 2 additions & 1 deletion src/prefixmaps/data/merged.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6932,7 +6932,8 @@ merged,ICD10,https://icdcodelookup.com/icd-10/codes/,prefix_alias,bioregistry
merged,ICD10,https://identifiers.org/icd/,prefix_alias,bioregistry
merged,ICD10,https://identifiers.org/icd:,prefix_alias,bioregistry
merged,ICD10,https://n2t.net/icd:,prefix_alias,bioregistry
merged,ICD10CM,https://icd.codes/icd10cm/,canonical,bioregistry
merged,ICD10CM,https://www.icd10data.com/search?s=,canonical,linkml
merged,ICD10CM,https://icd.codes/icd10cm/,prefix_alias,bioregistry
merged,ICD10CM,http://bioregistry.io/ICD10CM:,prefix_alias,bioregistry
merged,ICD10CM,http://icd.codes/icd10cm/,prefix_alias,bioregistry
merged,ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/,prefix_alias,bioregistry
Expand Down
3 changes: 2 additions & 1 deletion src/prefixmaps/data/merged.monarch.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6932,7 +6932,8 @@ merged.monarch,ICD10,https://icdcodelookup.com/icd-10/codes/,prefix_alias,bioreg
merged.monarch,ICD10,https://identifiers.org/icd/,prefix_alias,bioregistry
merged.monarch,ICD10,https://identifiers.org/icd:,prefix_alias,bioregistry
merged.monarch,ICD10,https://n2t.net/icd:,prefix_alias,bioregistry
merged.monarch,ICD10CM,https://icd.codes/icd10cm/,canonical,bioregistry
merged.monarch,ICD10CM,https://www.icd10data.com/search?s=,canonical,linkml
merged.monarch,ICD10CM,https://icd.codes/icd10cm/,prefix_alias,bioregistry
merged.monarch,ICD10CM,http://bioregistry.io/ICD10CM:,prefix_alias,bioregistry
merged.monarch,ICD10CM,http://icd.codes/icd10cm/,prefix_alias,bioregistry
merged.monarch,ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/,prefix_alias,bioregistry
Expand Down
3 changes: 2 additions & 1 deletion src/prefixmaps/data/merged.oak.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6932,7 +6932,8 @@ merged.oak,ICD10,https://icdcodelookup.com/icd-10/codes/,prefix_alias,bioregistr
merged.oak,ICD10,https://identifiers.org/icd/,prefix_alias,bioregistry
merged.oak,ICD10,https://identifiers.org/icd:,prefix_alias,bioregistry
merged.oak,ICD10,https://n2t.net/icd:,prefix_alias,bioregistry
merged.oak,ICD10CM,https://icd.codes/icd10cm/,canonical,bioregistry
merged.oak,ICD10CM,https://www.icd10data.com/search?s=,canonical,linkml
merged.oak,ICD10CM,https://icd.codes/icd10cm/,prefix_alias,bioregistry
merged.oak,ICD10CM,http://bioregistry.io/ICD10CM:,prefix_alias,bioregistry
merged.oak,ICD10CM,http://icd.codes/icd10cm/,prefix_alias,bioregistry
merged.oak,ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/,prefix_alias,bioregistry
Expand Down
20 changes: 20 additions & 0 deletions tests/test_core/test_prefixmaps.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -229,3 +229,23 @@ def test_synonyms(self):
for curie in others:
with self.subTest(curie=curie):
self.assertEqual(canonical, converter.standardize_curie(curie))

def test_curated_icd10cm_prefix(self):
"""ICD10CM is curated in linked_data to follow Bioregistry's URI format.

Older bioregistry releases made the dead icd.codes namespace canonical, see #80.
"""
canonical = "https://www.icd10data.com/search?s="
for name in ["linked_data", "merged", "merged.monarch", "merged.oak"]:
with self.subTest(context=name):
ctxt = load_context(name)
self.assertEqual(canonical, ctxt.as_dict()["ICD10CM"])
self.assertEqual("ICD10CM", ctxt.as_inverted_dict()[canonical])
# the dead icd.codes namespace and the BioPortal PURL stay as aliases
aliases = {
pe.namespace
for pe in self.dyn_merged_context.prefix_expansions
if pe.prefix == "ICD10CM" and pe.status == StatusType.prefix_alias
}
self.assertIn("https://icd.codes/icd10cm/", aliases)
self.assertIn("http://purl.bioontology.org/ontology/ICD10CM/", aliases)
Loading