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Include ICD11 mappings #486

Merged
merged 2 commits into from
Apr 4, 2024
Merged

Include ICD11 mappings #486

merged 2 commits into from
Apr 4, 2024

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hrshdhgd
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@hrshdhgd hrshdhgd commented Apr 4, 2024

Resolves #140 and Addresses #16 (bullet 3)

Overview

This PR:

  • Removes filter to ignore ICD11 refs.

New Packages

Were any new Python packages added?

Were any other non-Python packages added?

PR Review and Conversations Resolved

Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?

  • Yes

@hrshdhgd hrshdhgd mentioned this pull request Apr 4, 2024
@hrshdhgd hrshdhgd requested a review from matentzn April 4, 2024 14:38
@@ -16,5 +16,5 @@ WHERE {
oboInOwl:hasDbXref ?xref ;
?p1 ?o2 .
}
FILTER( STRSTARTS(str(?xref), "UMLS_ICD9CM_2005_AUI:") || STRSTARTS(str(?xref), "ICD11:") || STRSTARTS(str(?xref), "SNOMEDCT_US_") || STRSTARTS(str(?xref), "IMDRF:") || STRSTARTS(str(?xref), "url:") )
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Just commenting on my understanding.
I see what's going on here to address #140. So this deletion query gets run on the DOID and NCIT components, removing these xrefs. You're removing ICD11 from this query, so thus we're adding the mappings back from these files, as they won't be removed any longer.

I thought that #140 had something to do with my new ICD11Foundation work but it does not.

@@ -16,5 +16,5 @@ WHERE {
oboInOwl:hasDbXref ?xref ;
?p1 ?o2 .
}
FILTER( STRSTARTS(str(?xref), "UMLS_ICD9CM_2005_AUI:") || STRSTARTS(str(?xref), "ICD11:") || STRSTARTS(str(?xref), "SNOMEDCT_US_") || STRSTARTS(str(?xref), "IMDRF:") || STRSTARTS(str(?xref), "url:") )
FILTER( STRSTARTS(str(?xref), "UMLS_ICD9CM_2005_AUI:") || STRSTARTS(str(?xref), "SNOMEDCT_US_") || STRSTARTS(str(?xref), "IMDRF:") || STRSTARTS(str(?xref), "url:") )
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Merging into develop or main

@hrshdhgd I see that this is merging into main, but basically from now on, per #405 (which isn't completed yet) we're going to follow the normal git flow of main <-- develop <-- feature branches.

We could change the base on this PR but IDK how much it matters. I update develop from master regularly as needed anyway.

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@hrshdhgd I approve as well as Nico. Prolly good to merge. I can update develop later.

@joeflack4 joeflack4 added the icd11 label Apr 4, 2024
@hrshdhgd hrshdhgd merged commit 3c353fb into main Apr 4, 2024
@hrshdhgd hrshdhgd deleted the issue-140 branch April 4, 2024 23:03
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Add ICD11 mappings back
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