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Add Cancer Codes to TEFCA DB #2617

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merged 3 commits into from
Sep 24, 2024
Merged

Add Cancer Codes to TEFCA DB #2617

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03b3eaa
add relevant cancer codes
m-goggins Sep 24, 2024
011e808
updates to reorganize labs
m-goggins Sep 24, 2024
6f500ee
Merge branch 'main' into add-cancer-codes
m-goggins Sep 24, 2024
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35 changes: 31 additions & 4 deletions containers/tefca-viewer/flyway/sql/V01_03__insert_hardcoded_values.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,15 @@ INSERT INTO conditions VALUES('3','DIBBs Local Code System','Social Determinants
INSERT INTO valuesets VALUES('1_20240909','1','20240909','Newborn Screening','DIBBs','lotc');

-- Cancer (Leukemia) valueset(s)
INSERT INTO valuesets VALUES('2_20240909','2','20240909','Cancer (Leukemia)','DIBBs','dxtc');
INSERT INTO valuesets VALUES('3_20240909','3','20240909','Cancer Leukemia','DIBBs','mrtc');
INSERT INTO valuesets VALUES('2_20240909','2','20240909','Cancer (Leukemia) Diagnosis Problem','DIBBs','dxtc');
INSERT INTO valuesets VALUES('3_20240909','3','20240909','Cancer (Leukemia) Medication','DIBBs','mrtc');

-- Missing Syphilis valueset(s)
INSERT INTO valuesets VALUES('4_20240909','4','20240909','Syphilis Medication','DIBBs','mrtc');
INSERT INTO valuesets VALUES('5_20240909','5','20240909','Syphilis Diagnosis Problem','DIBBs','dxtc');
INSERT INTO valuesets VALUES('6_20240909','6','20240909','Suspected Syphilis Disorder','DIBBs','sdtc');

-- Missing Gonorhea valueset(s)
-- Missing Gonorrhea valueset(s)
INSERT INTO valuesets VALUES('7_20240909','7','20240909','Gonorrhea Medication','DIBBs','mrtc');
INSERT INTO valuesets VALUES('8_20240909','8','20240909','Gonorrhea Diagnosis Problem','DIBBs','dxtc');
INSERT INTO valuesets VALUES('9_20240909','9','20240909','Gonorrhea Lab Organism','DIBBs','lotc');
Expand All @@ -27,6 +27,9 @@ INSERT INTO valuesets VALUES('11_20240910','11','20240910','Chlamydia Medication
INSERT INTO valuesets VALUES('12_20240910','12','20240910','Chlamydia Lab Result','DIBBs','lrtc');
INSERT INTO valuesets VALUES('13_20240910','13','20240910','Suspected Chlamydia Diagnosis','DIBBs','sdtc');

-- Cancer (CAP) valueset(s)
INSERT INTO valuesets VALUES('14_20240923','14','20240923','Cancer (Leukemia) Lab Result','DIBBs','lrtc');
INSERT INTO valuesets VALUES('15_20240923','15','20240923','Suspected Cancer (Leukemia) Diagnosis','DIBBs','sdtc');

-- Newborn Screening concepts
INSERT INTO concepts VALUES('1_73700-7','73700-7','http://loinc.org','CCHD newborn screening interpretation','737007','2024-09');
Expand Down Expand Up @@ -61,12 +64,23 @@ INSERT INTO concepts VALUES('1_1649987','1649987','http://www.nlm.nih.gov/resear
INSERT INTO concepts VALUES('1_72828-7','72828-7','http://loinc.org','Chlamydia trachomatis and Neisseria gonorrhoeae DNA panel - Specimen','728287','2024-09');
INSERT INTO concepts VALUES('1_2339001','2339001','http://snomed.info/sct','Sexual overexposure','2339001','2024-09');

-- Cancer (Leukemia) concepts from CAP
INSERT INTO concepts VALUES('1_21908-9','21908-9','http://loinc.org','Stage group.clinical Cancer','219089','2024-09');
INSERT INTO concepts VALUES('1_36929009','36929009','http://snomed.info/sct','Stage II (localized)','36929009','2024-09');
INSERT INTO concepts VALUES('1_60568-3','60568-3','http://loinc.org','Pathology Synoptic report','605683','2024-09');
INSERT INTO concepts VALUES('1_30000.100004300','30000.100004300','http://cap.org/eCC','MSH2 Result','30000.100004300','2024-09');
INSERT INTO concepts VALUES('1_1255068005','1255068005','http://snomed.info/sct','Presence of DNA mismatch repair protein MSH2 in primary malignant neoplasm of colon by immunohistochemistry (observable entity)','1255068005','2024-09');
INSERT INTO concepts VALUES('1_9484.100004300','9484.100004300','http://cap.org/eCC','RESULTS','9484.100004300','2024-09');
INSERT INTO concepts VALUES('1_363346000','363346000','http://snomed.info/sct','Malignant neoplastic disease (disorder)','363346000','2024-09');
INSERT INTO concepts VALUES('1_418689008','418689008','http://snomed.info/sct','Allergy to sulfonamide','418689008','2024-09');


-- Newborn Screening condition to valueset mappings
INSERT INTO condition_to_valueset VALUES('1514','1','1_20240909','DIBBs');

-- Cancer (Leukemia) condition to valueset mappings
INSERT INTO condition_to_valueset VALUES('1515','2','2_20240909','DIBBs');
INSERT INTO condition_to_valueset VALUES('1516','3','3_20240909','DIBBs');
INSERT INTO condition_to_valueset VALUES('1516','2','3_20240909','DIBBs');

-- Missing Syphilis condition to valueset mappings
INSERT INTO condition_to_valueset VALUES('1517','35742006','4_20240909','DIBBs');
Expand All @@ -84,6 +98,10 @@ INSERT INTO condition_to_valueset VALUES('1524','240589008','11_20240910','DIBBs
INSERT INTO condition_to_valueset VALUES('1525','240589008','12_20240910','DIBBs');
INSERT INTO condition_to_valueset VALUES('1526','240589008','13_20240910','DIBBs');

-- Missing Cancer condition to valueset mappings (CAP)
INSERT INTO condition_to_valueset VALUES('1527','2','14_20240923','DIBBs');
INSERT INTO condition_to_valueset VALUES('1528','2','15_20240923','DIBBs');

-- Newborn Screening valueset to concept mappings
INSERT INTO valueset_to_concept VALUES('45274','1_20240909','1_73700-7');
INSERT INTO valueset_to_concept VALUES('45275','1_20240909','1_73698-3');
Expand Down Expand Up @@ -130,6 +148,15 @@ INSERT INTO valueset_to_concept VALUES('45307','12_20240910','1_72828-7');
INSERT INTO valueset_to_concept VALUES('45308','13_20240910','1_72531000052105');
INSERT INTO valueset_to_concept VALUES('45309','13_20240910','1_2339001');

-- Missing Cancer valueset to concept mapping (CAP)
INSERT INTO valueset_to_concept VALUES('45310','2_20240909','1_21908-9');
INSERT INTO valueset_to_concept VALUES('45311','2_20240909','1_36929009');
INSERT INTO valueset_to_concept VALUES('45312','2_20240909','1_60568-3');
INSERT INTO valueset_to_concept VALUES('45313','14_20240923','1_30000.100004300');
INSERT INTO valueset_to_concept VALUES('45314','14_20240923','1_1255068005');
INSERT INTO valueset_to_concept VALUES('45315','14_20240923','1_9484.100004300');
INSERT INTO valueset_to_concept VALUES('45316','15_20240923','1_363346000');
INSERT INTO valueset_to_concept VALUES('45317','2_20240909','1_418689008');



Expand Down
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