Concept map v1.3: Dexcom qualifier, cmtrt_lfst Yes answer, four healt…

CHANGELOG.md

@@ -11,6 +11,31 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## [Unreleased]
 
+## [v1.3] - 2026-10-17
+
+### Changed — target concept
+
+- `cmtrt_lfst_1` "Yes" (line 1873), answer to `cmtrt_lfst` "Do you use lifestyle changes to control your A1C and blood glucose levels?": 607008 (Able to modify behavior and lifestyle to support health improvement, SNOMED Clinical Finding) → 45877994 (Yes, LOINC LA33-6, Meas Value), exactMatch 1. The previous concept described ability rather than practice and did not pair with the "No" answer (`cmtrt_lfst_0`, 45878245 No, LA32-8). In the current OMOP survey data this affects 1,245 participants' "Yes" responses (`value_as_concept_id`); `value_as_string` is unaffected.
+
+- Health history "Has a doctor or other healthcare professional ever told you that you have/had..." (`2005200014`): four condition concepts corrected. Each change updates the "Yes" answer row (CONDITION_OCCURRENCE target) and the matching question row (`MODIFIER`, `qualifier_concept_id`, `qualifier_source_value` on the OBSERVATION record), so both tables carry the same concept.
+  - `mhoccur_cns` "Other neurological conditions" (lines 303, 371): 46271045 Neurocognitive disorder → 376337 Disorder of nervous system (SNOMED 118940003), closeMatch 0.75. Neurocognitive disorder covers only cognitive conditions, which have their own questions (dementia, mild cognitive impairment).
+  - `mhoccur_ua` "Urinary problems (Examples: urinary tract infections, incontinence, prostate problems)" (lines 309, 389): 81902 Urinary tract infectious disease → 75865 Disorder of urinary system (SNOMED 128606002), closeMatch 0.75. The previous concept covered infections only.
+  - `mhoccur_clsh` "High blood cholesterol" (lines 295, 346): 4159131 Dyslipidemia → 4029305 Hypercholesterolemia (SNOMED 13644009), exactMatch 1. The previous concept was broader than the question.
+  - `mhoccur_ca` "Cancer (any type)" (lines 306, 380): 4194405 Cancer confirmed (Context-dependent) → 443392 Malignant neoplastic disease (SNOMED 363346000, Disorder), exactMatch 1, the standard concept used for "any cancer" cohort definitions.
+
+### Fixed
+
+- `dcvgmenyn` "Dexcom G6 transmitter returned?" (line 127): `qualifier_concept_id` 1615066 → 2615313 (Transmitter; external, for use with non-durable medical equipment interstitial continuous glucose monitoring system; HCPCS, Device, standard). Concept 1615066 (GLUCOSE TRANSMITTER DEXCOM G6) is not present in the deployed OMOP vocabulary (Databricks `omop_vocab`), and no Dexcom G6 device concept exists there. 2615313 was chosen over 45764014 (Invasive interstitial-fluid glucose monitoring system, SNOMED) because the question and `qualifier_source_value` refer specifically to the transmitter. `qualifier_source_value` is unchanged. Target concept 2005200589 is unchanged.
+
+### Regenerated
+
+- map2omop and open-source public versions, SSSOM and LinkML from the v1.3 common file. Counts (`run_counts.py`): standard 1,409 elements (379 distinct concepts, down from 380 because 607008 is no longer used; the four condition replacements are one-for-one); custom 489 (344); mapped 1,898 (723); designated but unmapped 106.
+
+### Downstream
+
+- Survey ETL must be re-run to apply all v1.3 changes.
+- Note for the ETL team: in the current OMOP survey data, "Yes" answers to the `2005200014` health history questions are written as `value_as_concept_id` 4188539 (SNOMED Yes), while the map specifies 45877994 (LOINC Yes, LA33-6).
+
 ## [v1.2.1] - 2026-10-16
 
 ### Fixed

CITATION.cff

@@ -16,8 +16,8 @@ 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: "v1.2.1"
-date-released: "2026-10-16" 
+version: "v1.3"
+date-released: "2026-10-17" 
 identifiers:
    - type: doi
      value: "10.5281/zenodo.23375723"

codemeta.json

@@ -7,9 +7,9 @@
     "codeRepository": "https://github.com/AI-READI/DataElementMaps",
     "downloadUrl": "https://github.com/AI-READI/DataElementMaps",
     "issueTracker": "https://github.com/AI-READI/DataElementMaps/issues",
-    "version": "v1.2.1",
-    "datePublished": "2026-10-16",
-    "releaseNotes": "Concept map v1.2.1: 4 rows restore concept name changes to v1.1. See CHANGELOG.md.",
+    "version": "v1.3",
+    "datePublished": "2026-10-17",
+    "releaseNotes": "Concept map v1.3: line 127 qualifier 1615066 replaced with 2615313; cmtrt_lfst_1 Yes answer 607008 replaced with 45877994; four health history condition concepts corrected (neurological, urinary, high cholesterol, cancer). See CHANGELOG.md.",
     "dateCreated": "2023-06-28",
     "dateModified": "2026-10-16",
     "applicationCategory": "Scientific",

redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml

@@ -2614,7 +2614,7 @@ mappings:
   predicate_id: skos:exactMatch
   confidence: 1.0
   modifier: Dexcom G6 transmitter returned?
-  qualifier_concept_id: 1615066
+  qualifier_concept_id: 2615313
   qualifier_source_value: GLUCOSE TRANSMITTER DEXCOM G6
 - mapping_record_id: AIREADI_MAPPING_0127
   map_to_omop: 'Yes'
@@ -6268,9 +6268,9 @@ mappings:
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
-  modifier: '4159131'
-  qualifier_concept_id: 4159131
-  qualifier_source_value: Dyslipidemia
+  modifier: '4029305'
+  qualifier_concept_id: 4029305
+  qualifier_source_value: Hypercholesterolemia
 - mapping_record_id: AIREADI_MAPPING_0295
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
@@ -6453,9 +6453,9 @@ mappings:
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
-  modifier: '46271045'
-  qualifier_concept_id: 46271045
-  qualifier_source_value: Neurocognitive disorder
+  modifier: '376337'
+  qualifier_concept_id: 376337
+  qualifier_source_value: Disorder of nervous system
 - mapping_record_id: AIREADI_MAPPING_0303
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
@@ -6522,9 +6522,9 @@ mappings:
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
-  modifier: '4194405'
-  qualifier_concept_id: 4194405
-  qualifier_source_value: Cancer confirmed
+  modifier: '443392'
+  qualifier_concept_id: 443392
+  qualifier_source_value: Malignant neoplastic disease
 - mapping_record_id: AIREADI_MAPPING_0306
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
@@ -6591,9 +6591,9 @@ mappings:
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
-  modifier: '81902'
-  qualifier_concept_id: 81902
-  qualifier_source_value: Urinary tract problems
+  modifier: '75865'
+  qualifier_concept_id: 75865
+  qualifier_source_value: Disorder of urinary system
 - mapping_record_id: AIREADI_MAPPING_0309
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
@@ -7385,12 +7385,12 @@ mappings:
   src_code: '1'
   src_code_id: mhoccur_clsh_1
   src_cd_description: 'Yes'
-  target_concept_id: 4159131
-  target_concept_name: Dyslipidemia
+  target_concept_id: 4029305
+  target_concept_name: Hypercholesterolemia
   target_domain_id: Condition
   target_vocabulary_id: SNOMED
   target_concept_class_id: Disorder
-  target_concept_code: '370992007'
+  target_concept_code: '13644009'
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
@@ -7935,15 +7935,15 @@ mappings:
   src_code: '1'
   src_code_id: mhoccur_cns_1
   src_cd_description: 'Yes'
-  target_concept_id: 46271045
-  target_concept_name: Neurocognitive disorder
+  target_concept_id: 376337
+  target_concept_name: Disorder of nervous system
   target_domain_id: Condition
   target_vocabulary_id: SNOMED
   target_concept_class_id: Disorder
-  target_concept_code: '709073001'
+  target_concept_code: '118940003'
   target_standard_concept: S
-  predicate_id: skos:exactMatch
-  confidence: 1.0
+  predicate_id: skos:closeMatch
+  confidence: 0.75
 - mapping_record_id: AIREADI_MAPPING_0371
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
@@ -8133,12 +8133,12 @@ mappings:
   src_code: '1'
   src_code_id: mhoccur_ca_1
   src_cd_description: 'Yes'
-  target_concept_id: 4194405
-  target_concept_name: Cancer confirmed
+  target_concept_id: 443392
+  target_concept_name: Malignant neoplastic disease
   target_domain_id: Condition
   target_vocabulary_id: SNOMED
-  target_concept_class_id: Context-dependent
-  target_concept_code: '395099008'
+  target_concept_class_id: Disorder
+  target_concept_code: '363346000'
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
@@ -8331,15 +8331,15 @@ mappings:
   src_code: '1'
   src_code_id: mhoccur_ua_1
   src_cd_description: 'Yes'
-  target_concept_id: 81902
-  target_concept_name: Urinary tract infectious disease
+  target_concept_id: 75865
+  target_concept_name: Disorder of urinary system
   target_domain_id: Condition
   target_vocabulary_id: SNOMED
   target_concept_class_id: Disorder
-  target_concept_code: '68566005'
+  target_concept_code: '128606002'
   target_standard_concept: S
-  predicate_id: skos:exactMatch
-  confidence: 1.0
+  predicate_id: skos:closeMatch
+  confidence: 0.75
 - mapping_record_id: AIREADI_MAPPING_0389
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
@@ -40310,12 +40310,12 @@ mappings:
   src_code: '1'
   src_code_id: cmtrt_lfst_1
   src_cd_description: 'Yes'
-  target_concept_id: 607008
-  target_concept_name: Able to modify behavior and lifestyle to support health improvement
-  target_domain_id: Observation
-  target_vocabulary_id: SNOMED
-  target_concept_class_id: Clinical Finding
-  target_concept_code: '1148971005'
+  target_concept_id: 45877994
+  target_concept_name: 'Yes'
+  target_domain_id: Meas Value
+  target_vocabulary_id: LOINC
+  target_concept_class_id: Answer
+  target_concept_code: LA33-6
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0

redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_summary.md

@@ -22,8 +22,8 @@
 - diabetes_survey: 53
 
 ### TARGET_DOMAIN_ID
-- Meas Value: 1247
-- Observation: 440
+- Meas Value: 1248
+- Observation: 439
 - Measurement: 115
 - [blank]: 72
 - Unit: 69
@@ -34,9 +34,9 @@
 - Route: 1
 
 ### TARGET_VOCABULARY_ID
-- LOINC: 1201
+- LOINC: 1202
 - AIREADI: 424
-- SNOMED: 129
+- SNOMED: 128
 - [blank]: 72
 - AIREADI-Vision: 69
 - UCUM: 69
@@ -46,8 +46,8 @@
 - OMOP Extension: 1
 
 ### PREDICATE_ID
-- skos:exactMatch: 1669
-- skos:closeMatch: 261
+- skos:exactMatch: 1667
+- skos:closeMatch: 263
 - [blank]: 72
 - skos:relatedMatch: 2