diff --git a/CHANGELOG.md b/CHANGELOG.md index beb68ff..e4dab98 100644 --- a/CHANGELOG.md +++ b/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) diff --git a/redCapDataDictionaryWithExtension/OHDSI-vocabulary-request/concept_manual.csv b/redCapDataDictionaryWithExtension/OHDSI-vocabulary-request/concept_manual.csv index eea1f32..8e1b6e5 100644 --- a/redCapDataDictionaryWithExtension/OHDSI-vocabulary-request/concept_manual.csv +++ b/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,, \ No newline at end of file +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,, \ No newline at end of file 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 d06a2fb..33bac3f 100644 --- a/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml +++ b/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' @@ -13795,19 +13796,19 @@ 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 @@ -13815,19 +13816,19 @@ 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: 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 diff --git a/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_summary.md b/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_summary.md index 19d86eb..0f72537 100644 --- a/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_summary.md +++ b/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 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 bd43677..d910727 100644 --- a/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.tsv +++ b/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.tsv @@ -130,7 +130,7 @@ AIREADI_REDCAP:diabetes_survey.dmlvex In a typical week, how often do you engage AIREADI_REDCAP:diabetes_survey.dmlact What would you consider your typical activity level to be? skos:closeMatch OMOP:44808782 Level of physical activity semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation diabetes_survey radio 1225 dmlact Question 44808782 Observation SNOMED Observable Entity 859981000000107 S No open-source Yes AIREADI_REDCAP:diabetes_survey.dmlhex How often would you say that you engage in daily home exercise? (Examples: stretching, calisthenics, or yoga) skos:exactMatch OMOP:2005200278 How often would you say that you engage in daily home exercise? (Examples: stretching, calisthenics, or yoga) semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation diabetes_survey radio 1226 dmlhex Question 2005200278 2005200278 Observation AIREADI Procedure S Yes open-source Yes AIREADI_REDCAP:diabetes_survey.dmlsugar When reflecting on your typical eating habits, which of the following options best describes how often you consume simple sugars? skos:exactMatch OMOP:2005200305 When reflecting on your typical eating habits, which of the following options best describes how often you consume simple sugars? semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation diabetes_survey radio 1227 dmlsugar Question 2005200305 2005200305 Observation AIREADI Procedure S Yes open-source Yes -AIREADI_REDCAP:diabetes_survey.dmlgrain In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice). skos:closeMatch OMOP:46272478 Assessment of eating and drinking behavior semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation diabetes_survey radio 1228 dmlgrain Question 46272478 Observation SNOMED Procedure 710848001 S Yes open-source Yes +AIREADI_REDCAP:diabetes_survey.dmlgrain In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice). skos:exactMatch OMOP:2005200633 In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice). semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation diabetes_survey radio 1228 dmlgrain Question 2005200633 2005200633 Observation AIREADI Survey S Yes open-source Yes AIREADI_REDCAP:diabetes_survey.dmlpor When reflecting on your typical eating habits, which of the following best describes your approach to portion control? skos:closeMatch OMOP:764035 Able to control portion size semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation diabetes_survey radio 1229 dmlpor Question 764035 Observation SNOMED Clinical Finding 449921000124105 S No open-source Yes AIREADI_REDCAP:diabetes_survey.dmlfrveg In a typical day, how many servings of fruits and vegetables do you consume? skos:closeMatch OMOP:4295005 Number of portions of fruit and vegetables daily semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation diabetes_survey radio 1230 dmlfrveg Question 4295005 Observation SNOMED Observable Entity 401070008 S No open-source Yes AIREADI_REDCAP:diabetes_survey.dmledu How often would you say that you engage in diabetes health education? (Examples: consulting with a dietician, attending support groups, reading books on diabetes, using diabetes-focused websites, watching TV shows on health, or using health-focused apps on your phone or tablet) skos:exactMatch OMOP:2005200307 How often would you say that you engage in diabetes health education? (Examples: consulting with a dietician, attending support groups, reading books on diabetes, using diabetes-focused websites, watching TV shows on health, or using health-focused apps on your phone or tablet) semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation diabetes_survey radio 1231 dmledu Question 2005200307 2005200307 Observation AIREADI Survey S Yes open-source Yes @@ -234,11 +234,11 @@ AIREADI_REDCAP:disposition.eos_dsdecod What was the primary reason the subject d AIREADI_REDCAP:disposition.eos_dsstdat What was the study discontinuation or completion date? skos:exactMatch OMOP:4260905 Date semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation What was the study discontinuation or completion date? disposition text 1730 eos_dsstdat Question 4260905 Observation SNOMED Qualifier Value 410672004 S No open-source Yes 2005200625 AI-READI study discontinuation or completion AIREADI_REDCAP:disposition.eos_dsdecodie Mark questions from Inclusion/Exclusion that were not met. skos:relatedMatch OMOP:44811374 Not eligible for participation in research study semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation disposition checkbox 1731 eos_dsdecodie Question 44811374 Observation SNOMED Clinical Finding 873751000000103 S No open-source Yes AIREADI_REDCAP:disposition.eos_dsvst Provide the last study visit/stage completed: skos:exactMatch OMOP:2005200632 Last study visit/stage completed semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation disposition radio 1732 eos_dsvst Question 2005200632 2005200632 Observation AIREADI Survey S Yes open-source Yes -AIREADI_REDCAP:disposition.1.eos_dsdecod_1 Did not meet Inclusion/Exclusion criteria skos:exactMatch OMOP:2005200280 Did not meet Inclusion/Exclusion criteria semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation disposition radio eos_dsdecod 3346 1 eos_dsdecod_1 Answer 2005200280 2005200280 Meas Value AIREADI Answer S Yes open-source Yes +AIREADI_REDCAP:disposition.1.eos_dsdecod_1 Did not meet Inclusion/Exclusion criteria skos:exactMatch OMOP:40480675 Does not meet eligibility criteria for clinical trial semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation disposition radio eos_dsdecod 3346 1 eos_dsdecod_1 Answer 40480675 Observation SNOMED Clinical Finding 444734003 S No open-source Yes AIREADI_REDCAP:disposition.2.eos_dsdecod_2 Lost to Follow-up skos:exactMatch OMOP:4163894 Lost to follow-up semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation disposition radio eos_dsdecod 3347 2 eos_dsdecod_2 Answer 4163894 Observation SNOMED Clinical Finding 399307001 S No open-source Yes AIREADI_REDCAP:disposition.3.eos_dsdecod_3 Withdrawal by Subject skos:exactMatch OMOP:2005200281 Withdrawal by Subject semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation disposition radio eos_dsdecod 3348 3 eos_dsdecod_3 Answer 2005200281 2005200281 Meas Value AIREADI Answer S Yes open-source Yes AIREADI_REDCAP:disposition.4.eos_dsdecod_4 Geographic Inaccessibility skos:exactMatch OMOP:2005200282 Geographic Inaccessibility semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation disposition radio eos_dsdecod 3349 4 eos_dsdecod_4 Answer 2005200282 2005200282 Observation AIREADI Context-dependent S Yes open-source Yes -AIREADI_REDCAP:disposition.5.eos_dsdecod_5 Investigator deemed not appropriate for study skos:closeMatch OMOP:40480675 Does not meet eligibility criteria for clinical trial semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation disposition radio eos_dsdecod 3350 5 eos_dsdecod_5 Answer 40480675 Observation SNOMED Clinical Finding 444734003 S No open-source Yes +AIREADI_REDCAP:disposition.5.eos_dsdecod_5 Investigator deemed not appropriate for study skos:exactMatch OMOP:2005200634 Investigator deemed not appropriate for study semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation disposition radio eos_dsdecod 3350 5 eos_dsdecod_5 Answer 2005200634 2005200634 Meas Value AIREADI Answer S Yes open-source Yes AIREADI_REDCAP:disposition.6.eos_dsdecod_6 Currently enrolled in a conflicting study skos:exactMatch OMOP:2005200283 Currently enrolled in a conflicting study semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation disposition radio eos_dsdecod 3351 6 eos_dsdecod_6 Answer 2005200283 2005200283 Observation AIREADI Clinical Finding S Yes open-source Yes AIREADI_REDCAP:disposition.7.eos_dsdecod_7 Death skos:exactMatch OMOP:45881348 Death semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation disposition radio eos_dsdecod 3352 7 eos_dsdecod_7 Answer 45881348 Meas Value LOINC Answer LA7424-0 S No open-source Yes AIREADI_REDCAP:disposition.8.eos_dsdecod_8 Adverse Event skos:exactMatch OMOP:45884383 Adverse event semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation disposition radio eos_dsdecod 3353 8 eos_dsdecod_8 Answer 45884383 Meas Value LOINC Answer LA7266-5 S No open-source Yes @@ -598,14 +598,14 @@ AIREADI_REDCAP:imported.s second skos:exactMatch OMOP:8555 second semapv:ManualM AIREADI_REDCAP:imported.second second skos:exactMatch OMOP:8555 second semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation imported text second second 8555 Unit UCUM Unit s S No open-source Yes AIREADI_REDCAP:imported.score [score] skos:exactMatch OMOP:44777566 score semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation imported text score score 44777566 Unit UCUM Unit [score] S No open-source Yes AIREADI_REDCAP:lab_results.lbdattim1 Date & time clinical labs performed skos:closeMatch OMOP:4160030 Performed semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation Date & time clinical labs performed lab_results text 1661 lbdattim1 Question 4160030 Observation SNOMED Qualifier Value 398166005 S No open-source Yes 2005200603 clinical labs -AIREADI_REDCAP:lab_results.lbscat_wbc White Blood Cells (WBC) - x10E3/µL skos:exactMatch OMOP:2005200182 White Blood Cells (WBC) - x10E3/µL semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation lab_results text 1665 lbscat_wbc Question 2005200182 2005200182 Measurement AIREADI Procedure S Yes open-source Yes -AIREADI_REDCAP:lab_results.lbscat_rbc Red Blood Cells (RBC) - x10E6/µL skos:exactMatch OMOP:2005200183 Red Blood Cells (RBC) - x10E6/µL semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation lab_results text 1666 lbscat_rbc Question 2005200183 2005200183 Measurement AIREADI Procedure S Yes open-source Yes +AIREADI_REDCAP:lab_results.lbscat_wbc White Blood Cells (WBC) - x10E3/µL skos:exactMatch OMOP:3000905 Leukocytes [#/volume] in Blood by Automated count semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1665 lbscat_wbc Question 3000905 Measurement LOINC Lab Test 6690-2 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_rbc Red Blood Cells (RBC) - x10E6/µL skos:exactMatch OMOP:3020416 Erythrocytes [#/volume] in Blood by Automated count semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1666 lbscat_rbc Question 3020416 Measurement LOINC Lab Test 789-8 S No open-source Yes AIREADI_REDCAP:lab_results.lbscat_a1c Hemoglobin - g/dL skos:exactMatch OMOP:3000963 Hemoglobin [Mass/volume] in Blood semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1667 lbscat_a1c Question 3000963 Measurement LOINC Lab Test 718-7 S No open-source Yes -AIREADI_REDCAP:lab_results.lbscat_hct Hematocrit  - % skos:exactMatch OMOP:3009542 Hematocrit [Volume Fraction] of Blood by calculation semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1668 lbscat_hct Question 3009542 Measurement LOINC Lab Test 20570-8 S No open-source Yes -AIREADI_REDCAP:lab_results.lbscat_mcv MCV - fL skos:exactMatch OMOP:3024731 MCV [Entitic mean volume] in Red Blood Cells semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1669 lbscat_mcv Question 3024731 Measurement LOINC Lab Test 30428-7 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_hct Hematocrit  - % skos:exactMatch OMOP:3009542 Hematocrit [Volume Fraction] of Blood semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1668 lbscat_hct Question 3009542 Measurement LOINC Lab Test 20570-8 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_mcv MCV - fL skos:exactMatch OMOP:3024731 MCV [Entitic volume] semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1669 lbscat_mcv Question 3024731 Measurement LOINC Lab Test 30428-7 S No open-source Yes AIREADI_REDCAP:lab_results.lbscat_mch MCH - pg skos:closeMatch OMOP:3035941 MCH [Entitic mass] semapv:ManualMappingCuration 0.75 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1670 lbscat_mch Question 3035941 Measurement LOINC Lab Test 28539-5 S No open-source Yes -AIREADI_REDCAP:lab_results.lbscat_mchc MCHC - g/dL skos:exactMatch OMOP:3003338 MCHC [Entitic Mass/volume] in Red Blood Cells semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1671 lbscat_mchc Question 3003338 Measurement LOINC Lab Test 28540-3 S No open-source Yes -AIREADI_REDCAP:lab_results.lbscat_rdw RDW - % skos:exactMatch OMOP:3002385 Erythrocyte [DistWidth] in Red Blood Cells semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1672 lbscat_rdw Question 3002385 Measurement LOINC Lab Test 30385-9 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_mchc MCHC - g/dL skos:exactMatch OMOP:3003338 MCHC [Mass/volume] semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1671 lbscat_mchc Question 3003338 Measurement LOINC Lab Test 28540-3 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_rdw RDW - % skos:exactMatch OMOP:3002385 Erythrocyte distribution width [Ratio] semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1672 lbscat_rdw Question 3002385 Measurement LOINC Lab Test 30385-9 S No open-source Yes AIREADI_REDCAP:lab_results.lbscat_plt Platelets - x10E3/µL skos:closeMatch OMOP:3007461 Platelets [#/volume] in Blood semapv:ManualMappingCuration 0.75 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1673 lbscat_plt Question 3007461 Measurement LOINC Lab Test 26515-7 S No open-source Yes AIREADI_REDCAP:meds_assessment.cmcmpdat Date medications assessment conducted skos:exactMatch OMOP:4260905 Date semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation Date medications assessment conducted meds_assessment text 1456 cmcmpdat Question 4260905 Observation SNOMED Qualifier Value 410672004 S No open-source Yes 2005200593 medications assessment conducted AIREADI_REDCAP:meds_assessment.cm_asp Have you taken aspirin in the past 2 weeks? skos:exactMatch OMOP:2005200145 Have you taken aspirin in the past 2 weeks? semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation meds_assessment radio 1461 cm_asp Question 2005200145 2005200145 Observation AIREADI Survey S Yes open-source Yes @@ -738,7 +738,7 @@ AIREADI_REDCAP:ophthalmic_survey.4.via6_4 2 or more years ago skos:closeMatch OM AIREADI_REDCAP:ophthalmic_survey.5.via6_5 Never skos:exactMatch OMOP:45876662 Never semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation ophthalmic_survey radio via6 2254 5 via6_5 Answer 45876662 Meas Value LOINC Answer LA6270-8 S No open-source Yes AIREADI_REDCAP:ophthalmic_survey.777.via6_777 Prefer not to say skos:exactMatch OMOP:36311156 Prefer not to say semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation ophthalmic_survey radio via6 2255 777 via6_777 Answer 36311156 Meas Value LOINC Answer LA28803-7 S No open-source Yes AIREADI_REDCAP:paid5_dm_survey.paidcmpdat PAID-5 DM survey date skos:closeMatch OMOP:4160030 Performed semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation PAID-5 DM survey date paid5_dm_survey text 1210 paidcmpdat Question 4160030 Observation SNOMED Qualifier Value 398166005 S No open-source Yes 2005200571 PAID-5 DM Survey -AIREADI_REDCAP:paid5_dm_survey.paid_scrd Feeling scared when you think about living with diabetes skos:exactMatch OMOP:36716888 Fear of metabolic disease semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation paid5_dm_survey radio 1213 paid_scrd Question 36716888 Observation SNOMED Clinical Finding 723113005 S Yes open-source Yes +AIREADI_REDCAP:paid5_dm_survey.paid_scrd Feeling scared when you think about living with diabetes skos:exactMatch OMOP:2005200635 Feeling scared when you think about living with diabetes semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation paid5_dm_survey radio 1213 paid_scrd Question 2005200635 2005200635 Observation AIREADI Survey S Yes open-source Yes AIREADI_REDCAP:paid5_dm_survey.paid_dpr Feeling depressed when you think about living with diabetes skos:exactMatch OMOP:2005200045 Feeling depressed when you think about living with diabetes semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation paid5_dm_survey radio 1214 paid_dpr Question 2005200045 2005200045 Observation AIREADI Survey S Yes open-source Yes AIREADI_REDCAP:paid5_dm_survey.paid_wr Worrying about the future and the possibility of serious complications skos:exactMatch OMOP:2005200046 Worrying about the future and the possibility of serious complications semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation paid5_dm_survey radio 1215 paid_wr Question 2005200046 2005200046 Observation AIREADI Survey S Yes open-source Yes AIREADI_REDCAP:paid5_dm_survey.paid_eng Feeling that diabetes is taking up too much of your mental and physical energy every day skos:exactMatch OMOP:2005200047 Feeling that diabetes is taking up too much of your mental and physical energy every day semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation paid5_dm_survey radio 1216 paid_eng Question 2005200047 2005200047 Observation AIREADI Survey S Yes open-source Yes 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 af21dad..50be2ec 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 @@ -143,7 +143,7 @@ Yes,Yes,open-source,Yes,diabetes_survey,radio,,1224,Question,dmlvex,,"In a typic Yes,Yes,open-source,No,diabetes_survey,radio,,1225,Question,dmlact,,What would you consider your typical activity level to be?,44808782,,Level of physical activity,Observation,SNOMED,Observable Entity,859981000000107,S,skos:closeMatch,1,,,, Yes,Yes,open-source,Yes,diabetes_survey,radio,,1226,Question,dmlhex,,"How often would you say that you engage in daily home exercise? (Examples: stretching, calisthenics, or yoga)",2005200278,2005200278,"How often would you say that you engage in daily home exercise? (Examples: stretching, calisthenics, or yoga)",Observation,AIREADI,Procedure,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,diabetes_survey,radio,,1227,Question,dmlsugar,,"When reflecting on your typical eating habits, which of the following options best describes how often you consume simple sugars?",2005200305,2005200305,"When reflecting on your typical eating habits, which of the following options best describes how often you consume simple sugars?",Observation,AIREADI,Procedure,,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,Yes,diabetes_survey,radio,,1228,Question,dmlgrain,,"In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice).",46272478,,Assessment of eating and drinking behavior,Observation,SNOMED,Procedure,710848001,S,skos:closeMatch,0.75,,,, +Yes,Yes,open-source,Yes,diabetes_survey,radio,,1228,Question,dmlgrain,,"In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice).",2005200633,2005200633,"In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice).",Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,diabetes_survey,radio,,1229,Question,dmlpor,,"When reflecting on your typical eating habits, which of the following best describes your approach to portion control?",764035,,Able to control portion size,Observation,SNOMED,Clinical Finding,449921000124105,S,skos:closeMatch,0.75,,,, Yes,Yes,open-source,No,diabetes_survey,radio,,1230,Question,dmlfrveg,,"In a typical day, how many servings of fruits and vegetables do you consume?",4295005,,Number of portions of fruit and vegetables daily,Observation,SNOMED,Observable Entity,401070008,S,skos:closeMatch,0.75,,,, Yes,Yes,open-source,Yes,diabetes_survey,radio,,1231,Question,dmledu,,"How often would you say that you engage in diabetes health education? (Examples: consulting with a dietician, attending support groups, reading books on diabetes, using diabetes-focused websites, watching TV shows on health, or using health-focused apps on your phone or tablet)",2005200307,2005200307,"How often would you say that you engage in diabetes health education? (Examples: consulting with a dietician, attending support groups, reading books on diabetes, using diabetes-focused websites, watching TV shows on health, or using health-focused apps on your phone or tablet)",Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, @@ -247,11 +247,11 @@ Yes,Yes,open-source,No,disposition,radio,,1728,Question,eos_dsdecod,,What was th Yes,Yes,open-source,No,disposition,text,,1730,Question,eos_dsstdat,,What was the study discontinuation or completion date?,4260905,,Date,Observation,SNOMED,Qualifier Value,410672004,S,skos:exactMatch,1,What was the study discontinuation or completion date?,,2005200625,AI-READI study discontinuation or completion Yes,Yes,open-source,No,disposition,checkbox,,1731,Question,eos_dsdecodie,,Mark questions from Inclusion/Exclusion that were not met.,44811374,,Not eligible for participation in research study,Observation,SNOMED,Clinical Finding,873751000000103,S,skos:relatedMatch,0.75,,,, Yes,Yes,open-source,Yes,disposition,radio,,1732,Question,eos_dsvst,,Provide the last study visit/stage completed:,2005200632,2005200632,Last study visit/stage completed,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3346,Answer,1,eos_dsdecod_1,Did not meet Inclusion/Exclusion criteria,2005200280,2005200280,Did not meet Inclusion/Exclusion criteria,Meas Value,AIREADI,Answer,,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3346,Answer,1,eos_dsdecod_1,Did not meet Inclusion/Exclusion criteria,40480675,,Does not meet eligibility criteria for clinical trial,Observation,SNOMED,Clinical Finding,444734003,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3347,Answer,2,eos_dsdecod_2,Lost to Follow-up,4163894,,Lost to follow-up,Observation,SNOMED,Clinical Finding,399307001,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3348,Answer,3,eos_dsdecod_3,Withdrawal by Subject,2005200281,2005200281,Withdrawal by Subject,Meas Value,AIREADI,Answer,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3349,Answer,4,eos_dsdecod_4,Geographic Inaccessibility,2005200282,2005200282,Geographic Inaccessibility,Observation,AIREADI,Context-dependent,,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3350,Answer,5,eos_dsdecod_5,Investigator deemed not appropriate for study,40480675,,Does not meet eligibility criteria for clinical trial,Observation,SNOMED,Clinical Finding,444734003,S,skos:closeMatch,0.75,,,, +Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3350,Answer,5,eos_dsdecod_5,Investigator deemed not appropriate for study,2005200634,2005200634,Investigator deemed not appropriate for study,Meas Value,AIREADI,Answer,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3351,Answer,6,eos_dsdecod_6,Currently enrolled in a conflicting study,2005200283,2005200283,Currently enrolled in a conflicting study,Observation,AIREADI,Clinical Finding,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3352,Answer,7,eos_dsdecod_7,Death,45881348,,Death,Meas Value,LOINC,Answer,LA7424-0,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3353,Answer,8,eos_dsdecod_8,Adverse Event,45884383,,Adverse event,Meas Value,LOINC,Answer,LA7266-5,S,skos:exactMatch,1,,,, @@ -669,14 +669,14 @@ Yes,Yes,open-source,No,imported,text,s,,,s,,second,8555,,second,Unit,UCUM,Unit,s Yes,Yes,open-source,No,imported,text,second,,,second,,second,8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,score,,,score,,[score],44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,lab_results,text,,1661,Question,lbdattim1,,Date & time clinical labs performed,4160030,,Performed,Observation,SNOMED,Qualifier Value,398166005,S,skos:closeMatch,0.75,Date & time clinical labs performed,,2005200603,clinical labs -Yes,Yes,open-source,Yes,lab_results,text,,1665,Question,lbscat_wbc,,White Blood Cells (WBC) - x10E3/µL,2005200182,2005200182,White Blood Cells (WBC) - x10E3/µL,Measurement,AIREADI,Procedure,,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,Yes,lab_results,text,,1666,Question,lbscat_rbc,,Red Blood Cells (RBC) - x10E6/µL,2005200183,2005200183,Red Blood Cells (RBC) - x10E6/µL,Measurement,AIREADI,Procedure,,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1665,Question,lbscat_wbc,,White Blood Cells (WBC) - x10E3/µL,3000905,,Leukocytes [#/volume] in Blood by Automated count,Measurement,LOINC,Lab Test,6690-2,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1666,Question,lbscat_rbc,,Red Blood Cells (RBC) - x10E6/µL,3020416,,Erythrocytes [#/volume] in Blood by Automated count,Measurement,LOINC,Lab Test,789-8,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,lab_results,text,,1667,Question,lbscat_a1c,,Hemoglobin - g/dL,3000963,,Hemoglobin [Mass/volume] in Blood,Measurement,LOINC,Lab Test,718-7,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,lab_results,text,,1668,Question,lbscat_hct,,Hematocrit  - %,3009542,,Hematocrit [Volume Fraction] of Blood by calculation,Measurement,LOINC,Lab Test,20570-8,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,lab_results,text,,1669,Question,lbscat_mcv,,MCV - fL,3024731,,MCV [Entitic mean volume] in Red Blood Cells,Measurement,LOINC,Lab Test,30428-7,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1668,Question,lbscat_hct,,Hematocrit  - %,3009542,,Hematocrit [Volume Fraction] of Blood,Measurement,LOINC,Lab Test,20570-8,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1669,Question,lbscat_mcv,,MCV - fL,3024731,,MCV [Entitic volume],Measurement,LOINC,Lab Test,30428-7,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,lab_results,text,,1670,Question,lbscat_mch,,MCH - pg,3035941,,MCH [Entitic mass],Measurement,LOINC,Lab Test,28539-5,S,skos:closeMatch,0.75,,,, -Yes,Yes,open-source,No,lab_results,text,,1671,Question,lbscat_mchc,,MCHC - g/dL,3003338,,MCHC [Entitic Mass/volume] in Red Blood Cells,Measurement,LOINC,Lab Test,28540-3,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,lab_results,text,,1672,Question,lbscat_rdw,,RDW - %,3002385,,Erythrocyte [DistWidth] in Red Blood Cells,Measurement,LOINC,Lab Test,30385-9,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1671,Question,lbscat_mchc,,MCHC - g/dL,3003338,,MCHC [Mass/volume],Measurement,LOINC,Lab Test,28540-3,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1672,Question,lbscat_rdw,,RDW - %,3002385,,Erythrocyte distribution width [Ratio],Measurement,LOINC,Lab Test,30385-9,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,lab_results,text,,1673,Question,lbscat_plt,,Platelets - x10E3/µL,3007461,,Platelets [#/volume] in Blood,Measurement,LOINC,Lab Test,26515-7,S,skos:closeMatch,0.75,,,, Yes,Yes,open-source,No,meds_assessment,text,,1456,Question,cmcmpdat,,Date medications assessment conducted,4260905,,Date,Observation,SNOMED,Qualifier Value,410672004,S,skos:exactMatch,1,Date medications assessment conducted,,2005200593,medications assessment conducted Yes,Yes,open-source,Yes,meds_assessment,radio,,1461,Question,cm_asp,,Have you taken aspirin in the past 2 weeks?,2005200145,2005200145,Have you taken aspirin in the past 2 weeks?,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, @@ -809,7 +809,7 @@ Yes,Yes,open-source,No,ophthalmic_survey,radio,via6,2253,Answer,4,via6_4,2 or mo Yes,Yes,open-source,No,ophthalmic_survey,radio,via6,2254,Answer,5,via6_5,Never,45876662,,Never,Meas Value,LOINC,Answer,LA6270-8,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,ophthalmic_survey,radio,via6,2255,Answer,777,via6_777,Prefer not to say,36311156,,Prefer not to say,Meas Value,LOINC,Answer,LA28803-7,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,paid5_dm_survey,text,,1210,Question,paidcmpdat,,PAID-5 DM survey date,4160030,,Performed,Observation,SNOMED,Qualifier Value,398166005,S,skos:closeMatch,0.75,PAID-5 DM survey date,,2005200571,PAID-5 DM Survey -Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1213,Question,paid_scrd,,Feeling scared when you think about living with diabetes,36716888,,Fear of metabolic disease,Observation,SNOMED,Clinical Finding,723113005,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1213,Question,paid_scrd,,Feeling scared when you think about living with diabetes,2005200635,2005200635,Feeling scared when you think about living with diabetes,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1214,Question,paid_dpr,,Feeling depressed when you think about living with diabetes,2005200045,2005200045,Feeling depressed when you think about living with diabetes,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1215,Question,paid_wr,,Worrying about the future and the possibility of serious complications,2005200046,2005200046,Worrying about the future and the possibility of serious complications,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1216,Question,paid_eng,,Feeling that diabetes is taking up too much of your mental and physical energy every day,2005200047,2005200047,Feeling that diabetes is taking up too much of your mental and physical energy every day,Observation,AIREADI,Survey,,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 adae3a6..f7cfb39 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 @@ -128,7 +128,7 @@ Yes,Yes,open-source,Yes,diabetes_survey,radio,,1224,Question,dmlvex,,"In a typic Yes,Yes,open-source,No,diabetes_survey,radio,,1225,Question,dmlact,,What would you consider your typical activity level to be?,44808782,,Level of physical activity,Observation,SNOMED,Observable Entity,859981000000107,S,skos:closeMatch,1,,,, Yes,Yes,open-source,Yes,diabetes_survey,radio,,1226,Question,dmlhex,,"How often would you say that you engage in daily home exercise? (Examples: stretching, calisthenics, or yoga)",2005200278,2005200278,"How often would you say that you engage in daily home exercise? (Examples: stretching, calisthenics, or yoga)",Observation,AIREADI,Procedure,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,diabetes_survey,radio,,1227,Question,dmlsugar,,"When reflecting on your typical eating habits, which of the following options best describes how often you consume simple sugars?",2005200305,2005200305,"When reflecting on your typical eating habits, which of the following options best describes how often you consume simple sugars?",Observation,AIREADI,Procedure,,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,Yes,diabetes_survey,radio,,1228,Question,dmlgrain,,"In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice).",46272478,,Assessment of eating and drinking behavior,Observation,SNOMED,Procedure,710848001,S,skos:closeMatch,0.75,,,, +Yes,Yes,open-source,Yes,diabetes_survey,radio,,1228,Question,dmlgrain,,"In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice).",2005200633,2005200633,"In a typical day, how often do you consume whole grains? (Examples: include whole wheat, brown bread, or brown rice).",Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,diabetes_survey,radio,,1229,Question,dmlpor,,"When reflecting on your typical eating habits, which of the following best describes your approach to portion control?",764035,,Able to control portion size,Observation,SNOMED,Clinical Finding,449921000124105,S,skos:closeMatch,0.75,,,, Yes,Yes,open-source,No,diabetes_survey,radio,,1230,Question,dmlfrveg,,"In a typical day, how many servings of fruits and vegetables do you consume?",4295005,,Number of portions of fruit and vegetables daily,Observation,SNOMED,Observable Entity,401070008,S,skos:closeMatch,0.75,,,, Yes,Yes,open-source,Yes,diabetes_survey,radio,,1231,Question,dmledu,,"How often would you say that you engage in diabetes health education? (Examples: consulting with a dietician, attending support groups, reading books on diabetes, using diabetes-focused websites, watching TV shows on health, or using health-focused apps on your phone or tablet)",2005200307,2005200307,"How often would you say that you engage in diabetes health education? (Examples: consulting with a dietician, attending support groups, reading books on diabetes, using diabetes-focused websites, watching TV shows on health, or using health-focused apps on your phone or tablet)",Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, @@ -230,11 +230,11 @@ Yes,Yes,open-source,No,disposition,radio,,1728,Question,eos_dsdecod,,What was th Yes,Yes,open-source,No,disposition,text,,1730,Question,eos_dsstdat,,What was the study discontinuation or completion date?,4260905,,Date,Observation,SNOMED,Qualifier Value,410672004,S,skos:exactMatch,1,What was the study discontinuation or completion date?,,2005200625,AI-READI study discontinuation or completion Yes,Yes,open-source,No,disposition,checkbox,,1731,Question,eos_dsdecodie,,Mark questions from Inclusion/Exclusion that were not met.,44811374,,Not eligible for participation in research study,Observation,SNOMED,Clinical Finding,873751000000103,S,skos:relatedMatch,0.75,,,, Yes,Yes,open-source,Yes,disposition,radio,,1732,Question,eos_dsvst,,Provide the last study visit/stage completed:,2005200632,2005200632,Last study visit/stage completed,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3346,Answer,1,eos_dsdecod_1,Did not meet Inclusion/Exclusion criteria,2005200280,2005200280,Did not meet Inclusion/Exclusion criteria,Meas Value,AIREADI,Answer,,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3346,Answer,1,eos_dsdecod_1,Did not meet Inclusion/Exclusion criteria,40480675,,Does not meet eligibility criteria for clinical trial,Observation,SNOMED,Clinical Finding,444734003,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3347,Answer,2,eos_dsdecod_2,Lost to Follow-up,4163894,,Lost to follow-up,Observation,SNOMED,Clinical Finding,399307001,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3348,Answer,3,eos_dsdecod_3,Withdrawal by Subject,2005200281,2005200281,Withdrawal by Subject,Meas Value,AIREADI,Answer,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3349,Answer,4,eos_dsdecod_4,Geographic Inaccessibility,2005200282,2005200282,Geographic Inaccessibility,Observation,AIREADI,Context-dependent,,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3350,Answer,5,eos_dsdecod_5,Investigator deemed not appropriate for study,40480675,,Does not meet eligibility criteria for clinical trial,Observation,SNOMED,Clinical Finding,444734003,S,skos:closeMatch,0.75,,,, +Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3350,Answer,5,eos_dsdecod_5,Investigator deemed not appropriate for study,2005200634,2005200634,Investigator deemed not appropriate for study,Meas Value,AIREADI,Answer,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,disposition,radio,eos_dsdecod,3351,Answer,6,eos_dsdecod_6,Currently enrolled in a conflicting study,2005200283,2005200283,Currently enrolled in a conflicting study,Observation,AIREADI,Clinical Finding,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3352,Answer,7,eos_dsdecod_7,Death,45881348,,Death,Meas Value,LOINC,Answer,LA7424-0,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,disposition,radio,eos_dsdecod,3353,Answer,8,eos_dsdecod_8,Adverse Event,45884383,,Adverse event,Meas Value,LOINC,Answer,LA7266-5,S,skos:exactMatch,1,,,, @@ -611,14 +611,14 @@ Yes,Yes,open-source,No,imported,text,s,,,s,,second,8555,,second,Unit,UCUM,Unit,s Yes,Yes,open-source,No,imported,text,second,,,second,,second,8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,score,,,score,,[score],44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,lab_results,text,,1661,Question,lbdattim1,,Date & time clinical labs performed,4160030,,Performed,Observation,SNOMED,Qualifier Value,398166005,S,skos:closeMatch,0.75,Date & time clinical labs performed,,2005200603,clinical labs -Yes,Yes,open-source,Yes,lab_results,text,,1665,Question,lbscat_wbc,,White Blood Cells (WBC) - x10E3/µL,2005200182,2005200182,White Blood Cells (WBC) - x10E3/µL,Measurement,AIREADI,Procedure,,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,Yes,lab_results,text,,1666,Question,lbscat_rbc,,Red Blood Cells (RBC) - x10E6/µL,2005200183,2005200183,Red Blood Cells (RBC) - x10E6/µL,Measurement,AIREADI,Procedure,,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1665,Question,lbscat_wbc,,White Blood Cells (WBC) - x10E3/µL,3000905,,Leukocytes [#/volume] in Blood by Automated count,Measurement,LOINC,Lab Test,6690-2,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1666,Question,lbscat_rbc,,Red Blood Cells (RBC) - x10E6/µL,3020416,,Erythrocytes [#/volume] in Blood by Automated count,Measurement,LOINC,Lab Test,789-8,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,lab_results,text,,1667,Question,lbscat_a1c,,Hemoglobin - g/dL,3000963,,Hemoglobin [Mass/volume] in Blood,Measurement,LOINC,Lab Test,718-7,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,lab_results,text,,1668,Question,lbscat_hct,,Hematocrit  - %,3009542,,Hematocrit [Volume Fraction] of Blood by calculation,Measurement,LOINC,Lab Test,20570-8,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,lab_results,text,,1669,Question,lbscat_mcv,,MCV - fL,3024731,,MCV [Entitic mean volume] in Red Blood Cells,Measurement,LOINC,Lab Test,30428-7,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1668,Question,lbscat_hct,,Hematocrit  - %,3009542,,Hematocrit [Volume Fraction] of Blood,Measurement,LOINC,Lab Test,20570-8,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1669,Question,lbscat_mcv,,MCV - fL,3024731,,MCV [Entitic volume],Measurement,LOINC,Lab Test,30428-7,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,lab_results,text,,1670,Question,lbscat_mch,,MCH - pg,3035941,,MCH [Entitic mass],Measurement,LOINC,Lab Test,28539-5,S,skos:closeMatch,0.75,,,, -Yes,Yes,open-source,No,lab_results,text,,1671,Question,lbscat_mchc,,MCHC - g/dL,3003338,,MCHC [Entitic Mass/volume] in Red Blood Cells,Measurement,LOINC,Lab Test,28540-3,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,lab_results,text,,1672,Question,lbscat_rdw,,RDW - %,3002385,,Erythrocyte [DistWidth] in Red Blood Cells,Measurement,LOINC,Lab Test,30385-9,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1671,Question,lbscat_mchc,,MCHC - g/dL,3003338,,MCHC [Mass/volume],Measurement,LOINC,Lab Test,28540-3,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1672,Question,lbscat_rdw,,RDW - %,3002385,,Erythrocyte distribution width [Ratio],Measurement,LOINC,Lab Test,30385-9,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,lab_results,text,,1673,Question,lbscat_plt,,Platelets - x10E3/µL,3007461,,Platelets [#/volume] in Blood,Measurement,LOINC,Lab Test,26515-7,S,skos:closeMatch,0.75,,,, Yes,Yes,open-source,No,meds_assessment,text,,1456,Question,cmcmpdat,,Date medications assessment conducted,4260905,,Date,Observation,SNOMED,Qualifier Value,410672004,S,skos:exactMatch,1,Date medications assessment conducted,,2005200593,medications assessment conducted Yes,Yes,open-source,Yes,meds_assessment,radio,,1461,Question,cm_asp,,Have you taken aspirin in the past 2 weeks?,2005200145,2005200145,Have you taken aspirin in the past 2 weeks?,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, @@ -751,7 +751,7 @@ Yes,Yes,open-source,No,ophthalmic_survey,radio,via6,2253,Answer,4,via6_4,2 or mo Yes,Yes,open-source,No,ophthalmic_survey,radio,via6,2254,Answer,5,via6_5,Never,45876662,,Never,Meas Value,LOINC,Answer,LA6270-8,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,ophthalmic_survey,radio,via6,2255,Answer,777,via6_777,Prefer not to say,36311156,,Prefer not to say,Meas Value,LOINC,Answer,LA28803-7,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,paid5_dm_survey,text,,1210,Question,paidcmpdat,,PAID-5 DM survey date,4160030,,Performed,Observation,SNOMED,Qualifier Value,398166005,S,skos:closeMatch,0.75,PAID-5 DM survey date,,2005200571,PAID-5 DM Survey -Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1213,Question,paid_scrd,,Feeling scared when you think about living with diabetes,36716888,,Fear of metabolic disease,Observation,SNOMED,Clinical Finding,723113005,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1213,Question,paid_scrd,,Feeling scared when you think about living with diabetes,2005200635,2005200635,Feeling scared when you think about living with diabetes,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1214,Question,paid_dpr,,Feeling depressed when you think about living with diabetes,2005200045,2005200045,Feeling depressed when you think about living with diabetes,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1215,Question,paid_wr,,Worrying about the future and the possibility of serious complications,2005200046,2005200046,Worrying about the future and the possibility of serious complications,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,Yes,paid5_dm_survey,radio,,1216,Question,paid_eng,,Feeling that diabetes is taking up too much of your mental and physical energy every day,2005200047,2005200047,Feeling that diabetes is taking up too much of your mental and physical energy every day,Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,,