commit v1.6 labs and vitals to LOINC, ratio units, - Lines 584, 554, …

CHANGELOG.md

@@ -11,6 +11,45 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## [Unreleased]
 
+## [v1.6] - 2026-10-22
+
+Lab and vital-sign measurements moved from SNOMED to standard LOINC concepts, unit rows added for the three ratio fields, and the leftover answers of two removed questions excluded. Target concepts change on 4 rows, `Map_to_OMOP` on 4 rows, and 3 unit rows are appended, so the ETL must be re-run to apply these changes. Edits to existing rows are in place and the new rows are appended at the end (lines 2078–2080), so every existing line number is the same as in v1.5. Concept IDs and names were confirmed in the deployed OMOP vocabulary (Databricks `omop_vocab`).
+
+### Changed — target concept (SNOMED → LOINC)
+
+- `import_ag_ratio` "A/G Ratio (calculated field)" (line 584): 4288601 *Albumin/Globulin ratio* (SNOMED 687005) → 3020509 *Albumin/Globulin [Mass Ratio] in Serum or Plasma* (LOINC 1759-0, Lab Test), exactMatch 1. Every other imported lab already maps to a LOINC lab test. Current OMOP data: 3,984 values, median 1.72.
+- `import_buncreatinineratio` "BUN/Creatinine ratio" (line 554): 4112223 *BUN/Creatinine ratio* (SNOMED 18207002) → **3033837 *Creatinine/Urea nitrogen [Mass Ratio] in Serum or Plasma*** (LOINC 31045-8, Lab Test), exactMatch 1. The REDCap calculated field stores **creatinine ÷ BUN**, the inverse of its label: compared with each person's own BUN and creatinine on the same date, all 3,981 values in the current OMOP data match creatinine ÷ BUN (median 0.053; BUN ÷ creatinine would be 18.75). The row is mapped to what is stored, with `MODIFIER` "Stored value is creatinine/BUN (REDCap calculation inverted; field label says BUN/Creatinine); remap to 3018311 (LOINC 3097-3) when the REDCap formula and values are corrected". `SRC_CD_DESCRIPTION` keeps the REDCap label. The data team has been asked to correct the formula.
+- `bmi_vsorres` "BMI" (line 858): 4245997 *Body mass index* (SNOMED 60621009) → 3038553 *Body mass index (BMI) [Ratio]* (LOINC 39156-5), exactMatch 1, the standard BMI concept used in OHDSI phenotypes.
+- `waist_vsorres` "Waist Circumference (cm)" (line 859): 4172830 *Waist circumference* (SNOMED 276361009) → 3016258 *Waist Circumference at umbilicus by Tape measure* (LOINC 8280-0), closeMatch 1. Measurement at the umbilicus with a tape measure is accepted for AI-READI; closeMatch because the site is not stated on the form.
+- Kept on SNOMED: hip circumference (line 860; LOINC has only a protocol term, 62409-8) and waist/hip ratio (line 861; no LOINC term).
+
+### Added — units
+
+- Fixed-unit rows for the three ratio fields, same format as the v1.4 fixed-unit rows (`MODIFIER` "fixed unit; no REDCap unit field"): `import_ag_ratio_u` (line 2078), `whr_vsorres_u` (line 2079) and `import_buncreatinineratio_u` (line 2080) → 8523 *ratio* (UCUM `{ratio}`). A ratio of two values in the same unit is dimensionless; the unit is the same whichever way the BUN/creatinine ratio is calculated. v1.4 had left these fields without a unit.
+- `unit_concept_lookup.csv` (and `01_create_unit_lookup.sql`): 113 rows (field 88, string 25), up from 110; row counts updated in the scripts' README, USAGE and SQL comments.
+
+### Changed — Map_to_OMOP
+
+- `dri3` "Driver's License photocopied" answers (lines 277–278) and `cmotyn` "Are there any other medications that you are currently taking that are not included here?" answers (lines 730–731): `Map_to_OMOP` Yes → No. In the master REDCap dictionary the `dri3` question was deleted (6/27/2023) and the `cmotyn` question was excluded from mapping (4/25/2024), but their Yes/No answer rows had been left as Yes. Neither field appears in the current OMOP survey data. map2omop and the open-source public file each lose these 4 rows.
+
+### Changed — scripts
+
+- `count_concept_map.sql`: answer rows of an excluded question (`Map_to_OMOP` = No) are reported as designated-but-unmapped with the reason "Answer to an excluded question"; expected values updated to v1.6.
+- `audit_concept_map.py` (check A8) and `validate_concept_map_vocab.sql` (check V9): answer rows already excluded (`Map_to_OMOP` = No) are no longer flagged. A8 now lists 3 rows (administrative BCVA "not done" and satisfaction-survey rows).
+
+### Regenerated
+
+- map2omop (2,074 rows) and open-source public (1,965) versions, SSSOM (2,003 rows; 76 incomplete) and LinkML (2,079 records) from the v1.6 common file. `medication_route_lookup.csv` checked against the map: unchanged.
+- Counts (`run_counts.py`): standard 1,478 (392 concepts); custom 487 (342); mapped 1,965 (734 concepts); designated but unmapped 114. The 3 added unit rows lower "not designated" from 830 to 827 against the fixed total of 2,906.
+
+### Reviewed and not changed
+
+- LDL cholesterol (lines 537–538): the unit row `import_ldl_cholesterol_u` does not follow the `<field>_u` pattern because the REDCap names differ: the data uses `import_ldl_cholesterol_calculation` (3,984 rows in the current OMOP data) and the REDCap unit field is `import_ldl_cholesterol_u`. The extra key in `unit_concept_lookup.csv` (and the UNION in `01_create_unit_lookup.sql`) is the documented exception.
+
+### Not yet included
+
+- CBC method codes: hematocrit (line 675) stays *by calculation* (20570-8, 3009542) unless the lab confirms it is measured directly (then 4544-3, 3023314); MCV, MCH, MCHC, RDW and platelets (676–680) may move to their "by Automated count" codes (3023599, 3012030, 3009744, 3019897, 3024929) once the lab confirms an automated analyzer. Waiting on the performing labs.
+
 ## [v1.5] - 2026-10-19 - 10.5281/zenodo.23488128
 
 Corrections from a full review of all 2,076 rows of v1.4 (the first review of the whole file; earlier releases reviewed only the rows in each batch of changes). Target concepts change on 10 rows, qualifier concepts on 2 rows and field names on 5 answer rows, so the ETL must be re-run to apply these changes. All edits are in place: no rows are added or removed, so every line number is the same as in v1.4. Concept IDs and names for the new standard concepts were confirmed in the deployed OMOP vocabulary (Databricks `omop_vocab`).

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: "v1.5"
-date-released: "2026-10-19" 
+version: "v1.6"
+date-released: "2026-10-22" 
 identifiers:
    - type: doi
      value: "10.5281/zenodo.23375723"

codemeta.json

@@ -7,11 +7,11 @@
     "codeRepository": "https://github.com/AI-READI/DataElementMaps",
     "downloadUrl": "https://github.com/AI-READI/DataElementMaps",
     "issueTracker": "https://github.com/AI-READI/DataElementMaps/issues",
-    "version": "v1.5",
-    "datePublished": "2026-10-19",
-    "releaseNotes": "Concept map v1.5: maps stroke and kidney disease to standard SNOMED concepts, separates the 31-40 cigarettes-per-day answer from the LOINC \"31 or more\" answer (new custom concept 2005200636), maps \"less than once a week\" medication-use answers to LOINC LA27722-0, sets the medication route question to 0, cleans metadata, and adds release audit scripts. ETL re-run required. See CHANGELOG.md.",
+    "version": "v1.6",
+    "datePublished": "2026-10-22",
+    "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",
-    "dateModified": "2026-10-19",
+    "dateModified": "2026-10-22",
     "applicationCategory": "Scientific",
     "developmentStatus": "active",
     "isPartOf": "https://aireadi.org/",

redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml

@@ -5827,7 +5827,7 @@ mappings:
   predicate_id: skos:exactMatch
   confidence: 1.0
 - mapping_record_id: AIREADI_MAPPING_0276
-  map_to_omop: 'Yes'
+  map_to_omop: 'No'
   transferred_to_fairhub_redcap_dataset: 'Yes'
   protected_or_open_source: open-source
   extension_needed: 'No'
@@ -5849,7 +5849,7 @@ mappings:
   predicate_id: skos:exactMatch
   confidence: 1.0
 - mapping_record_id: AIREADI_MAPPING_0277
-  map_to_omop: 'Yes'
+  map_to_omop: 'No'
   transferred_to_fairhub_redcap_dataset: 'Yes'
   protected_or_open_source: open-source
   extension_needed: 'No'
@@ -11627,15 +11627,17 @@ mappings:
   question_or_answer: Question
   src_code_id: BUN/Creatinine ratio
   src_cd_description: BUN/Creatinine ratio
-  target_concept_id: 4112223
-  target_concept_name: BUN/Creatinine ratio
+  target_concept_id: 3033837
+  target_concept_name: Creatinine/Urea nitrogen [Mass Ratio] in Serum or Plasma
   target_domain_id: Measurement
-  target_vocabulary_id: SNOMED
-  target_concept_class_id: Procedure
-  target_concept_code: '18207002'
+  target_vocabulary_id: LOINC
+  target_concept_class_id: Lab Test
+  target_concept_code: 31045-8
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
+  modifier: Stored value is creatinine/BUN (REDCap calculation inverted; field label says BUN/Creatinine); remap to 3018311
+    (LOINC 3097-3) when the REDCap formula and values are corrected
 - mapping_record_id: AIREADI_MAPPING_0554
   map_to_omop: 'Yes'
   transferred_to_fairhub_redcap_dataset: 'Yes'
@@ -12146,12 +12148,12 @@ mappings:
   question_or_answer: Question
   src_code_id: A/G Ratio (calculated field)
   src_cd_description: Albumin/Globulin ratio
-  target_concept_id: 4288601
-  target_concept_name: Albumin/Globulin ratio
+  target_concept_id: 3020509
+  target_concept_name: Albumin/Globulin [Mass Ratio] in Serum or Plasma
   target_domain_id: Measurement
-  target_vocabulary_id: SNOMED
-  target_concept_class_id: Procedure
-  target_concept_code: '687005'
+  target_vocabulary_id: LOINC
+  target_concept_class_id: Lab Test
+  target_concept_code: 1759-0
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
@@ -15019,7 +15021,7 @@ mappings:
   predicate_id: skos:exactMatch
   confidence: 1.0
 - mapping_record_id: AIREADI_MAPPING_0729
-  map_to_omop: 'Yes'
+  map_to_omop: 'No'
   transferred_to_fairhub_redcap_dataset: 'Yes'
   protected_or_open_source: open-source
   extension_needed: 'No'
@@ -15041,7 +15043,7 @@ mappings:
   predicate_id: skos:exactMatch
   confidence: 1.0
 - mapping_record_id: AIREADI_MAPPING_0730
-  map_to_omop: 'Yes'
+  map_to_omop: 'No'
   transferred_to_fairhub_redcap_dataset: 'Yes'
   protected_or_open_source: open-source
   extension_needed: 'No'
@@ -17856,12 +17858,12 @@ mappings:
   question_or_answer: Question
   src_code: bmi_vsorres
   src_cd_description: BMI
-  target_concept_id: 4245997
-  target_concept_name: Body mass index
+  target_concept_id: 3038553
+  target_concept_name: Body mass index (BMI) [Ratio]
   target_domain_id: Measurement
-  target_vocabulary_id: SNOMED
-  target_concept_class_id: Observable Entity
-  target_concept_code: '60621009'
+  target_vocabulary_id: LOINC
+  target_concept_class_id: Clinical Observation
+  target_concept_code: 39156-5
   target_standard_concept: S
   predicate_id: skos:exactMatch
   confidence: 1.0
@@ -17876,14 +17878,14 @@ mappings:
   question_or_answer: Question
   src_code: waist_vsorres
   src_cd_description: Waist Circumference (cm)
-  target_concept_id: 4172830
-  target_concept_name: Waist circumference
+  target_concept_id: 3016258
+  target_concept_name: Waist Circumference at umbilicus by Tape measure
   target_domain_id: Measurement
-  target_vocabulary_id: SNOMED
-  target_concept_class_id: Observable Entity
-  target_concept_code: '276361009'
+  target_vocabulary_id: LOINC
+  target_concept_class_id: Clinical Observation
+  target_concept_code: 8280-0
   target_standard_concept: S
-  predicate_id: skos:exactMatch
+  predicate_id: skos:closeMatch
   confidence: 1.0
 - mapping_record_id: AIREADI_MAPPING_0859
   map_to_omop: 'Yes'
@@ -44604,3 +44606,69 @@ mappings:
   predicate_id: skos:exactMatch
   confidence: 1.0
   modifier: fixed unit; no REDCap unit field
+- mapping_record_id: AIREADI_MAPPING_2077
+  map_to_omop: 'Yes'
+  transferred_to_fairhub_redcap_dataset: 'Yes'
+  protected_or_open_source: open-source
+  extension_needed: 'No'
+  form_name: imported
+  field_type: text
+  field_id: import_ag_ratio_u
+  question_or_answer: Unit
+  src_code: ratio
+  src_code_id: import_ag_ratio_u
+  src_cd_description: ratio
+  target_concept_id: 8523
+  target_concept_name: ratio
+  target_domain_id: Unit
+  target_vocabulary_id: UCUM
+  target_concept_class_id: Unit
+  target_concept_code: '{ratio}'
+  target_standard_concept: S
+  predicate_id: skos:exactMatch
+  confidence: 1.0
+  modifier: fixed unit; no REDCap unit field
+- mapping_record_id: AIREADI_MAPPING_2078
+  map_to_omop: 'Yes'
+  transferred_to_fairhub_redcap_dataset: 'Yes'
+  protected_or_open_source: open-source
+  extension_needed: 'No'
+  form_name: physical_assessment
+  field_type: text
+  field_id: whr_vsorres_u
+  question_or_answer: Unit
+  src_code: ratio
+  src_code_id: whr_vsorres_u
+  src_cd_description: ratio
+  target_concept_id: 8523
+  target_concept_name: ratio
+  target_domain_id: Unit
+  target_vocabulary_id: UCUM
+  target_concept_class_id: Unit
+  target_concept_code: '{ratio}'
+  target_standard_concept: S
+  predicate_id: skos:exactMatch
+  confidence: 1.0
+  modifier: fixed unit; no REDCap unit field
+- mapping_record_id: AIREADI_MAPPING_2079
+  map_to_omop: 'Yes'
+  transferred_to_fairhub_redcap_dataset: 'Yes'
+  protected_or_open_source: open-source
+  extension_needed: 'No'
+  form_name: imported
+  field_type: text
+  field_id: import_buncreatinineratio_u
+  question_or_answer: Unit
+  src_code: ratio
+  src_code_id: import_buncreatinineratio_u
+  src_cd_description: ratio
+  target_concept_id: 8523
+  target_concept_name: ratio
+  target_domain_id: Unit
+  target_vocabulary_id: UCUM
+  target_concept_class_id: Unit
+  target_concept_code: '{ratio}'
+  target_standard_concept: S
+  predicate_id: skos:exactMatch
+  confidence: 1.0
+  modifier: fixed unit; no REDCap unit field

redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_summary.md

@@ -1,7 +1,7 @@
 # AI-READI REDCap Value Set Mapping LinkML Conversion Summary
 
 - Source file: `_ai_readi_redcap_value_set_mapping_common.csv`
-- Rows converted: 2076
+- Rows converted: 2079
 - Source columns: 26
 
 ## Generated files
@@ -12,7 +12,7 @@
 ### FORM_NAME
 - px_racial_ethnic_discrimination_survey: 364
 - px_sdoh_combined_survey: 267
-- imported: 203
+- imported: 205
 - health_survey: 174
 - retinal_imaging_v2: 133
 - px_neighborhood_environment_survey: 126
@@ -24,7 +24,7 @@
 ### TARGET_DOMAIN_ID
 - Meas Value: 1231
 - Observation: 439
-- Unit: 145
+- Unit: 148
 - Measurement: 114
 - [blank]: 76
 - Condition: 32
@@ -34,10 +34,10 @@
 - Device: 1
 
 ### TARGET_VOCABULARY_ID
-- LOINC: 1183
+- LOINC: 1187
 - AIREADI: 422
-- UCUM: 145
-- SNOMED: 141
+- UCUM: 148
+- SNOMED: 137
 - [blank]: 76
 - AIREADI-Vision: 69
 - AIREADI-MOCA: 30
@@ -46,12 +46,12 @@
 - OMOP Extension: 1
 
 ### PREDICATE_ID
-- skos:exactMatch: 1734
-- skos:closeMatch: 264
+- skos:exactMatch: 1736
+- skos:closeMatch: 265
 - [blank]: 76
 - skos:relatedMatch: 2
 
 ### Extension_Needed
-- No: 1554
+- No: 1557
 - Yes: 521
 - [blank]: 1

redCapDataDictionaryWithExtension/scripts/audit_concept_map.py

@@ -12,8 +12,8 @@
   A6  Leading/trailing spaces or non-breaking spaces in key columns
   A7  Custom concept used as a Condition/answer target where a review is due
       (lists every custom Condition target; check whether a standard concept exists)
-  A8  Answer rows whose FIELD_ID matches no question row (a field-name typo stops the
-      ETL from linking the answers; e.g. pxne9_ and pxrd9 before v1.5)
+  A8  Answer rows (Map_to_OMOP = Yes) whose FIELD_ID matches no question row (a field-name
+      typo stops the ETL from linking the answers; e.g. pxne9_ and pxrd9 before v1.5)
 
 Part B - review lists (read every row; nothing here is automatically wrong):
   B1  Answer rows whose source text differs from the target concept name
@@ -218,7 +218,8 @@ def audit(rows, cm, out, label):
     # A8
     qcodes = {r["SRC_CODE"] for r in rows if r["temp_Question_or_Answer"] == "Question"}
     a8 = [(r["_ln"], r["FORM_NAME"], r["FIELD_ID"], r["SRC_CODE"], r["SRC_CD_DESCRIPTION"][:60], r["TARGET_CONCEPT_ID"])
-          for r in rows if r["temp_Question_or_Answer"] == "Answer" and r["FIELD_ID"] not in qcodes]
+          for r in rows if r["temp_Question_or_Answer"] == "Answer" and r["FIELD_ID"] not in qcodes
+          and r.get("Map_to_OMOP", "Yes") == "Yes"]  # rows already excluded (Map_to_OMOP = No) are not flagged
     sections.append(("A8 Answers whose FIELD_ID matches no question row (field-name typos; administrative fields expected)",
                      ["Line", "Form", "FIELD_ID", "SRC_CODE", "Source text", "Concept"], a8, False))