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Added ICD10 description tiers #12

Merged
merged 4 commits into from
Jan 14, 2025
Merged

Added ICD10 description tiers #12

merged 4 commits into from
Jan 14, 2025

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dogversioning
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This PR aims to add some utility views into the data around ICD coding, by doing the following:

  • providing slices of mrconso/mrrel pointed at the ICD10cm subset of codes
  • providing slices, and a tree representation, of the ICD10 code hierarchy

It also updates the UMLS study to be compatible with library v4, and writes the version of UMLS data used to the transaction log.

-- A collection of convenience views for UMLS data

-- Selecting only child relationships FROM mrrel
CREATE TABLE IF NOT EXISTS umls__mrrel_is_a AS

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This umls__mrrel_is_a only applies to DRUGS, recommend changing name to
umls__mrrel_drug_is_a

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ok, done

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@comorbidity comorbidity left a comment

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From reading "Files Changed" looks good, only change recommended is the name for the umls MRREL "is a" ... that's only for drugs wouldn't want users to be confused.

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Looks good very minor requested name change.

cumulus_library_umls/.DS_Store Outdated Show resolved Hide resolved
@@ -44,7 +44,8 @@ testpaths = [
]

[tool.ruff]
target-version = "py310"
target-version = "py311"
line-length = 100
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You were feeling like 100 was too much for your tastes, after living with it for a bit, yeah? I'm fine if you want to keep the default going.

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Yeah it's fine - mostly I'm here for 'just do it this one way and don't spend time debating it'.

cumulus_library_umls/umls_builder.py Outdated Show resolved Hide resolved
cumulus_library_umls/umls_builder.py Outdated Show resolved Hide resolved
cumulus_library_umls/manifest.toml Outdated Show resolved Hide resolved
cumulus_library_umls/ancilary_tables.sql Outdated Show resolved Hide resolved
@dogversioning dogversioning merged commit bfc451e into main Jan 14, 2025
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@dogversioning dogversioning deleted the mg/umls_descriptions branch January 14, 2025 14:45
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3 participants