From e7e1a77f0ce6523ea4054c1ed1b06c50c745b2cd Mon Sep 17 00:00:00 2001 From: peterprinsen Date: Fri, 15 Dec 2023 10:51:36 +0100 Subject: [PATCH 1/2] Replaced deprecated SNOMED concept with new concept and fixed error (concept_id was used instead of concept_code) --- ICDO3/load_stage.sql | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ICDO3/load_stage.sql b/ICDO3/load_stage.sql index 41b2ffef7..5f8f8c69a 100644 --- a/ICDO3/load_stage.sql +++ b/ICDO3/load_stage.sql @@ -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 @@ -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 @@ -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 From 114b5109d8fbd365f38f221673b9d8845c52d80c Mon Sep 17 00:00:00 2001 From: Eduard Korchmar Date: Fri, 29 Dec 2023 12:51:30 +0100 Subject: [PATCH 2/2] Bump version and fix bug breaking hierarchy Fixes a bug preventing 'Is a' relationships from being built for concepts which had _any_ relationships comming from manual tables. --- ICDO3/load_stage.sql | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/ICDO3/load_stage.sql b/ICDO3/load_stage.sql index 5f8f8c69a..8920c75c0 100644 --- a/ICDO3/load_stage.sql +++ b/ICDO3/load_stage.sql @@ -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' ); @@ -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 @@ -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',