Repository navigation
fix: curate ICD10CM to Bioregistry's icd10data URI format - #80
Open
kevinschaper wants to merge 3 commits into
Open
kevinschaper wants to merge 3 commits into
kevinschaper wants to merge 3 commits into
Conversation
matentzn
reviewed
Feb 20, 2026
| linkml,biolink,https://w3id.org/biolink/vocab/,canonical | ||
| linkml,dcterms,http://purl.org/dc/terms/,canonical | ||
| linkml,foaf,http://xmlns.com/foaf/0.1/,canonical | ||
| linkml,ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/,canonical |
There was a problem hiding this comment.
I am not against this, note that Bioregistrysuggests this:
https://www.icd10data.com/search?s=
Which is a bit of a hack - redirecting to the search page rather than the concept page for which you cant construct a URI.
Contributor
Author
There was a problem hiding this comment.
Good call, thanks. I've switched this to Bioregistry's https://www.icd10data.com/search?s= so we follow upstream rather than carrying a local opinion. Bioregistry now marks the icd.codes provider as gone (2025-07-28), so the pinned release here is just behind. The BioPortal PURL and icd.codes remain as prefix aliases. Branch is rebuilt on current main with only the ICD10CM rows changed.
kevinschaper
force-pushed
the
fix/icd10cm-prefix
branch
from
May 9, 2026 00:42
f6d8f92 to
0e4d169
Compare
|
Did you think about this @kevinschaper |
Older bioregistry releases, including the one pinned here, make https://icd.codes/icd10cm/ the canonical ICD10CM namespace. That host has been dead since 2025-07 and Bioregistry now marks the provider as gone; its own URI format is https://www.icd10data.com/search?s=. Add ICD10CM to linked_data.curated.yaml with that namespace, so the merged contexts follow Bioregistry regardless of the pinned release. icd.codes and the BioPortal PURL stay as prefix aliases. The CSV rows were produced with the package's own ingest, merge and writer, and only the ICD10CM rows change. A full `make etl` was not run, to avoid burying this in an upstream refresh. Claude-Session: https://claude.ai/code/session_01GvqCPLs6vPfQbS73ca2jJw
kevinschaper
changed the title
kevinschaper
force-pushed
the
fix/icd10cm-prefix
branch
from
November 6, 2026 17:17
0e4d169 to
a296506
Compare
This branch has not been deployed
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
https://icd.codes/icd10cm/the canonical ICD10CM namespace. That host has been dead since 2025-07 and Bioregistry now marks the provider asgone.https://www.icd10data.com/search?s=, by addingICD10CMtolinked_data.curated.yaml. It is a search page rather than a concept URI, but it is what Bioregistry resolves to, and a later bioregistry bump will agree with it instead of fighting the override.icd.codesand the BioPortal PURL stay asprefix_aliasrows, so compression of existing URIs keeps working.linked_dataand the three merged contexts, and the aliases in the dynamically merged context.For reviewers
main. The earlier version of this PR carried a stalemake etlrefresh and a Poetry 2 lock file; both are gone.make etlwas not run, to avoid burying this in an upstream refresh.test_w3idfailure until fix: read w3id namespaces from ids/ after upstream move #84 is merged. It also fails onmain.https://claude.ai/code/session_01GvqCPLs6vPfQbS73ca2jJw