v1.2 supporting files

CHANGELOG.md

@@ -11,6 +11,40 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## [Unreleased]
 
+### Concept map v1.2 (`_ai_readi_redcap_value_set_mapping_common.csv`)
+
+10 rows changed from `v1.1`: 6 target-concept corrections and 4 concept-name fixes. Line numbers refer to the CSV file (header = line 1).
+
+#### Changed — target concept
+
+- `dmlgrain` (line 146): 46272478 (Assessment of eating and drinking behavior, a SNOMED procedure used with a domain override) → custom 2005200633 (Observation, Survey), exactMatch 1. No standard concept matches the question; LOINC 90725-3 differs in time frame, foods and answer type.
+- `eos_dsdecod_1` "Did not meet Inclusion/Exclusion criteria" (line 250): custom 2005200280 → 40480675 (Does not meet eligibility criteria for clinical trial, SNOMED 444734003), exactMatch 1.
+- `eos_dsdecod_5` "Investigator deemed not appropriate for study" (line 254): 40480675 (closeMatch 0.75; investigator judgment is not ineligibility) → custom 2005200634 (Meas Value, Answer), exactMatch 1.
+- `lbscat_wbc` (line 672): custom 2005200182 → 3000905 (Leukocytes [#/volume] in Blood by Automated count, LOINC 6690-2).
+- `lbscat_rbc` (line 673): custom 2005200183 → 3020416 (Erythrocytes [#/volume] in Blood by Automated count, LOINC 789-8).
+- `paid_scrd` (line 813): 36716888 (Fear of metabolic disease, a SNOMED Condition-domain clinical finding used with a domain override) → custom 2005200635 (Observation, Survey), exactMatch 1, consistent with the other PAID-5 items.
+
+#### Changed — concept name only (target concept unchanged)
+
+- `lbscat_hct` (675): Hematocrit [Volume Fraction] of Blood (removed "by calculation").
+- `lbscat_mcv` (676): MCV [Entitic volume].
+- `lbscat_mchc` (678): MCHC [Mass/volume].
+- `lbscat_rdw` (679): Erythrocyte distribution width [Ratio].
+
+#### Added
+
+- AI-READI custom concepts 2005200633 (`dmlgrain`), 2005200634 (`eos_dsdecod_5`) and 2005200635 (`paid_scrd`) in `OHDSI-vocabulary-request/concept_manual.csv`. Custom concepts 2005200182, 2005200183 and 2005200280 are no longer referenced but are kept (IDs are not reused).
+
+#### Regenerated
+
+- map2omop and open-source public versions from the v1.2 common file.
+- SSSOM and LinkML with `generate_linkml_sssom.py`.
+- Counts (`redCapDataDictionaryWithExtension/scripts/run_counts.py`): standard 1,409 (380 concepts); custom 489 (344); mapped 1,898 (724); designated but unmapped 106.
+
+#### Downstream
+
+- Survey ETL must be re-run to apply v1.2.
+
 
 ## [v1.1] - 2026-10-16
 
@@ -51,9 +85,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `_ai_readi_redcap_value_set_mapping_common_map2omop.csv` (Map_to_OMOP = Yes; 2,003 rows) and `_ai_readi_redcap_value_set_mapping_map2omop_open_source_public_version.csv` (open-source rows; 1,895 rows) from the v1.1 common file.
 - SSSOM and LinkML (`redCapDataDictionaryWithExtension/sssom/`, `linkml/`) with `generate_linkml_sssom.py`: SSSOM 1,932 rows, 72 incomplete (`ethnicscore` and `brthyy` now listed as incomplete); `Ethnicity` added to the LinkML domain and vocabulary enums.
 
-#### Downstream
-
-- Survey ETL must be re-run to apply v1.1.
 
 ### Manuscript package (changes since v1.0-tvst)
 

redCapDataDictionaryWithExtension/OHDSI-vocabulary-request/concept_manual.csv

@@ -414,4 +414,7 @@ Stroke,,2005200628,AIREADI,Condition,,Disorder,,1/1/1970,,
 "Have you had anything to eat or drink in the last six hours, including coffee or tea with milk or sugar or any other drink other than water?",,2005200629,AIREADI,Observation,survey_conduct,Survey,,1/1/1970,,
 Discrimination in Medical Settings (DMS) total score [PhenX],pxdhc_sum,2005200630,AIREADI,Observation,,Survey,,1/1/1970,,
 Location of environmental sensor within home,dvenvlocn,2005200631,AIREADI,Observation,,Survey,,1/1/1970,,
-Last study visit/stage completed,eos_dsvst,2005200632,AIREADI,Observation,survey_conduct,Survey,,1/1/1970,,
+Last study visit/stage completed,eos_dsvst,2005200632,AIREADI,Observation,survey_conduct,Survey,,1/1/1970,,
+"In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice).",dmlgrain,2005200633,AIREADI,Observation,survey_conduct,Survey,,1/1/1970,,
+Investigator deemed not appropriate for study,eos_dsdecod_5,2005200634,AIREADI,Meas Value,,Answer,,1/1/1970,,
+Feeling scared when you think about living with diabetes,paid_scrd,2005200635,AIREADI,Observation,survey_conduct,Survey,,1/1/1970,,

redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml

@@ -2998,15 +2998,16 @@ mappings:
   src_code: dmlgrain
   src_cd_description: 'In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread,
     or brown rice).'
-  target_concept_id: 46272478
-  target_concept_name: Assessment of eating and drinking behavior
+  target_concept_id: 2005200633
+  local_concept_id: 2005200633
+  target_concept_name: 'In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread,
+    or brown rice).'
   target_domain_id: Observation
-  target_vocabulary_id: SNOMED
-  target_concept_class_id: Procedure
-  target_concept_code: '710848001'
+  target_vocabulary_id: AIREADI
+  target_concept_class_id: Survey
   target_standard_concept: S
-  predicate_id: skos:closeMatch
-  confidence: 0.75
+  predicate_id: skos:exactMatch
+  confidence: 1.0
 - mapping_record_id: AIREADI_MAPPING_0146
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
@@ -5248,7 +5249,7 @@ mappings:
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
   protected_or_open_source: open-source
-  extension_needed: 'Yes'
+  extension_needed: 'No'
   form_name: disposition
   field_type: radio
   field_id: eos_dsdecod
@@ -5257,12 +5258,12 @@ mappings:
   src_code: '1'
   src_code_id: eos_dsdecod_1
   src_cd_description: Did not meet Inclusion/Exclusion criteria
-  target_concept_id: 2005200280
-  local_concept_id: 2005200280
-  target_concept_name: Did not meet Inclusion/Exclusion criteria
-  target_domain_id: Meas Value
-  target_vocabulary_id: AIREADI
-  target_concept_class_id: Answer
+  target_concept_id: 40480675
+  target_concept_name: Does not meet eligibility criteria for clinical trial
+  target_domain_id: Observation
+  target_vocabulary_id: SNOMED
+  target_concept_class_id: Clinical Finding
+  target_concept_code: '444734003'
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
@@ -5336,7 +5337,7 @@ mappings:
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
   protected_or_open_source: open-source
-  extension_needed: 'No'
+  extension_needed: 'Yes'
   form_name: disposition
   field_type: radio
   field_id: eos_dsdecod
@@ -5345,15 +5346,15 @@ mappings:
   src_code: '5'
   src_code_id: eos_dsdecod_5
   src_cd_description: Investigator deemed not appropriate for study
-  target_concept_id: 40480675
-  target_concept_name: Does not meet eligibility criteria for clinical trial
-  target_domain_id: Observation
-  target_vocabulary_id: SNOMED
-  target_concept_class_id: Clinical Finding
-  target_concept_code: '444734003'
+  target_concept_id: 2005200634
+  local_concept_id: 2005200634
+  target_concept_name: Investigator deemed not appropriate for study
+  target_domain_id: Meas Value
+  target_vocabulary_id: AIREADI
+  target_concept_class_id: Answer
   target_standard_concept: S
-  predicate_id: skos:closeMatch
-  confidence: 0.75
+  predicate_id: skos:exactMatch
+  confidence: 1.0
 - mapping_record_id: AIREADI_MAPPING_0254
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
@@ -13795,39 +13796,39 @@ mappings:
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
   protected_or_open_source: open-source
-  extension_needed: 'Yes'
+  extension_needed: 'No'
   form_name: lab_results
   field_type: text
   field_id_num: 1665
   question_or_answer: Question
   src_code: lbscat_wbc
   src_cd_description: White Blood Cells (WBC) - x10E3/µL
-  target_concept_id: 2005200182
-  local_concept_id: 2005200182
-  target_concept_name: White Blood Cells (WBC) - x10E3/µL
+  target_concept_id: 3000905
+  target_concept_name: Leukocytes [#/volume] in Blood by Automated count
   target_domain_id: Measurement
-  target_vocabulary_id: AIREADI
-  target_concept_class_id: Procedure
+  target_vocabulary_id: LOINC
+  target_concept_class_id: Lab Test
+  target_concept_code: 6690-2
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
 - mapping_record_id: AIREADI_MAPPING_0672
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
   protected_or_open_source: open-source
-  extension_needed: 'Yes'
+  extension_needed: 'No'
   form_name: lab_results
   field_type: text
   field_id_num: 1666
   question_or_answer: Question
   src_code: lbscat_rbc
   src_cd_description: Red Blood Cells (RBC) - x10E6/µL
-  target_concept_id: 2005200183
-  local_concept_id: 2005200183
-  target_concept_name: Red Blood Cells (RBC) - x10E6/µL
+  target_concept_id: 3020416
+  target_concept_name: Erythrocytes [#/volume] in Blood by Automated count
   target_domain_id: Measurement
-  target_vocabulary_id: AIREADI
-  target_concept_class_id: Procedure
+  target_vocabulary_id: LOINC
+  target_concept_class_id: Lab Test
+  target_concept_code: 789-8
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
@@ -13863,7 +13864,7 @@ mappings:
   src_code: lbscat_hct
   src_cd_description: Hematocrit  - %
   target_concept_id: 3009542
-  target_concept_name: Hematocrit [Volume Fraction] of Blood by calculation
+  target_concept_name: Hematocrit [Volume Fraction] of Blood
   target_domain_id: Measurement
   target_vocabulary_id: LOINC
   target_concept_class_id: Lab Test
@@ -13883,7 +13884,7 @@ mappings:
   src_code: lbscat_mcv
   src_cd_description: MCV - fL
   target_concept_id: 3024731
-  target_concept_name: MCV [Entitic mean volume] in Red Blood Cells
+  target_concept_name: MCV [Entitic volume]
   target_domain_id: Measurement
   target_vocabulary_id: LOINC
   target_concept_class_id: Lab Test
@@ -13923,7 +13924,7 @@ mappings:
   src_code: lbscat_mchc
   src_cd_description: MCHC - g/dL
   target_concept_id: 3003338
-  target_concept_name: MCHC [Entitic Mass/volume] in Red Blood Cells
+  target_concept_name: MCHC [Mass/volume]
   target_domain_id: Measurement
   target_vocabulary_id: LOINC
   target_concept_class_id: Lab Test
@@ -13943,7 +13944,7 @@ mappings:
   src_code: lbscat_rdw
   src_cd_description: RDW - %
   target_concept_id: 3002385
-  target_concept_name: Erythrocyte [DistWidth] in Red Blood Cells
+  target_concept_name: Erythrocyte distribution width [Ratio]
   target_domain_id: Measurement
   target_vocabulary_id: LOINC
   target_concept_class_id: Lab Test
@@ -16895,12 +16896,12 @@ mappings:
   question_or_answer: Question
   src_code: paid_scrd
   src_cd_description: Feeling scared when you think about living with diabetes
-  target_concept_id: 36716888
-  target_concept_name: Fear of metabolic disease
+  target_concept_id: 2005200635
+  local_concept_id: 2005200635
+  target_concept_name: Feeling scared when you think about living with diabetes
   target_domain_id: Observation
-  target_vocabulary_id: SNOMED
-  target_concept_class_id: Clinical Finding
-  target_concept_code: '723113005'
+  target_vocabulary_id: AIREADI
+  target_concept_class_id: Survey
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0

redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_summary.md

@@ -34,9 +34,9 @@
 - Route: 1
 
 ### TARGET_VOCABULARY_ID
-- LOINC: 1199
+- LOINC: 1201
 - AIREADI: 424
-- SNOMED: 131
+- SNOMED: 129
 - [blank]: 72
 - AIREADI-Vision: 69
 - UCUM: 69
@@ -46,12 +46,12 @@
 - OMOP Extension: 1
 
 ### PREDICATE_ID
-- skos:exactMatch: 1667
-- skos:closeMatch: 263
+- skos:exactMatch: 1669
+- skos:closeMatch: 261
 - [blank]: 72
 - skos:relatedMatch: 2
 
 ### Extension_Needed
-- No: 1511
-- Yes: 492
+- No: 1513
+- Yes: 490
 - [blank]: 1