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Corrections in ICDO3 script #925

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Corrections in ICDO3 script #925

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e7e1a77
Replaced deprecated SNOMED concept with new concept and fixed error (…
peterprinsen-iknl Dec 15, 2023
114b510
Bump version and fix bug breaking hierarchy
ekorchmar Dec 29, 2023
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21 changes: 13 additions & 8 deletions ICDO3/load_stage.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ DO $_$
BEGIN
PERFORM VOCABULARY_PACK.SetLatestUpdate(
pVocabularyName => 'ICDO3',
pVocabularyDate => TO_DATE ('20200630', 'yyyymmdd'), -- https://seer.cancer.gov/ICDO3/
pVocabularyDate => TO_DATE ('20231129', 'yyyymmdd'), -- https://seer.cancer.gov/ICDO3/
pVocabularyVersion => 'ICDO3 SEER Site/Histology Released 06/2020',
pVocabularyDevSchema => 'DEV_icdo3'
);
Expand Down Expand Up @@ -110,7 +110,7 @@ FROM snomed_ancestor hc
;
--3.3. Add missing relation to Primary Malignant Neoplasm where needed
insert into snomed_ancestor (ancestor_concept_code, descendant_concept_code)
select distinct '86049000', snomed_code
select distinct '1240414004', snomed_code
from r_to_c_all r
where
r.concept_code ~ '\d{4}\/3' and
Expand All @@ -120,7 +120,7 @@ where
select 1
from snomed_ancestor a
where
a.ancestor_concept_code = '86049000' and --PMN
a.ancestor_concept_code = '1240414004' and --PMN
a.descendant_concept_code = r.snomed_code
)
/* and not exists -- no common descendants with Secondary malignant neoplasm
Expand Down Expand Up @@ -590,7 +590,7 @@ snomed_concept as
ancestor_concept_code in
(
'400177003', --Neoplasm
'4216275', --Proliferation of hematopoietic cell type
'415181008', --Proliferation of hematopoietic cell type
'25723000', --Dysplasia
'76197007' --Hyperplasia
) and
Expand Down Expand Up @@ -1586,7 +1586,8 @@ select distinct
TO_DATE ('20991231', 'yyyymmdd')
from match_blob m
left join concept_relationship_stage r on
m.i_code = r.concept_code_1
m.i_code = r.concept_code_1
AND r.relationship_id = 'Maps to'
where r.concept_code_1 is null
;
--17. Write relations for attributes
Expand Down Expand Up @@ -1897,11 +1898,15 @@ where
;
--23. Populate concept_synonym_stage
--23.1. with morphologies
insert into concept_synonym_stage
insert into concept_synonym_stage (
synonym_name,
synonym_concept_code,
synonym_vocabulary_id,
language_concept_id
)
--we ignore obsoletion status of synonyms for now: concepts may still be referenced by their old names in historical classifications
--ICDO3 does not distinguish between 'old' and 'wrong'
select
null,
select distinct
trim (term),
icdo32,
'ICDO3',
Expand Down