Concept map v1.8.3; two unit fixes -

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.

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

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",

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

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,,,,,,,,,,,,,

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			

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,,,,