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Refresh basic #18

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c4252eb
Update 04_DE_ID_CDM_Table_ddl.sql
matthewlrobinson Nov 13, 2023
862752e
Add files via upload
benwmar Nov 17, 2023
b00b621
Add files via upload
benwmar Nov 17, 2023
f9dacd6
Delete Cohort curation scripts/00_CURE_ID_create_concept_table.sql
benwmar Nov 17, 2023
e24597b
Update and rename 00_CURE_ID_create_concept_table_working.sql to 00_C…
benwmar Nov 17, 2023
864f4c9
Merge branch 'refresh_advance' into refresh_basic
benwmar Nov 17, 2023
567a78d
Added updated concepts and earlier code for measurements and drugs
jhajagos Feb 27, 2024
e23625e
Merge pull request #27 from jhajagos/refresh_basic
DBJHU Feb 27, 2024
8dd545d
Committing update to measurement profile
jhajagos Feb 28, 2024
3ece43d
Merge pull request #28 from jhajagos/refresh_basic
DBJHU Feb 28, 2024
9b0f56a
Added Loinc expansion fix
jhajagos Mar 7, 2024
7dc5d4c
Merge pull request #31 from jhajagos/refresh_basic
DBJHU May 6, 2024
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26,586 changes: 13,295 additions & 13,291 deletions CURE ID Concepts/CureID_concepts_all_Working.csv
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32 changes: 16 additions & 16 deletions CURE ID Concepts/CureID_concepts_parents_Working.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -141,22 +141,22 @@
"140","3045524","34543-9","Bilirubin direct and total panel [Mass/volume] - Serum or Plasma","Measurement","LOINC","S",FALSE
"141","3036277","8302-2","Body height","Measurement","LOINC","S",FALSE
"142","3038553","39156-5","Body mass index (BMI) [Ratio]","Measurement","LOINC","S",FALSE
"143","3025315","29463-7","Body weight","Measurement","LOINC","S",FALSE
"144","3020460","1988-5","C reactive protein [Mass/volume] in Serum or Plasma","Measurement","LOINC","S",FALSE
"145","3027801","2703-7","Oxygen [Partial pressure] in Arterial blood","Measurement","LOINC","S",FALSE
"146","3016502","2708-6","Oxygen saturation in Arterial blood","Measurement","LOINC","S",FALSE
"147","40762499","59408-5","Oxygen saturation in Arterial blood by Pulse oximetry","Measurement","LOINC","S",FALSE
"148","3026238","19996-8","Oxygen/Inspired gas Respiratory system --on ventilator","Measurement","LOINC","S",FALSE
"149","3025634","29908-1","Parainfluenza virus 1 RNA [Presence] in Specimen by NAA with probe detection","Measurement","LOINC","S",FALSE
"150","3007461","26515-7","Platelets [#/volume] in Blood","Measurement","LOINC","S",FALSE
"151","3024929","777-3","Platelets [#/volume] in Blood by Automated count","Measurement","LOINC","S",FALSE
"152","3010834","778-1","Platelets [#/volume] in Blood by Manual count","Measurement","LOINC","S",FALSE
"153","3046279","33959-8","Procalcitonin [Mass/volume] in Serum or Plasma","Measurement","LOINC","S",FALSE
"154","3034426","5902-2","Prothrombin time (PT)","Measurement","LOINC","S",FALSE
"155","3024171","9279-1","Respiratory rate","Measurement","LOINC","S",FALSE
"156","37065137","LP378960-1","Respiratory syncytial virus RNA | XXX | Microbiology","Measurement","LOINC","C",FALSE
"157","37055446","LP378971-8","Rhinovirus RNA | XXX | Microbiology","Measurement","LOINC","C",FALSE
"158","3004249","8480-6","Systolic blood pressure","Measurement","LOINC","S",FALSE
"143","3020460","1988-5","C reactive protein [Mass/volume] in Serum or Plasma","Measurement","LOINC","S",FALSE
"144","3027801","2703-7","Oxygen [Partial pressure] in Arterial blood","Measurement","LOINC","S",FALSE
"145","3016502","2708-6","Oxygen saturation in Arterial blood","Measurement","LOINC","S",FALSE
"146","40762499","59408-5","Oxygen saturation in Arterial blood by Pulse oximetry","Measurement","LOINC","S",FALSE
"147","3026238","19996-8","Oxygen/Inspired gas Respiratory system --on ventilator","Measurement","LOINC","S",FALSE
"148","3025634","29908-1","Parainfluenza virus 1 RNA [Presence] in Specimen by NAA with probe detection","Measurement","LOINC","S",FALSE
"149","3007461","26515-7","Platelets [#/volume] in Blood","Measurement","LOINC","S",FALSE
"150","3024929","777-3","Platelets [#/volume] in Blood by Automated count","Measurement","LOINC","S",FALSE
"151","3010834","778-1","Platelets [#/volume] in Blood by Manual count","Measurement","LOINC","S",FALSE
"152","3046279","33959-8","Procalcitonin [Mass/volume] in Serum or Plasma","Measurement","LOINC","S",FALSE
"153","3034426","5902-2","Prothrombin time (PT)","Measurement","LOINC","S",FALSE
"154","3024171","9279-1","Respiratory rate","Measurement","LOINC","S",FALSE
"155","37065137","LP378960-1","Respiratory syncytial virus RNA | XXX | Microbiology","Measurement","LOINC","C",FALSE
"156","37055446","LP378971-8","Rhinovirus RNA | XXX | Microbiology","Measurement","LOINC","C",FALSE
"157","3004249","8480-6","Systolic blood pressure","Measurement","LOINC","S",FALSE
"158","1004141","LP415675-0","Body weight | Patient | General body weight","Measurement","LOINC","C",TRUE
"159","45889365","1012740","Dialysis Services and Procedures","Observation","CPT4","C",TRUE
"160","46235215","76691-5","Gender identity","Observation","LOINC","S",TRUE
"161","4039922","229306004","Positive pressure therapy","Observation","SNOMED","S",TRUE
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38 changes: 19 additions & 19 deletions CURE ID Concepts/CureID_concepts_parents_Working.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2394,25 +2394,6 @@
"includeDescendants": false,
"includeMapped": false
},
{
"concept": {
"CONCEPT_CLASS_ID": "Clinical Observation",
"CONCEPT_CODE": "29463-7",
"CONCEPT_ID": 3025315,
"CONCEPT_NAME": "Body weight",
"DOMAIN_ID": "Measurement",
"INVALID_REASON": "V",
"INVALID_REASON_CAPTION": "Valid",
"STANDARD_CONCEPT": "S",
"STANDARD_CONCEPT_CAPTION": "Standard",
"VOCABULARY_ID": "LOINC",
"VALID_START_DATE": "1969-12-31",
"VALID_END_DATE": "2099-12-30"
},
"isExcluded": false,
"includeDescendants": false,
"includeMapped": false
},
{
"concept": {
"CONCEPT_CLASS_ID": "Lab Test",
Expand Down Expand Up @@ -3704,6 +3685,25 @@
"isExcluded": false,
"includeDescendants": false,
"includeMapped": false
},
{
"concept": {
"CONCEPT_CLASS_ID": "LOINC Hierarchy",
"CONCEPT_CODE": "LP415675-0",
"CONCEPT_ID": 1004141,
"CONCEPT_NAME": "Body weight | Patient | General body weight",
"DOMAIN_ID": "Measurement",
"INVALID_REASON": "V",
"INVALID_REASON_CAPTION": "Valid",
"STANDARD_CONCEPT": "C",
"STANDARD_CONCEPT_CAPTION": "Classification",
"VOCABULARY_ID": "LOINC",
"VALID_START_DATE": "2019-12-12",
"VALID_END_DATE": "2099-12-30"
},
"isExcluded": false,
"includeDescendants": true,
"includeMapped": false
}
]
}
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