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Include ICD11 mappings #486

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merged 2 commits into from
Apr 4, 2024
Merged

Include ICD11 mappings #486

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0f04f58
Include ICD11 mappings
hrshdhgd Apr 4, 2024
dbdc652
ran make mappings
hrshdhgd Apr 4, 2024
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104 changes: 84 additions & 20 deletions src/mappings/doid.sssom.tsv
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2 changes: 1 addition & 1 deletion src/mappings/gard.sssom.tsv
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Expand Up @@ -9,7 +9,7 @@
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/fba76c0f-e243-4b76-84be-13031a56bcfa
# mapping_set_id: https://w3id.org/sssom/mappings/a2d27ac8-e35c-4370-a09d-803978eaa02f
subject_id subject_label predicate_id object_id mapping_justification
obo:GARD_1 GRACILE syndrome skos:exactMatch Orphanet:53693 semapv:UnspecifiedMatching
obo:GARD_1 GRACILE syndrome skos:narrowMatch OMIM:603358 semapv:UnspecifiedMatching
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2 changes: 1 addition & 1 deletion src/mappings/icd10cm.sssom.tsv
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Expand Up @@ -6,6 +6,6 @@
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/505bfd44-9435-45eb-be59-3c19aa83d3e3
# mapping_set_id: https://w3id.org/sssom/mappings/c15beb32-c0a5-4a9f-bff3-337c52503878


2 changes: 1 addition & 1 deletion src/mappings/icd10who.sssom.tsv
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Expand Up @@ -6,6 +6,6 @@
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/69a61798-1eb3-45d6-a3fa-bcd03dc5cf25
# mapping_set_id: https://w3id.org/sssom/mappings/8e08c2db-8891-4a5e-990e-1a50b1b83041


2 changes: 1 addition & 1 deletion src/mappings/ncit.sssom.tsv
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Expand Up @@ -9,7 +9,7 @@
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://w3id.org/sssom/license/unspecified
# mapping_set_id: https://w3id.org/sssom/mappings/9367551c-034c-40d2-881a-2a73c73020a2
# mapping_set_id: https://w3id.org/sssom/mappings/644cb230-28fb-4860-b973-21bd6950b861
subject_id subject_label predicate_id object_id mapping_justification
NCIT:C103222 Popliteal Fossa oboInOwl:hasDbXref UBERON:0013069 semapv:UnspecifiedMatching
NCIT:C103384 Common Iliac Lymph Node oboInOwl:hasDbXref UBERON:0015878 semapv:UnspecifiedMatching
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5,028 changes: 2,541 additions & 2,487 deletions src/mappings/omim.sssom.tsv
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2 changes: 1 addition & 1 deletion src/sparql/rm_xref_by_prefix.ru
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Expand Up @@ -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.

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.

}