From afd7d870d7b13f0688e61d410e909ed6d22fcf33 Mon Sep 17 00:00:00 2001 From: "Stephanie S. Hong" Date: Tue, 27 Oct 2026 18:15:41 -0400 Subject: [PATCH] Concept map v1.8.3; unit fixes - import_c_peptide ng/mL (8842), import_urine_albumin mg/dL (8840) --- CHANGELOG.md | 23 +++++++++++++++++++ CITATION.cff | 2 +- codemeta.json | 2 +- ...i_readi_redcap_value_set_mapping_data.yaml | 20 ++++++++-------- ...ed_cap_data_dictionary_with_extensions.csv | 4 ++-- ...i_readi_redcap_value_set_mapping.sssom.tsv | 4 ++-- ..._readi_redcap_value_set_mapping_common.csv | 4 ++-- ...dcap_value_set_mapping_common_map2omop.csv | 4 ++-- ...ng_map2omop_open_source_public_version.csv | 4 ++-- .../scripts/README.md | 4 ++-- .../scripts/unit_concept_lookup.csv | 4 ++-- .../scripts/unit_concept_lookup_extended.csv | 4 ++-- 12 files changed, 51 insertions(+), 28 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1855375..9d678bb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,29 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/). ## [Unreleased] +## [v1.8.3] - 2026-10-27 + +Two lab unit rows are corrected to the units the data is reported in. A check of the delivered OMOP survey data against the v1.8.2 unit lookup found that the unit text in the data and the value ranges disagree with the map for C-peptide and urine albumin; the field key (which the join applies first) would have labeled C-peptide 1,000× and urine albumin 10× off. Two rows are edited in place, so every line number is the same as in v1.8.2. The ETL must apply this change (`MEASUREMENT.unit_concept_id`). + +### Fixed — unit rows + +| Line | Unit row | v1.8.2 | v1.8.3 | Evidence (current OMOP data) | +|---|---|---|---|---| +| 514 | `import_c_peptide_u` | 8725 *nanogram per liter* (`ng/L`) | **8842** *nanogram per milliliter* (`ng/mL`) | unit text `ng/mL`; 3,981 values, median 2.64 (p05 0.86, p95 7.39): ng/mL range (ng/L would be about 1,000× higher) | +| 613 | `import_urine_albumin_u` | 8751 *milligram per liter* (`mg/L`) | **8840** *milligram per deciliter* (`mg/dL`) | unit text `mg/dL`; 3,984 values, median 0.54 (p95 9.6) | + +- `SRC_CODE`, `SRC_CD_DESCRIPTION`, `TARGET_CONCEPT_NAME` and `TARGET_CONCEPT_CODE` follow the new unit. The other imported lab units were checked against the data's unit text and agree (e.g. insulin `ng/mL`, median 0.60; urine creatinine `mg/dL`, median 66.8; troponin T `ng/L`; NT-proBNP `pg/mL`; CRP-HS `mg/L`). +- `unit_concept_lookup.csv`: field keys `import_c_peptide` → 8842 `ng/mL` and `import_urine_albumin` → 8840 `mg/dL` (still 114 rows; `01_create_unit_lookup.sql` gives the same result). The unit-text keys `ng/L` and `mg/L` are unchanged (generic rows). `unit_concept_lookup_extended.csv` rebuilt; scripts README updated. +- Not changed: the vision and monofilament measurements (BCVA, MARS contrast sensitivity, monofilament; 26 fields) have no unit rows: logMAR and log contrast sensitivity are dimensionless, the others are letter counts or scores; `unit_concept_id` stays 0. + +### Changed — master REDCap data dictionary + +- The two unit rows (master records 2844 and 2939) take the new values; `Origin` = Changed, `Date_of_Variable_Modification` 10/27/2026. 3,150 rows; every concept map row has a master row with the same values. + +### Regenerated + +- map2omop (2,112 rows) and open-source public (1,997) versions, SSSOM (2,067 rows; 75 incomplete) and LinkML (2,142 records). Counts unchanged from v1.8.2 (UCUM 132/40: 8725 and 8751 are still used by troponin T and CRP-HS). + ## [v1.8.2] - 2026-10-27 The new BUN/creatinine field holds BUN ÷ creatinine, so it moves to the BUN/creatinine LOINC code. The data team confirmed the values (for example BUN 15 mg/dL, creatinine 0.77 mg/dL → ratio 19.5; BUN 37, creatinine 1.01 → 36.6). One row is edited in place, so every line number is the same as in v1.8.1. The ETL must apply this change: the field's MEASUREMENT concept changes. Also added: an extended unit lookup that pairs each measurement field's concept with its unit concept. diff --git a/CITATION.cff b/CITATION.cff index 2d93ca2..e7a5f32 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -16,7 +16,7 @@ repository-code: "https://github.com/AI-READI/DataElementMaps" repository-artifact: "https://github.com/AI-READI/DataElementMaps/blob/main/manuscript-tvst2026/ai_readi_redcap_value_set_mapping_common.csv" url: "https://aireadi.org" license: MIT -version: "v1.8.2" +version: "v1.8.3" date-released: "2026-10-27" identifiers: - type: doi diff --git a/codemeta.json b/codemeta.json index 7d1f7a4..ba6d1c5 100644 --- a/codemeta.json +++ b/codemeta.json @@ -7,7 +7,7 @@ "codeRepository": "https://github.com/AI-READI/DataElementMaps", "downloadUrl": "https://github.com/AI-READI/DataElementMaps", "issueTracker": "https://github.com/AI-READI/DataElementMaps/issues", - "version": "v1.8.2", + "version": "v1.8.3", "datePublished": "2026-10-27", "releaseNotes": "Concept map v1.6: maps the A/G ratio, BUN/creatinine ratio (stored as creatinine/BUN), BMI and waist circumference to standard LOINC concepts, adds the unit ratio for the three ratio fields, and excludes the leftover answers of two removed questions. ETL re-run required. See CHANGELOG.md.", "dateCreated": "2023-06-28", diff --git a/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml b/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml index c7a77f5..42a06f9 100644 --- a/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml +++ b/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml @@ -10964,15 +10964,15 @@ mappings: field_id: import_c_peptide_u field_id_num: 2922 question_or_answer: Unit - src_code: ng/L + src_code: ng/mL src_code_id: import_c_peptide_u - src_cd_description: nanogram per liter - target_concept_id: 8725 - target_concept_name: nanogram per liter + src_cd_description: nanogram per milliliter + target_concept_id: 8842 + target_concept_name: nanogram per milliliter target_domain_id: Unit target_vocabulary_id: UCUM target_concept_class_id: Unit - target_concept_code: ng/L + target_concept_code: ng/mL target_standard_concept: S predicate_id: skos:exactMatch confidence: 1.0 @@ -12628,15 +12628,15 @@ mappings: field_id: import_urine_albumin_u field_id_num: 3017 question_or_answer: Unit - src_code: mg/L + src_code: mg/dL src_code_id: import_urine_albumin_u - src_cd_description: milligram per liter - target_concept_id: 8751 - target_concept_name: milligram per liter + src_cd_description: milligram per deciliter + target_concept_id: 8840 + target_concept_name: milligram per deciliter target_domain_id: Unit target_vocabulary_id: UCUM target_concept_class_id: Unit - target_concept_code: mg/L + target_concept_code: mg/dL target_standard_concept: S predicate_id: skos:exactMatch confidence: 1.0 diff --git a/redCapDataDictionaryWithExtension/redcap-data-dictionary/_master_red_cap_data_dictionary_with_extensions.csv b/redCapDataDictionaryWithExtension/redcap-data-dictionary/_master_red_cap_data_dictionary_with_extensions.csv index 49a2976..ea67c13 100644 --- a/redCapDataDictionaryWithExtension/redcap-data-dictionary/_master_red_cap_data_dictionary_with_extensions.csv +++ b/redCapDataDictionaryWithExtension/redcap-data-dictionary/_master_red_cap_data_dictionary_with_extensions.csv @@ -2934,7 +2934,7 @@ Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_troponin_t,2918,Q Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_troponin_t_u,2919,Unit,ng/L,import_troponin_t_u,nanogram per liter,8725,,nanogram per liter,Unit,UCUM,Unit,ng/L,S,skos:exactMatch,1,,,,,, Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_troponin_t_max,2920,Question,,,NORC analyses,,,Troponin-T max,,,,,,,,,,,,, Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_c_peptide,2921,Question,1986-9,C-Peptide,C peptide [Mass/volume] in Serum or Plasma,3010084,,C peptide [Mass/volume] in Serum or Plasma,Measurement,LOINC,Lab Test,1986-9,S,skos:exactMatch,1,,,,,, -Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_c_peptide_u,2922,Unit,ng/L,import_c_peptide_u,nanogram per liter,8725,,nanogram per liter,Unit,UCUM,Unit,ng/L,S,skos:exactMatch,1,,,,,, +Changed,10/27/2026,Yes,Yes,open-source,No,imported,text,import_c_peptide_u,2922,Unit,ng/mL,import_c_peptide_u,nanogram per milliliter,8842,,nanogram per milliliter,Unit,UCUM,Unit,ng/mL,S,skos:exactMatch,1,,,,,, Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_c_peptide_min,2923,Question,,,NORC analyses,,,C-Peptide min,,,,,,,,,,,,, Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_c_peptide_max,2924,Question,,,NORC analyses,,,C-Peptide max,,,,,,,,,,,,, Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_insulin,2925,Question,3695-4,Insulin,Insulin [Mass/volume] in Serum or Plasma,3022466,,Insulin [Mass/volume] in Serum or Plasma,Measurement,LOINC,Lab Test,3695-4,S,skos:exactMatch,1,,,,,, @@ -3029,7 +3029,7 @@ Changed,10/14/2026,Yes,Yes,open-source,No,imported,notes,import_notes_urine,3013 Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_urine_creatinine,3014,Question,2161-8,Urine creatinine,Creatinine [Mass/volume] in Urine,3017250,,Creatinine [Mass/volume] in Urine,Measurement,LOINC,Lab Test,2161-8,S,skos:exactMatch,1,,,,,, Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_urine_creatinine_u,3015,Unit,mg/dL,import_urine_creatinine_u,milligram per deciliter,8840,,milligram per deciliter,Unit,UCUM,Unit,mg/dL,S,skos:exactMatch,1,,,,,, Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_urine_albumin,3016,Question,1754-1,Urine Albumin,Albumin [Mass/volume] in Urine,3012516,,Albumin [Mass/volume] in Urine,Measurement,LOINC,Lab Test,1754-1,S,skos:exactMatch,1,,,,,, -Changed,10/14/2026,Yes,Yes,open-source,No,imported,text,import_urine_albumin_u,3017,Unit,mg/L,import_urine_albumin_u,milligram per liter,8751,,milligram per liter,Unit,UCUM,Unit,mg/L,S,skos:exactMatch,1,,,,,, +Changed,10/27/2026,Yes,Yes,open-source,No,imported,text,import_urine_albumin_u,3017,Unit,mg/dL,import_urine_albumin_u,milligram per deciliter,8840,,milligram per deciliter,Unit,UCUM,Unit,mg/dL,S,skos:exactMatch,1,,,,,, Added,10/14/2026,Yes,Yes,open-source,No,imported,text,import_troponin_t_max2,2920,Question,,,NORC analyses,,,Troponin-T max,,,,,,,,,,,,, Added,10/14/2026,Yes,Yes,open-source,No,imported,text,import_creatinine_min2,,Question,,,COMP,,,Creatinine min,,,,,,,,,,,,, Added,10/14/2026,Yes,Yes,open-source,No,imported,text,import_creatinine_max2,,Question,,,COMP,,,Creatinine max,,,,,,,,,,,,, diff --git a/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.tsv b/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.tsv index 15f73e8..aa1f314 100644 --- a/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.tsv +++ b/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.tsv @@ -490,7 +490,7 @@ AIREADI_REDCAP:imported.pg_mL.import_nt_probnp_u picogram per milliliter skos:ex AIREADI_REDCAP:imported.67151-1.Troponin-T Troponin T.cardiac [Mass/volume] in Serum or Plasma by High sensitivity method skos:exactMatch OMOP:40769783 Troponin T.cardiac [Mass/volume] in Serum or Plasma by High sensitivity method semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation imported text import_troponin_t 2918 67151-1 Troponin-T Question 40769783 Measurement LOINC Lab Test 67151-1 S No open-source Yes AIREADI_REDCAP:imported.ng_L.import_troponin_t_u nanogram per liter skos:exactMatch OMOP:8725 nanogram per liter semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation imported text import_troponin_t_u 2919 ng/L import_troponin_t_u Unit 8725 Unit UCUM Unit ng/L S No open-source Yes AIREADI_REDCAP:imported.1986-9.C-Peptide C peptide [Mass/volume] in Serum or Plasma skos:exactMatch OMOP:3010084 C peptide [Mass/volume] in Serum or Plasma semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation imported text import_c_peptide 2921 1986-9 C-Peptide Question 3010084 Measurement LOINC Lab Test 1986-9 S No open-source Yes -AIREADI_REDCAP:imported.ng_L.import_c_peptide_u nanogram per liter skos:exactMatch OMOP:8725 nanogram per liter semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation imported text import_c_peptide_u 2922 ng/L import_c_peptide_u Unit 8725 Unit UCUM Unit ng/L S No open-source Yes +AIREADI_REDCAP:imported.ng_mL.import_c_peptide_u nanogram per milliliter skos:exactMatch OMOP:8842 nanogram per milliliter semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation imported text import_c_peptide_u 2922 ng/mL import_c_peptide_u Unit 8842 Unit UCUM Unit ng/mL S No open-source Yes AIREADI_REDCAP:imported.3695-4.Insulin Insulin [Mass/volume] in Serum or Plasma skos:exactMatch OMOP:3022466 Insulin [Mass/volume] in Serum or Plasma semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation imported text import_insulin 2925 3695-4 Insulin Question 3022466 Measurement LOINC Lab Test 3695-4 S No open-source Yes AIREADI_REDCAP:imported.ng_mL.import_insulin_u nanogram per milliliter skos:exactMatch OMOP:8842 nanogram per milliliter semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation imported text import_insulin_u 2926 ng/mL import_insulin_u Unit 8842 Unit UCUM Unit ng/mL S No open-source Yes AIREADI_REDCAP:imported.30522-7.CRP-HS C reactive protein [Mass/volume] in Serum or Plasma by High sensitivity method skos:exactMatch OMOP:3010156 C reactive protein [Mass/volume] in Serum or Plasma by High sensitivity method semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation imported text import_crp_hs 2932 30522-7 CRP-HS Question 3010156 Measurement LOINC Lab Test 30522-7 S No open-source Yes @@ -538,7 +538,7 @@ AIREADI_REDCAP:imported.missing.import_hba1c_u percent skos:exactMatch OMOP:8554 AIREADI_REDCAP:imported.2161-8.Urine_creatinine Creatinine [Mass/volume] in Urine skos:exactMatch OMOP:3017250 Creatinine [Mass/volume] in Urine semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation imported text import_urine_creatinine 3014 2161-8 Urine creatinine Question 3017250 Measurement LOINC Lab Test 2161-8 S No open-source Yes AIREADI_REDCAP:imported.mg_dL.import_urine_creatinine_u milligram per deciliter skos:exactMatch OMOP:8840 milligram per deciliter semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation imported text import_urine_creatinine_u 3015 mg/dL import_urine_creatinine_u Unit 8840 Unit UCUM Unit mg/dL S No open-source Yes AIREADI_REDCAP:imported.1754-1.Urine_Albumin Albumin [Mass/volume] in Urine skos:exactMatch OMOP:3012516 Albumin [Mass/volume] in Urine semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation imported text import_urine_albumin 3016 1754-1 Urine Albumin Question 3012516 Measurement LOINC Lab Test 1754-1 S No open-source Yes -AIREADI_REDCAP:imported.mg_L.import_urine_albumin_u milligram per liter skos:exactMatch OMOP:8751 milligram per liter semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation imported text import_urine_albumin_u 3017 mg/L import_urine_albumin_u Unit 8751 Unit UCUM Unit mg/L S No open-source Yes +AIREADI_REDCAP:imported.mg_dL.import_urine_albumin_u milligram per deciliter skos:exactMatch OMOP:8840 milligram per deciliter semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation imported text import_urine_albumin_u 3017 mg/dL import_urine_albumin_u Unit 8840 Unit UCUM Unit mg/dL S No open-source Yes AIREADI_REDCAP:imported.test_upload_date MOCA Date skos:exactMatch OMOP:3006440 Date form completed semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation imported text test_upload_date Question 3006440 Observation LOINC Clinical Observation 30947-6 S No open-source Yes AIREADI_REDCAP:imported.trails_visuospatial_executive Visuospatial Executive - Trails skos:exactMatch OMOP:2005200344 Trail drawings score semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI-MOCA AI-READI manual_curation imported text trails_visuospatial_executive trails_visuospatial_executive Question 2005200344 2005200344 Measurement AIREADI-MOCA Assessment Item S Yes open-source Yes AIREADI_REDCAP:imported.trails_visuospatial_executive_time Visuospatial Executive - Trails (Time) skos:exactMatch OMOP:2005200345 Time taken to do trails in seconds semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI-MOCA AI-READI manual_curation imported text trails_visuospatial_executive_time trails_visuospatial_executive_time Question 2005200345 2005200345 Measurement AIREADI-MOCA Assessment Item S Yes open-source Yes diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common.csv b/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common.csv index 3d19fce..6988f58 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common.csv +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common.csv @@ -511,7 +511,7 @@ Yes,Yes,open-source,No,imported,text,import_troponin_t_u,2919,Unit,ng/L,import_t Yes,Yes,open-source,No,imported,text,import_troponin_t_max,2920,Question,,,NORC analyses,,,Troponin-T max,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_troponin_t_max2,2920,Question,,,NORC analyses,,,Troponin-T max,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_c_peptide,2921,Question,1986-9,C-Peptide,C peptide [Mass/volume] in Serum or Plasma,3010084,,C peptide [Mass/volume] in Serum or Plasma,Measurement,LOINC,Lab Test,1986-9,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,import_c_peptide_u,2922,Unit,ng/L,import_c_peptide_u,nanogram per liter,8725,,nanogram per liter,Unit,UCUM,Unit,ng/L,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,imported,text,import_c_peptide_u,2922,Unit,ng/mL,import_c_peptide_u,nanogram per milliliter,8842,,nanogram per milliliter,Unit,UCUM,Unit,ng/mL,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,import_c_peptide_min,2923,Question,,,NORC analyses,,,C-Peptide min,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_c_peptide_max,2924,Question,,,NORC analyses,,,C-Peptide max,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_insulin,2925,Question,3695-4,Insulin,Insulin [Mass/volume] in Serum or Plasma,3022466,,Insulin [Mass/volume] in Serum or Plasma,Measurement,LOINC,Lab Test,3695-4,S,skos:exactMatch,1,,,, @@ -610,7 +610,7 @@ Yes,Yes,open-source,No,imported,notes,import_notes_urine,3013,Question,,,NORC an Yes,Yes,open-source,No,imported,text,import_urine_creatinine,3014,Question,2161-8,Urine creatinine,Creatinine [Mass/volume] in Urine,3017250,,Creatinine [Mass/volume] in Urine,Measurement,LOINC,Lab Test,2161-8,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,import_urine_creatinine_u,3015,Unit,mg/dL,import_urine_creatinine_u,milligram per deciliter,8840,,milligram per deciliter,Unit,UCUM,Unit,mg/dL,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,import_urine_albumin,3016,Question,1754-1,Urine Albumin,Albumin [Mass/volume] in Urine,3012516,,Albumin [Mass/volume] in Urine,Measurement,LOINC,Lab Test,1754-1,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,import_urine_albumin_u,3017,Unit,mg/L,import_urine_albumin_u,milligram per liter,8751,,milligram per liter,Unit,UCUM,Unit,mg/L,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,imported,text,import_urine_albumin_u,3017,Unit,mg/dL,import_urine_albumin_u,milligram per deciliter,8840,,milligram per deciliter,Unit,UCUM,Unit,mg/dL,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,test_upload_date,,Question,,,MOCA Date,3006440,,Date form completed,Observation,LOINC,Clinical Observation,30947-6,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,imported,text,trails_visuospatial_executive,,Question,trails_visuospatial_executive,,Visuospatial Executive - Trails,2005200344,2005200344,Trail drawings score,Measurement,AIREADI-MOCA,Assessment Item,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,imported,text,trails_visuospatial_executive_time,,Question,trails_visuospatial_executive_time,,Visuospatial Executive - Trails (Time),2005200345,2005200345,Time taken to do trails in seconds,Measurement,AIREADI-MOCA,Assessment Item,,S,skos:exactMatch,1,,,, diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common_map2omop.csv b/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common_map2omop.csv index bd08a53..5030046 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common_map2omop.csv +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common_map2omop.csv @@ -509,7 +509,7 @@ Yes,Yes,open-source,No,imported,text,import_troponin_t_u,2919,Unit,ng/L,import_t Yes,Yes,open-source,No,imported,text,import_troponin_t_max,2920,Question,,,NORC analyses,,,Troponin-T max,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_troponin_t_max2,2920,Question,,,NORC analyses,,,Troponin-T max,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_c_peptide,2921,Question,1986-9,C-Peptide,C peptide [Mass/volume] in Serum or Plasma,3010084,,C peptide [Mass/volume] in Serum or Plasma,Measurement,LOINC,Lab Test,1986-9,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,import_c_peptide_u,2922,Unit,ng/L,import_c_peptide_u,nanogram per liter,8725,,nanogram per liter,Unit,UCUM,Unit,ng/L,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,imported,text,import_c_peptide_u,2922,Unit,ng/mL,import_c_peptide_u,nanogram per milliliter,8842,,nanogram per milliliter,Unit,UCUM,Unit,ng/mL,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,import_c_peptide_min,2923,Question,,,NORC analyses,,,C-Peptide min,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_c_peptide_max,2924,Question,,,NORC analyses,,,C-Peptide max,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_insulin,2925,Question,3695-4,Insulin,Insulin [Mass/volume] in Serum or Plasma,3022466,,Insulin [Mass/volume] in Serum or Plasma,Measurement,LOINC,Lab Test,3695-4,S,skos:exactMatch,1,,,, @@ -608,7 +608,7 @@ Yes,Yes,open-source,No,imported,notes,import_notes_urine,3013,Question,,,NORC an Yes,Yes,open-source,No,imported,text,import_urine_creatinine,3014,Question,2161-8,Urine creatinine,Creatinine [Mass/volume] in Urine,3017250,,Creatinine [Mass/volume] in Urine,Measurement,LOINC,Lab Test,2161-8,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,import_urine_creatinine_u,3015,Unit,mg/dL,import_urine_creatinine_u,milligram per deciliter,8840,,milligram per deciliter,Unit,UCUM,Unit,mg/dL,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,import_urine_albumin,3016,Question,1754-1,Urine Albumin,Albumin [Mass/volume] in Urine,3012516,,Albumin [Mass/volume] in Urine,Measurement,LOINC,Lab Test,1754-1,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,import_urine_albumin_u,3017,Unit,mg/L,import_urine_albumin_u,milligram per liter,8751,,milligram per liter,Unit,UCUM,Unit,mg/L,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,imported,text,import_urine_albumin_u,3017,Unit,mg/dL,import_urine_albumin_u,milligram per deciliter,8840,,milligram per deciliter,Unit,UCUM,Unit,mg/dL,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,test_upload_date,,Question,,,MOCA Date,3006440,,Date form completed,Observation,LOINC,Clinical Observation,30947-6,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,imported,text,trails_visuospatial_executive,,Question,trails_visuospatial_executive,,Visuospatial Executive - Trails,2005200344,2005200344,Trail drawings score,Measurement,AIREADI-MOCA,Assessment Item,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,imported,text,trails_visuospatial_executive_time,,Question,trails_visuospatial_executive_time,,Visuospatial Executive - Trails (Time),2005200345,2005200345,Time taken to do trails in seconds,Measurement,AIREADI-MOCA,Assessment Item,,S,skos:exactMatch,1,,,, diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_map2omop_open_source_public_version.csv b/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_map2omop_open_source_public_version.csv index 4b7bc99..8f46ab1 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_map2omop_open_source_public_version.csv +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_map2omop_open_source_public_version.csv @@ -451,7 +451,7 @@ Yes,Yes,open-source,No,imported,text,import_troponin_t_u,2919,Unit,ng/L,import_t Yes,Yes,open-source,No,imported,text,import_troponin_t_max,2920,Question,,,NORC analyses,,,Troponin-T max,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_troponin_t_max2,2920,Question,,,NORC analyses,,,Troponin-T max,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_c_peptide,2921,Question,1986-9,C-Peptide,C peptide [Mass/volume] in Serum or Plasma,3010084,,C peptide [Mass/volume] in Serum or Plasma,Measurement,LOINC,Lab Test,1986-9,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,import_c_peptide_u,2922,Unit,ng/L,import_c_peptide_u,nanogram per liter,8725,,nanogram per liter,Unit,UCUM,Unit,ng/L,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,imported,text,import_c_peptide_u,2922,Unit,ng/mL,import_c_peptide_u,nanogram per milliliter,8842,,nanogram per milliliter,Unit,UCUM,Unit,ng/mL,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,import_c_peptide_min,2923,Question,,,NORC analyses,,,C-Peptide min,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_c_peptide_max,2924,Question,,,NORC analyses,,,C-Peptide max,,,,,,,,,,, Yes,Yes,open-source,No,imported,text,import_insulin,2925,Question,3695-4,Insulin,Insulin [Mass/volume] in Serum or Plasma,3022466,,Insulin [Mass/volume] in Serum or Plasma,Measurement,LOINC,Lab Test,3695-4,S,skos:exactMatch,1,,,, @@ -550,7 +550,7 @@ Yes,Yes,open-source,No,imported,notes,import_notes_urine,3013,Question,,,NORC an Yes,Yes,open-source,No,imported,text,import_urine_creatinine,3014,Question,2161-8,Urine creatinine,Creatinine [Mass/volume] in Urine,3017250,,Creatinine [Mass/volume] in Urine,Measurement,LOINC,Lab Test,2161-8,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,import_urine_creatinine_u,3015,Unit,mg/dL,import_urine_creatinine_u,milligram per deciliter,8840,,milligram per deciliter,Unit,UCUM,Unit,mg/dL,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,import_urine_albumin,3016,Question,1754-1,Urine Albumin,Albumin [Mass/volume] in Urine,3012516,,Albumin [Mass/volume] in Urine,Measurement,LOINC,Lab Test,1754-1,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,import_urine_albumin_u,3017,Unit,mg/L,import_urine_albumin_u,milligram per liter,8751,,milligram per liter,Unit,UCUM,Unit,mg/L,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,imported,text,import_urine_albumin_u,3017,Unit,mg/dL,import_urine_albumin_u,milligram per deciliter,8840,,milligram per deciliter,Unit,UCUM,Unit,mg/dL,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,test_upload_date,,Question,,,MOCA Date,3006440,,Date form completed,Observation,LOINC,Clinical Observation,30947-6,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,imported,text,trails_visuospatial_executive,,Question,trails_visuospatial_executive,,Visuospatial Executive - Trails,2005200344,2005200344,Trail drawings score,Measurement,AIREADI-MOCA,Assessment Item,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,imported,text,trails_visuospatial_executive_time,,Question,trails_visuospatial_executive_time,,Visuospatial Executive - Trails (Time),2005200345,2005200345,Time taken to do trails in seconds,Measurement,AIREADI-MOCA,Assessment Item,,S,skos:exactMatch,1,,,, diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/README.md b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/README.md index 63b9426..1b374e5 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/README.md +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/README.md @@ -93,7 +93,7 @@ Notes: | `import_bun` | 8840 | mg/dL | | `import_bun_creatinine_ratio` | 8523 | ratio | | `import_buncreatinineratio` | 8523 | ratio | -| `import_c_peptide` | 8725 | ng/L | +| `import_c_peptide` | 8842 | ng/mL | | `import_calcium` | 8840 | mg/dL | | `import_carbon_dioxide_total` | 9557 | mEq/L | | `import_chloride` | 9557 | mEq/L | @@ -114,7 +114,7 @@ Notes: | `import_triglycerides` | 8840 | mg/dL | | `import_troponin_t` | 8725 | ng/L | | `import_uarc` | 8723 | mg/g | -| `import_urine_albumin` | 8751 | mg/L | +| `import_urine_albumin` | 8840 | mg/dL | | `import_urine_creatinine` | 8840 | mg/dL | | `lbscat_a1c` | 8713 | g/dL | | `lbscat_hct` | 8554 | % | diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup.csv b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup.csv index 42b553c..eacb4da 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup.csv +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup.csv @@ -25,7 +25,7 @@ field,import_bilirubin_total,8840,mg/dL field,import_bun,8840,mg/dL field,import_bun_creatinine_ratio,8523,ratio field,import_buncreatinineratio,8523,ratio -field,import_c_peptide,8725,ng/L +field,import_c_peptide,8842,ng/mL field,import_calcium,8840,mg/dL field,import_carbon_dioxide_total,9557,mEq/L field,import_chloride,9557,mEq/L @@ -46,7 +46,7 @@ field,import_total_cholesterol,8840,mg/dL field,import_triglycerides,8840,mg/dL field,import_troponin_t,8725,ng/L field,import_uarc,8723,mg/g -field,import_urine_albumin,8751,mg/L +field,import_urine_albumin,8840,mg/dL field,import_urine_creatinine,8840,mg/dL field,lbscat_a1c,8713,g/dL field,lbscat_hct,8554,% diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup_extended.csv b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup_extended.csv index 32c8df1..88fc5f7 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup_extended.csv +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup_extended.csv @@ -25,7 +25,7 @@ import_bilirubin_total,imported,"Bilirubin, Total",3024128,Bilirubin.total [Mass import_bun,imported,BUN,3013682,Urea nitrogen [Mass/volume] in Serum or Plasma,LOINC,3094-0,8840,milligram per deciliter,mg/dL,544,545, import_bun_creatinine_ratio,imported,BUN/Creatinine ratio,3018311,Urea nitrogen/Creatinine [Mass Ratio] in Serum or Plasma,LOINC,3097-3,8523,ratio,ratio,2125,2126, import_buncreatinineratio,imported,BUN/Creatinine ratio,3033837,Creatinine/Urea nitrogen [Mass Ratio] in Serum or Plasma,LOINC,31045-8,8523,ratio,ratio,554,2080, -import_c_peptide,imported,C-Peptide,3010084,C peptide [Mass/volume] in Serum or Plasma,LOINC,1986-9,8725,nanogram per liter,ng/L,513,514, +import_c_peptide,imported,C-Peptide,3010084,C peptide [Mass/volume] in Serum or Plasma,LOINC,1986-9,8842,nanogram per milliliter,ng/mL,513,514, import_calcium,imported,Calcium,3006906,Calcium [Mass/volume] in Serum or Plasma,LOINC,17861-6,8840,milligram per deciliter,mg/dL,571,572, import_carbon_dioxide_total,imported,"Carbon Dioxide, Total",3015632,"Carbon dioxide, total [Moles/volume] in Serum or Plasma",LOINC,2028-9,9557,milliequivalent per liter,mEq/L,567,568, import_chloride,imported,Chloride,3014576,Chloride [Moles/volume] in Serum or Plasma,LOINC,2075-0,9557,milliequivalent per liter,mEq/L,563,564, @@ -46,7 +46,7 @@ import_total_cholesterol,imported,Total Cholesterol,3027114,Cholesterol [Mass/vo import_triglycerides,imported,Triglycerides,3022192,Triglyceride [Mass/volume] in Serum or Plasma,LOINC,2571-8,8840,milligram per deciliter,mg/dL,531,532, import_troponin_t,imported,Troponin-T,40769783,Troponin T.cardiac [Mass/volume] in Serum or Plasma by High sensitivity method,LOINC,67151-1,8725,nanogram per liter,ng/L,509,510, import_uarc,imported,uACR,3020682,Albumin/Creatinine [Ratio] in Urine,LOINC,32294-1,8723,milligram per gram,mg/g,1715,2047, -import_urine_albumin,imported,Urine Albumin,3012516,Albumin [Mass/volume] in Urine,LOINC,1754-1,8751,milligram per liter,mg/L,612,613, +import_urine_albumin,imported,Urine Albumin,3012516,Albumin [Mass/volume] in Urine,LOINC,1754-1,8840,milligram per deciliter,mg/dL,612,613, import_urine_creatinine,imported,Urine creatinine,3017250,Creatinine [Mass/volume] in Urine,LOINC,2161-8,8840,milligram per deciliter,mg/dL,610,611, lbscat_a1c,lab_results,Hemoglobin - g/dL,3000963,Hemoglobin [Mass/volume] in Blood,LOINC,718-7,8713,gram per deciliter,g/dL,674,2034, lbscat_hct,lab_results,Hematocrit - %,3023314,Hematocrit [Volume Fraction] of Blood by Automated count,LOINC,4544-3,8554,percent,%,675,2035,