diff --git a/CHANGELOG.md b/CHANGELOG.md index 944c954..9dcb47d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,82 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/). ## [Unreleased] +## [v1.7] - 2026-10-24 + +Retinal imaging scans are recorded as procedures, the new BUN/creatinine ratio field is mapped, and the CBC results move to the lab's "by Automated count" LOINC codes. 48 rows are appended at the end of the file (lines 2081–2128), 6 rows are edited in place (lines 675–680), and 20 superseded MoCA unit rows are switched off (lines 648–667), so every existing line number is the same as in v1.6. The new rows write PROCEDURE_OCCURRENCE and MEASUREMENT, so the ETL must be re-run, with the ETL rules below. Concept IDs, names and domains were confirmed in the deployed OMOP vocabulary (Databricks `omop_vocab`). + +### Added — retinal imaging procedures + +- Form `retinal_imaging_v2` asks one yes/no question per scan type and eye (22 scan types × 2 eyes; questions on lines 1679–1741, answers on lines 1743–1846). Until v1.6 a completed scan was recorded only as an OBSERVATION (custom scan concept, value *Yes*), so a standard query for fundus photography or OCT found no AI-READI participants. +- For each of the 44 questions, a second "Yes" answer row (same `FIELD_ID`, `SRC_CODE` 1 and `SRC_CODE_ID` as the existing Yes row) maps to a standard procedure concept, domain Procedure. This follows the health-history pattern, where a "Yes" has a Yes value row and a Condition row (for example `mhoccur_mi`, lines 440 and 328). Right eye on lines 2081–2102 and left eye on lines 2103–2124, both in form order. + +| Scans (per eye) | Concept | Predicate | +|---|---|---| +| OptoMed disc and macula CFP; Eidon central, nasal, temporal CFP and mosaic (6) | 4063911 *Ocular fundus photography* (SNOMED 20067007) | exactMatch 1 | +| Eidon IR, Eidon FAF, FLIO (3) | 4063911 | closeMatch 0.75 (no infrared, autofluorescence or FLIO procedure concept exists) | +| Spectralis posterior pole, Cirrus macula cube, Maestro2 3D wide and 3D macula, Triton 3D (5) | 1073298 *Optical coherence tomography of posterior segment of eye* (SNOMED 1303746000) | exactMatch 1 | +| Spectralis ONH, Cirrus disc cube (2) | 1073298 | closeMatch 1 (optic nerve head scans) | +| Spectralis, Cirrus, Maestro2 and Triton macula OCTA (5) | 745759 *Computerized ophthalmic diagnostic imaging … retina, including OCT angiography* (CPT4 92137) | closeMatch 1 (no SNOMED OCT angiography concept) | +| Cirrus disc 6x6 OCTA (1) | 745759 | closeMatch 0.75 (the code says "retina") | + +- Laterality as a CPT4 modifier, the class OMOP intends for `PROCEDURE_OCCURRENCE.modifier_concept_id`: right-eye rows `qualifier_concept_id` 45888271 (RT), `qualifier_source_value` "Right eye", `MODIFIER` "right eye|45888271"; left-eye rows 45888270 (LT), "Left eye", "left eye|45888270". The existing imaging question and Yes rows keep the LOINC answers 45876703 *Right eye* / 45883829 *Left eye*. +- Not used: Measurement-domain concepts such as 4189584 *Confocal scanning laser ophthalmoscopy* and 45763633 *Optical coherence tomography of retina* (they would write MEASUREMENT), and Device-domain OCT scanner concepts. No new custom concepts. + +### Added — BUN/creatinine ratio, new REDCap field + +- `import_bun_creatinine_ratio` "Creatinine/BUN ratio" (line 2125, new) → **3033837** *Creatinine/Urea nitrogen [Mass Ratio] in Serum or Plasma* (LOINC 31045-8, Lab Test), exactMatch 1; `SRC_CODE` 31045-8, as for the other imported labs. This is the field the data team named for the ratio; it maps to what is stored now (creatinine ÷ BUN). +- Fixed-unit row `import_bun_creatinine_ratio_u` (line 2126) → 8523 *ratio* (UCUM `{ratio}`), same format as line 2080; `unit_concept_lookup.csv` (and `01_create_unit_lookup.sql`) gains `import_bun_creatinine_ratio` (with NRBC below: 115 rows, up from 113). +- Line 554 (`import_buncreatinineratio`) is unchanged from v1.6: 3033837, with the `MODIFIER` note that the stored value is creatinine ÷ BUN. Both fields therefore map to creatinine ÷ BUN (all 3,981 current values; median 0.053). 3018311 *Urea nitrogen/Creatinine [Mass Ratio]* (LOINC 3097-3) is not used; if a field is later recalculated as BUN ÷ creatinine (median about 18), remap that field to 3018311. + +### Changed — CBC method codes (lines 675–680) + +The performing lab's LOINC map (Labcorp test 028142 *CBC, Platelet, No Differential*) reports these results with the "by Automated count" codes; WBC (6690-2), RBC (789-8) and hemoglobin (718-7) already matched. All exactMatch 1; concept names from `omop_vocab`. + +| Line | Field | v1.6 | v1.7 | +|---|---|---|---| +| 675 | `lbscat_hct` Hematocrit - % | 3009542 *… by calculation* (20570-8) | **3023314** *Hematocrit [Volume Fraction] of Blood by Automated count* (4544-3) | +| 676 | `lbscat_mcv` MCV - fL | 3024731 (30428-7) | **3023599** *MCV [Entitic mean volume] in Red Blood Cells by Automated count* (787-2) | +| 677 | `lbscat_mch` MCH - pg | 3035941 (28539-5), closeMatch 0.75 | **3012030** *MCH [Entitic mass] by Automated count* (785-6) | +| 678 | `lbscat_mchc` MCHC - g/dL | 3003338 (28540-3) | **3009744** *MCHC [Entitic Mass/volume] in Red Blood Cells by Automated count* (786-4) | +| 679 | `lbscat_rdw` RDW - % | 3002385 (30385-9) | **3019897** *Erythrocyte [DistWidth] in Red Blood Cells by Automated count* (788-0) | +| 680 | `lbscat_plt` Platelets - x10E3/µL | 3007461 (26515-7), closeMatch 0.75 | **3024929** *Platelets [#/volume] in Blood by Automated count* (777-3) | + +Units are unchanged (the lab's units match the v1.4 CBC unit rows). The lab's NRBC result (58413-6) has no REDCap field yet; see *Added — NRBC* below. + +### Added — NRBC (proposed REDCap field) + +- Labcorp test 028142 also reports nucleated red blood cells (NRBC) per 100 white blood cells (LOINC 58413-6, unit %), but the REDCap CBC form has no NRBC field. Rows are added in advance for the proposed field `lbscat_nrbc`, so it maps as soon as it is added to the form: question row (line 2127) → **40761514** *Nucleated erythrocytes/Leukocytes [Ratio] in Blood by Automated count* (LOINC 58413-6), exactMatch 1; fixed-unit row `lbscat_nrbc_u` (line 2128) → 8554 *percent* (`%`), as for RDW and hematocrit. Both rows have `transferred_to_fairhub_REDCap_dataset` = Yes, as the other CBC rows: NRBC belongs in the dataset and was missed on the REDCap form. `MODIFIER` is blank on both rows. Note: `lbscat_nrbc` is a proposed REDCap field, not yet on the CBC form; Labcorp 028142 reports NRBC per 100 WBC (LOINC 58413-6), so it should have been included. `lbscat_nrbc` maps to **40761514** *Nucleated erythrocytes/Leukocytes [Ratio] in Blood by Automated count* (line 2127), with unit 8554 *percent* (`lbscat_nrbc_u`, line 2128); the value maps as soon as the field is added. `unit_concept_lookup.csv`: 115 rows (field 90, string 25). + +### Changed — Map_to_OMOP: old MoCA unit rows (lines 648–667) + +- The 20 original MoCA unit rows (14 `*_time_unit` → 8555 *second*, 6 `*_score_unit` → 44777566 *score*, e.g. `trails_time_unit`, `lettera_score_unit`) are not named after the MoCA measurement fields, so nothing links to them: in the current OMOP data all 30 MoCA measurement fields have `unit_concept_id` 0. They are superseded by the v1.4 `_u` rows (lines 2048–2077), which cover all 30 fields and are used by `unit_concept_lookup.csv`. +- `Map_to_OMOP` Yes → No on lines 648–667; no other column changes (`MODIFIER` stays blank). The rows are kept, not deleted, so the original content and line numbers are preserved, and there are no duplicate active MoCA unit rows. The replacement row for each is listed in the v1.7 decision record. map2omop and the open-source public file each lose these 20 rows; the unit lookup is unchanged (it never used them). +- The generic unit-text rows `s`, `second` → 8555 and `score` → 44777566 (lines 668–670) stay active; the lookup uses them. + +### ETL rules (for the survey ETL) + +1. **One procedure per "Yes".** Answers are matched on `FIELD_ID` (REDCap field) + `SRC_CODE` (answer code). A "Yes" (1) now matches two rows: the Yes row (Meas Value → `value_as_concept_id` on the OBSERVATION) and the procedure row (Procedure → one PROCEDURE_OCCURRENCE row). A "No" matches only the No row, so no procedure is written. Procedure rows are not merged: up to 22 per eye per visit. +2. **Date.** `procedure_date` = the form's Assessment Date (`rt_dat`, line 1742), the same date for every scan on the form. +3. **Laterality.** For Procedure rows whose `qualifier_concept_id` is a CPT4 Modifier (45888271, 45888270), write `qualifier_concept_id` to `modifier_concept_id` and `qualifier_source_value` to `modifier_source_value`. The monofilament Procedure rows (742–765) are unchanged and not covered by this rule. +4. **Source concept.** `procedure_source_concept_id` = the AI-READI custom concept of the imaging question (the `TARGET_CONCEPT_ID` of the question row whose `SRC_CODE` equals the procedure row's `FIELD_ID`; for example `rtso_odo` → 2005200297 *Spec-ONH-RC-HR-OCT*). `procedure_source_value` = the REDCap field, as for other tables. +5. **Units.** Fill `unit_concept_id` with `unit_concept_lookup.csv` (scripts `03_` / `04_`), matching on the trimmed field name and the trimmed unit text: the current data has `unit_source_value` " " (a single space) on the MoCA rows and a leading space on lab units (" mg/dL"). Write `unit_source_value` trimmed. + +### Changed — scripts + +- `count_concept_map.sql`: expected values updated to v1.7 (standard predicates: exact 1,267; close 257); the laterality query includes the CPT4 modifiers. +- `validate_concept_map_vocab.sql`: new check V10 (Procedure rows: the target is in the Procedure domain and a laterality qualifier is a CPT4 Modifier; expect only the two monofilament "Tested" rows); V0 row counts. +- Unit lookup scripts (`value-set-mapping-common/scripts/`): `03_left_join_unit_lookup_template.sql`, `04_example_omop_survey_measurement.sql`, `USAGE.md` and `README.md` write `unit_source_value` trimmed, with blank text as NULL (`NULLIF(TRIM(…), '')`, ETL rule 5); `USAGE.md` explains the MoCA unit rows, the generic `s`/`second`/`score` unit-text keys and blank unit text. +- `audit_concept_map.py`: A5 label lists Procedure among the expected duplicate-key pairs (A5 rises from 34 to 78 with the 44 new pairs). + +### Regenerated + +- map2omop (2,102 rows) and open-source public (1,993) versions, SSSOM (2,051 rows; 76 incomplete) and LinkML (2,127 records; `CPT4` added to the vocabulary enum) from the v1.7 common file. `unit_concept_lookup.csv` rebuilt (115 rows); `medication_route_lookup.csv` unchanged. +- Counts (`run_counts.py`): standard 1,506 (396 concepts); custom 487 (342); mapped 1,993 (738 concepts); designated but unmapped 134 (+20 "Superseded unit row"). The 44 procedure rows, the unit rows and the proposed NRBC field are not REDCap data elements in the curated dictionary, so, as with the earlier unit rows, "not designated" falls from 827 to 779 against the fixed total of 2,906. + +### Not yet included + +- Monofilament redesign (one procedure per foot, site results as measurements): deferred. + ## [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`). diff --git a/CITATION.cff b/CITATION.cff index 7cc9d43..f8931ef 100644 --- a/CITATION.cff +++ b/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: "v1.6" -date-released: "2026-10-22" +version: "v1.7" +date-released: "2026-10-24" identifiers: - type: doi value: "10.5281/zenodo.23375723" diff --git a/README.md b/README.md index 253de3e..2b89916 100644 --- a/README.md +++ b/README.md @@ -95,6 +95,7 @@ To report an incorrect mapping, suggest an improvement, or request a new feature This work is licensed under [MIT](https://opensource.org/licenses/mit). See [LICENSE](LICENSE) for more information. +[AI-READI](https://zenodo.org/records/17555036) The AI-READI dataset is shared under a custom license that has been developed as part of the project. The full license terms are available here. It is recommended to read them first to ensure that your envisioned use of the AI-READI dataset fits within the requirements of the license. @@ -119,4 +120,6 @@ The content is solely the responsibility of the authors and does not necessarily The funders/sponsors had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication. + +
diff --git a/codemeta.json b/codemeta.json index 5d441bc..e46d9ea 100644 --- a/codemeta.json +++ b/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": "v1.6", - "datePublished": "2026-10-22", + "version": "v1.7", + "datePublished": "2026-10-24", "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": "2026-10-22", + "dateModified": "2026-10-24", "applicationCategory": "Scientific", "developmentStatus": "active", "isPartOf": "https://aireadi.org/", 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 d1fc2a0..5e33d8c 100644 --- a/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml +++ b/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_data.yaml @@ -13313,7 +13313,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0647 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13332,7 +13332,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0648 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13351,7 +13351,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0649 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13370,7 +13370,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0650 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13389,7 +13389,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0651 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13408,7 +13408,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0652 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13427,7 +13427,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0653 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13446,7 +13446,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0654 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13465,7 +13465,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0655 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13484,7 +13484,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0656 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13503,7 +13503,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0657 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13522,7 +13522,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0658 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13541,7 +13541,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0659 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13560,7 +13560,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0660 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13579,7 +13579,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0661 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13598,7 +13598,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0662 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13617,7 +13617,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0663 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13636,7 +13636,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0664 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13655,7 +13655,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0665 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13675,7 +13675,7 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0666 - map_to_omop: 'Yes' + map_to_omop: 'No' transferred_to_fairhub_redcap_dataset: 'Yes' protected_or_open_source: open-source extension_needed: 'No' @@ -13844,12 +13844,12 @@ mappings: question_or_answer: Question src_code: lbscat_hct src_cd_description: Hematocrit - % - target_concept_id: 3009542 - target_concept_name: Hematocrit [Volume Fraction] of Blood by calculation + target_concept_id: 3023314 + target_concept_name: Hematocrit [Volume Fraction] of Blood by Automated count target_domain_id: Measurement target_vocabulary_id: LOINC target_concept_class_id: Lab Test - target_concept_code: 20570-8 + target_concept_code: 4544-3 target_standard_concept: S predicate_id: skos:exactMatch confidence: 1.0 @@ -13864,12 +13864,12 @@ mappings: question_or_answer: Question 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_id: 3023599 + target_concept_name: MCV [Entitic mean volume] in Red Blood Cells by Automated count target_domain_id: Measurement target_vocabulary_id: LOINC target_concept_class_id: Lab Test - target_concept_code: 30428-7 + target_concept_code: 787-2 target_standard_concept: S predicate_id: skos:exactMatch confidence: 1.0 @@ -13884,15 +13884,15 @@ mappings: question_or_answer: Question src_code: lbscat_mch src_cd_description: MCH - pg - target_concept_id: 3035941 - target_concept_name: MCH [Entitic mass] + target_concept_id: 3012030 + target_concept_name: MCH [Entitic mass] by Automated count target_domain_id: Measurement target_vocabulary_id: LOINC target_concept_class_id: Lab Test - target_concept_code: 28539-5 + target_concept_code: 785-6 target_standard_concept: S - predicate_id: skos:closeMatch - confidence: 0.75 + predicate_id: skos:exactMatch + confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0677 map_to_omop: 'Yes' transferred_to_fairhub_redcap_dataset: 'Yes' @@ -13904,12 +13904,12 @@ mappings: question_or_answer: Question 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_id: 3009744 + target_concept_name: MCHC [Entitic Mass/volume] in Red Blood Cells by Automated count target_domain_id: Measurement target_vocabulary_id: LOINC target_concept_class_id: Lab Test - target_concept_code: 28540-3 + target_concept_code: 786-4 target_standard_concept: S predicate_id: skos:exactMatch confidence: 1.0 @@ -13924,12 +13924,12 @@ mappings: question_or_answer: Question src_code: lbscat_rdw src_cd_description: RDW - % - target_concept_id: 3002385 - target_concept_name: Erythrocyte [DistWidth] in Red Blood Cells + target_concept_id: 3019897 + target_concept_name: Erythrocyte [DistWidth] in Red Blood Cells by Automated count target_domain_id: Measurement target_vocabulary_id: LOINC target_concept_class_id: Lab Test - target_concept_code: 30385-9 + target_concept_code: 788-0 target_standard_concept: S predicate_id: skos:exactMatch confidence: 1.0 @@ -13944,15 +13944,15 @@ mappings: question_or_answer: Question src_code: lbscat_plt src_cd_description: Platelets - x10E3/µL - target_concept_id: 3007461 - target_concept_name: Platelets [#/volume] in Blood + target_concept_id: 3024929 + target_concept_name: Platelets [#/volume] in Blood by Automated count target_domain_id: Measurement target_vocabulary_id: LOINC target_concept_class_id: Lab Test - target_concept_code: 26515-7 + target_concept_code: 777-3 target_standard_concept: S - predicate_id: skos:closeMatch - confidence: 0.75 + predicate_id: skos:exactMatch + confidence: 1.0 - mapping_record_id: AIREADI_MAPPING_0680 map_to_omop: 'Yes' transferred_to_fairhub_redcap_dataset: 'Yes' @@ -44672,3 +44672,1155 @@ mappings: predicate_id: skos:exactMatch confidence: 1.0 modifier: fixed unit; no REDCap unit field +- mapping_record_id: AIREADI_MAPPING_2080 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtop_odd + question_or_answer: Answer + src_code: '1' + src_code_id: rtop_odd_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2081 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtop_odm + question_or_answer: Answer + src_code: '1' + src_code_id: rtop_odm_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2082 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtei_odir + question_or_answer: Answer + src_code: '1' + src_code_id: rtei_odir_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 0.75 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2083 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtei_odfaf + question_or_answer: Answer + src_code: '1' + src_code_id: rtei_odfaf_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 0.75 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2084 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtsm_odc + question_or_answer: Answer + src_code: '1' + src_code_id: rtsm_odc_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2085 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtsm_odn + question_or_answer: Answer + src_code: '1' + src_code_id: rtsm_odn_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2086 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtsm_odt + question_or_answer: Answer + src_code: '1' + src_code_id: rtsm_odt_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2087 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtsm_odm + question_or_answer: Answer + src_code: '1' + src_code_id: rtsm_odm_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2088 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtso_odo + question_or_answer: Answer + src_code: '1' + src_code_id: rtso_odo_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2089 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtso_odp + question_or_answer: Answer + src_code: '1' + src_code_id: rtso_odp_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2090 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtso_odm + question_or_answer: Answer + src_code: '1' + src_code_id: rtso_odm_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2091 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtci_odm1 + question_or_answer: Answer + src_code: '1' + src_code_id: rtci_odm1_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2092 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtci_odd1 + question_or_answer: Answer + src_code: '1' + src_code_id: rtci_odd1_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2093 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtci_odm2 + question_or_answer: Answer + src_code: '1' + src_code_id: rtci_odm2_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2094 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtci_odd2 + question_or_answer: Answer + src_code: '1' + src_code_id: rtci_odd2_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 0.75 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2095 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtma_odw + question_or_answer: Answer + src_code: '1' + src_code_id: rtma_odw_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2096 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtma_odm + question_or_answer: Answer + src_code: '1' + src_code_id: rtma_odm_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2097 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtma_odm1 + question_or_answer: Answer + src_code: '1' + src_code_id: rtma_odm1_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2098 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rttr_odr + question_or_answer: Answer + src_code: '1' + src_code_id: rttr_odr_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2099 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rttr_odm1 + question_or_answer: Answer + src_code: '1' + src_code_id: rttr_odm1_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2100 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rttr_odm2 + question_or_answer: Answer + src_code: '1' + src_code_id: rttr_odm2_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2101 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtfl_od + question_or_answer: Answer + src_code: '1' + src_code_id: rtfl_od_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 0.75 + modifier: right eye|45888271 + qualifier_concept_id: 45888271 + qualifier_source_value: Right eye +- mapping_record_id: AIREADI_MAPPING_2102 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtop_osd + question_or_answer: Answer + src_code: '1' + src_code_id: rtop_osd_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2103 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtop_osm + question_or_answer: Answer + src_code: '1' + src_code_id: rtop_osm_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2104 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtei_osir + question_or_answer: Answer + src_code: '1' + src_code_id: rtei_osir_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 0.75 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2105 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtei_osfaf + question_or_answer: Answer + src_code: '1' + src_code_id: rtei_osfaf_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 0.75 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2106 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtsm_osc + question_or_answer: Answer + src_code: '1' + src_code_id: rtsm_osc_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2107 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtsm_osn + question_or_answer: Answer + src_code: '1' + src_code_id: rtsm_osn_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2108 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtsm_ost + question_or_answer: Answer + src_code: '1' + src_code_id: rtsm_ost_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2109 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtsm_osm + question_or_answer: Answer + src_code: '1' + src_code_id: rtsm_osm_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2110 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtso_oso + question_or_answer: Answer + src_code: '1' + src_code_id: rtso_oso_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2111 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtso_osp + question_or_answer: Answer + src_code: '1' + src_code_id: rtso_osp_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2112 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtso_osm + question_or_answer: Answer + src_code: '1' + src_code_id: rtso_osm_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2113 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtci_osm1 + question_or_answer: Answer + src_code: '1' + src_code_id: rtci_osm1_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2114 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtci_osd1 + question_or_answer: Answer + src_code: '1' + src_code_id: rtci_osd1_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2115 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtci_osm2 + question_or_answer: Answer + src_code: '1' + src_code_id: rtci_osm2_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2116 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtci_osd2 + question_or_answer: Answer + src_code: '1' + src_code_id: rtci_osd2_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 0.75 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2117 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtma_osw + question_or_answer: Answer + src_code: '1' + src_code_id: rtma_osw_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2118 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtma_osm + question_or_answer: Answer + src_code: '1' + src_code_id: rtma_osm_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2119 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtma_osm1 + question_or_answer: Answer + src_code: '1' + src_code_id: rtma_osm1_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2120 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rttr_osr + question_or_answer: Answer + src_code: '1' + src_code_id: rttr_osr_1 + src_cd_description: 'Yes' + target_concept_id: 1073298 + target_concept_name: Optical coherence tomography of posterior segment of eye + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '1303746000' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2121 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rttr_osm1 + question_or_answer: Answer + src_code: '1' + src_code_id: rttr_osm1_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2122 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rttr_osm2 + question_or_answer: Answer + src_code: '1' + src_code_id: rttr_osm2_1 + src_cd_description: 'Yes' + target_concept_id: 745759 + target_concept_name: Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, + with interpretation and report, unilateral or bilateral; retina, including OCT angiography + target_domain_id: Procedure + target_vocabulary_id: CPT4 + target_concept_class_id: CPT4 + target_concept_code: '92137' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 1.0 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2123 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: retinal_imaging_v2 + field_type: yesno + field_id: rtfl_os + question_or_answer: Answer + src_code: '1' + src_code_id: rtfl_os_1 + src_cd_description: 'Yes' + target_concept_id: 4063911 + target_concept_name: Ocular fundus photography + target_domain_id: Procedure + target_vocabulary_id: SNOMED + target_concept_class_id: Procedure + target_concept_code: '20067007' + target_standard_concept: S + predicate_id: skos:closeMatch + confidence: 0.75 + modifier: left eye|45888270 + qualifier_concept_id: 45888270 + qualifier_source_value: Left eye +- mapping_record_id: AIREADI_MAPPING_2124 + 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_bun_creatinine_ratio + question_or_answer: Question + src_code: 31045-8 + src_code_id: Creatinine/BUN ratio + src_cd_description: Creatinine/BUN ratio + target_concept_id: 3033837 + target_concept_name: Creatinine/Urea nitrogen [Mass Ratio] in Serum or Plasma + target_domain_id: Measurement + 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 +- mapping_record_id: AIREADI_MAPPING_2125 + 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_bun_creatinine_ratio_u + question_or_answer: Unit + src_code: ratio + src_code_id: import_bun_creatinine_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_2126 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: lab_results + field_type: text + question_or_answer: Question + src_code: lbscat_nrbc + src_cd_description: NRBC - % + target_concept_id: 40761514 + target_concept_name: Nucleated erythrocytes/Leukocytes [Ratio] in Blood by Automated count + target_domain_id: Measurement + target_vocabulary_id: LOINC + target_concept_class_id: Lab Test + target_concept_code: 58413-6 + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 +- mapping_record_id: AIREADI_MAPPING_2127 + map_to_omop: 'Yes' + transferred_to_fairhub_redcap_dataset: 'Yes' + protected_or_open_source: open-source + extension_needed: 'No' + form_name: lab_results + field_type: text + field_id: lbscat_nrbc_u + question_or_answer: Unit + src_code: '%' + src_code_id: lbscat_nrbc_u + src_cd_description: percent + target_concept_id: 8554 + target_concept_name: percent + target_domain_id: Unit + target_vocabulary_id: UCUM + target_concept_class_id: Unit + target_concept_code: '%' + target_standard_concept: S + predicate_id: skos:exactMatch + confidence: 1.0 + modifier: fixed unit; no REDCap unit field diff --git a/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_schema.yaml b/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_schema.yaml index a2d13e2..46cb67d 100644 --- a/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_schema.yaml +++ b/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_schema.yaml @@ -224,6 +224,7 @@ enums: AIREADI: {} AIREADI-MOCA: {} AIREADI-Vision: {} + CPT4: {} Ethnicity: {} LOINC: {} OMOP Extension: {} 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 2e15da6..9b24a66 100644 --- a/redCapDataDictionaryWithExtension/linkml/ai_readi_redcap_value_set_mapping_summary.md +++ b/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: 2079 +- Rows converted: 2127 - Source columns: 26 ## Generated files @@ -12,9 +12,9 @@ ### FORM_NAME - px_racial_ethnic_discrimination_survey: 364 - px_sdoh_combined_survey: 267 -- imported: 205 +- imported: 207 +- retinal_imaging_v2: 177 - health_survey: 174 -- retinal_imaging_v2: 133 - px_neighborhood_environment_survey: 126 - substance_use_survey: 111 - screening_survey: 77 @@ -24,34 +24,35 @@ ### TARGET_DOMAIN_ID - Meas Value: 1231 - Observation: 439 -- Unit: 148 -- Measurement: 114 +- Unit: 150 +- Measurement: 116 - [blank]: 76 +- Procedure: 66 - Condition: 32 -- Procedure: 22 - Route: 12 - Ethnicity: 4 - Device: 1 ### TARGET_VOCABULARY_ID -- LOINC: 1187 +- LOINC: 1189 - AIREADI: 422 -- UCUM: 148 -- SNOMED: 137 +- SNOMED: 169 +- UCUM: 150 - [blank]: 76 - AIREADI-Vision: 69 - AIREADI-MOCA: 30 +- CPT4: 12 - PPI: 5 - Ethnicity: 4 - OMOP Extension: 1 ### PREDICATE_ID -- skos:exactMatch: 1736 -- skos:closeMatch: 265 +- skos:exactMatch: 1764 +- skos:closeMatch: 285 - [blank]: 76 - skos:relatedMatch: 2 ### Extension_Needed -- No: 1557 +- No: 1605 - Yes: 521 - [blank]: 1 diff --git a/redCapDataDictionaryWithExtension/scripts/audit_concept_map.py b/redCapDataDictionaryWithExtension/scripts/audit_concept_map.py index f10a2be..4fa9961 100644 --- a/redCapDataDictionaryWithExtension/scripts/audit_concept_map.py +++ b/redCapDataDictionaryWithExtension/scripts/audit_concept_map.py @@ -7,7 +7,7 @@ A4 Predicate/confidence: exactMatch with confidence < 1; target 0 with a predicate; non-zero target without a predicate A5 Duplicate (FORM_NAME, FIELD_ID, SRC_CODE, row type) keys - (informational: Yes answers deliberately mapped to both a Condition/Observation + (informational: Yes answers deliberately mapped to both a Condition/Observation/Procedure concept and the Yes value are listed here) 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 @@ -197,7 +197,7 @@ def audit(rows, cm, out, label): if len(rs) > 1: a5.append((" / ".join(key), ", ".join(str(r["_ln"]) for r in rs), " | ".join(f"{r['TARGET_CONCEPT_ID']} {r['TARGET_CONCEPT_NAME'][:40]} ({r['TARGET_DOMAIN_ID']})" for r in rs))) - sections.append(("A5 Duplicate keys (informational: Yes -> Condition/Observation + Yes value pairs are expected)", + sections.append(("A5 Duplicate keys (informational: Yes -> Condition/Observation/Procedure + Yes value pairs are expected)", ["Form / field / code / type", "Lines", "Targets"], a5, False)) # A6 diff --git a/redCapDataDictionaryWithExtension/scripts/count_concept_map.sql b/redCapDataDictionaryWithExtension/scripts/count_concept_map.sql index 5b355ea..b643cd6 100644 --- a/redCapDataDictionaryWithExtension/scripts/count_concept_map.sql +++ b/redCapDataDictionaryWithExtension/scripts/count_concept_map.sql @@ -32,8 +32,13 @@ -- metadata, not survey content, and are reported as designated-but-unmapped. -- * Answer rows whose question was excluded or deleted (Map_to_OMOP = 'No', -- e.g. dri3, cmotyn since v1.6) are reported as designated-but-unmapped. --- * Not designated (827 in v1.6) = REDCap data elements in the curated dictionary --- (2,906) that are not rows in this mapping file. +-- * Unit rows switched off because a newer row replaces them (Map_to_OMOP = 'No', +-- the old MoCA *_time_unit / *_score_unit rows since v1.7) are reported as +-- designated-but-unmapped ("Superseded unit row"). +-- * Not designated (779 in v1.7) = REDCap data elements in the curated dictionary +-- (2,906) that are not rows in this mapping file. Rows that are not REDCap data +-- elements (the unit rows added in v1.4, v1.6 and v1.7, the 44 retinal imaging procedure +-- rows added in v1.7) are counted as mapped and lower this number. -- ============================================================================= -- 0. Load ------------------------------------------------------------------------ @@ -67,6 +72,7 @@ SELECT WHEN Map_to_OMOP <> 'Yes' AND SRC_CODE LIKE 'moca_paper%' THEN 'MoCA paper-administration flag' WHEN Map_to_OMOP <> 'Yes' AND temp_Question_or_Answer = 'Answer' THEN 'Answer to an excluded question' + WHEN Map_to_OMOP <> 'Yes' AND TARGET_DOMAIN_ID = 'Unit' THEN 'Superseded unit row' WHEN NULLIF(TRIM(TARGET_CONCEPT_ID), '') IS NOT NULL THEN NULL WHEN FIELD_ID LIKE 'import\_%\_min%' ESCAPE '\' OR FIELD_ID LIKE 'import\_%\_max%' ESCAPE '\' THEN 'Laboratory reference range' @@ -107,9 +113,9 @@ FROM rows ORDER BY CASE category WHEN 'Standard' THEN 1 WHEN 'Custom' THEN 2 WHEN 'Mapped total' THEN 3 WHEN 'Designated but unmapped' THEN 4 WHEN 'Not designated' THEN 5 ELSE 6 END; --- Expected (v1.6): Standard 1,478 (50.9%) / 392; Custom 487 (16.8%) / 342; --- Mapped 1,965 (67.6%) / 734; Designated-unmapped 114 (3.9%); --- Not designated 827 (28.5%); Total 2,906. +-- Expected (v1.7): Standard 1,506 (51.8%) / 396; Custom 487 (16.8%) / 342; +-- Mapped 1,993 (68.6%) / 738; Designated-unmapped 134 (4.6%); +-- Not designated 779 (26.8%); Total 2,906. -- 2. Elements and distinct concepts by vocabulary ---------------------------------- SELECT mapping_category, @@ -120,8 +126,8 @@ FROM mapping_classified WHERE mapping_category IN ('Standard','Custom') GROUP BY mapping_category, TARGET_VOCABULARY_ID ORDER BY mapping_category DESC, elements DESC; --- Expected (v1.6): LOINC 1,183/275; UCUM 148/38; SNOMED 137/71; PPI 5/5; Ethnicity 4/2; --- OMOP Extension 1/1; AIREADI 388/265; AIREADI-Vision 69/47; AIREADI-MOCA 30/30. +-- Expected (v1.7): LOINC 1,185/276; SNOMED 169/73; UCUM 130/38; CPT4 12/1; PPI 5/5; +-- Ethnicity 4/2; OMOP Extension 1/1; AIREADI 388/265; AIREADI-Vision 69/47; AIREADI-MOCA 30/30. -- 3. Designated-but-unmapped breakdown ------------------------------------------------- SELECT unmapped_reason, COUNT(*) AS n @@ -129,9 +135,9 @@ FROM mapping_classified WHERE mapping_category = 'Designated but unmapped' GROUP BY unmapped_reason ORDER BY n DESC; --- Expected (v1.6): reference range 46; survey timestamp 34; specimen handling 12; +-- Expected (v1.7): reference range 46; survey timestamp 34; superseded unit row 20; specimen handling 12; -- BCVA 10; no matching concept 6; answer to an excluded question 4; --- REDCap administrative 1; MoCA paper flag 1 (total 114). +-- REDCap administrative 1; MoCA paper flag 1 (total 134). -- 4. Confidence and SKOS predicate distribution ----------------------------------------- SELECT mapping_category, @@ -142,18 +148,20 @@ FROM mapping_classified WHERE mapping_category IN ('Standard','Custom') GROUP BY mapping_category, PREDICATE_ID, CONFIDENCE ORDER BY mapping_category DESC, PREDICATE_ID, CONFIDENCE DESC; --- Expected (v1.6, standard): exact 1,239; close 237 (156 at 1, 81 at 0.75); related 2; --- confidence 1 = 1,395; 0.75 = 82; 0.5 = 1. --- Expected (v1.6, custom): all 487 exact match at confidence 1. +-- Expected (v1.7, standard): exact 1,247; close 257 (170 at 1, 87 at 0.75); related 2; +-- confidence 1 = 1,417; 0.75 = 88; 0.5 = 1. +-- Expected (v1.7, custom): all 487 exact match at confidence 1. -- 5. Laterality qualifiers --------------------------------------------------------------- SELECT qualifier_concept_id, qualifier_source_value, COUNT(*) AS n FROM mapping_classified WHERE mapping_category IN ('Standard','Custom') - AND qualifier_concept_id IN ('45876703','45883829','4298982','4320144') + AND qualifier_concept_id IN ('45876703','45883829','4298982','4320144','45888271','45888270') GROUP BY qualifier_concept_id, qualifier_source_value ORDER BY qualifier_concept_id; --- Expected: Right eye 78; Left eye 78; Structure of right foot 2; Structure of left foot 2. +-- Expected: Right eye 78 (45876703) and 22 (45888271, CPT4 RT, v1.7 procedure rows); +-- Left eye 78 (45883829) and 22 (45888270, CPT4 LT); Structure of right foot 2; +-- Structure of left foot 2. -- 6. Integrity checks (each should return 0 rows) --------------------------------------- -- 6a. Custom concepts missing LOCAL_CONCEPT_ID diff --git a/redCapDataDictionaryWithExtension/scripts/validate_concept_map_vocab.sql b/redCapDataDictionaryWithExtension/scripts/validate_concept_map_vocab.sql index 920f51a..a6b2a9c 100644 --- a/redCapDataDictionaryWithExtension/scripts/validate_concept_map_vocab.sql +++ b/redCapDataDictionaryWithExtension/scripts/validate_concept_map_vocab.sql @@ -19,7 +19,7 @@ SELECT *, TRY_CAST(TRIM(CAST(qualifier_concept_id AS STRING)) AS BIGINT) AS qid FROM redcapsurveydb.ai_readi_redcap_value_set_mapping_common; --- V0. Row count (v1.4 and v1.5: 2,076) +-- V0. Row count (v1.4 and v1.5: 2,076; v1.6: 2,079; v1.7: 2,127) SELECT COUNT(*) AS n_rows FROM cmap; -- V1. Standard (non-custom) targets missing from the vocabulary, not standard, or invalid. Expect 0 rows. @@ -231,3 +231,19 @@ LEFT JOIN cmap q ON TRIM(q.temp_Question_or_Answer) = 'Question' AND TRIM(CAST(q WHERE TRIM(a.temp_Question_or_Answer) = 'Answer' AND q.SRC_CODE IS NULL AND TRIM(CAST(a.Map_to_OMOP AS STRING)) = 'Yes' ORDER BY a.FIELD_ID, a.SRC_CODE; + +-- V10. Procedure-domain rows (v1.7 retinal imaging: "Yes" -> PROCEDURE_OCCURRENCE). The target must be a +-- standard Procedure-domain concept, and a laterality qualifier must be a CPT4 Modifier (45888271 RT, +-- 45888270 LT), which the ETL writes to PROCEDURE_OCCURRENCE.modifier_concept_id. Expect 2 rows: the +-- monofilament "Tested" rows mssrftt and msslftt (qualifiers 4298982 / 4320144 Structure of right/left foot), +-- kept unchanged in v1.7 (monofilament redesign deferred). +SELECT m.FORM_NAME, m.FIELD_ID, m.SRC_CODE, m.tid, t.domain_id AS target_domain, + m.qid, q.concept_name AS qualifier_name, q.concept_class_id AS qualifier_class +FROM cmap m +LEFT JOIN omop_vocab.concept t ON t.concept_id = m.tid +LEFT JOIN omop_vocab.concept q ON q.concept_id = m.qid +WHERE TRIM(m.TARGET_DOMAIN_ID) = 'Procedure' + AND TRIM(CAST(m.Map_to_OMOP AS STRING)) = 'Yes' + AND ( (m.tid < 2000000000 AND t.domain_id IS DISTINCT FROM 'Procedure') + OR (m.qid IS NOT NULL AND m.qid < 2000000000 AND q.concept_class_id IS DISTINCT FROM 'CPT4 Modifier')) +ORDER BY m.FORM_NAME, m.FIELD_ID; 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 c5315d9..0b67f3c 100644 --- a/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.tsv +++ b/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.tsv @@ -600,12 +600,12 @@ AIREADI_REDCAP:lab_results.lbdattim1 Date & time clinical labs performed skos:cl 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_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_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:lab_results.lbscat_hct Hematocrit - % skos:exactMatch OMOP:3023314 Hematocrit [Volume Fraction] of Blood by Automated count semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1668 lbscat_hct Question 3023314 Measurement LOINC Lab Test 4544-3 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_mcv MCV - fL skos:exactMatch OMOP:3023599 MCV [Entitic mean volume] in Red Blood Cells by Automated count semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1669 lbscat_mcv Question 3023599 Measurement LOINC Lab Test 787-2 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_mch MCH - pg skos:exactMatch OMOP:3012030 MCH [Entitic mass] by Automated count semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1670 lbscat_mch Question 3012030 Measurement LOINC Lab Test 785-6 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_mchc MCHC - g/dL skos:exactMatch OMOP:3009744 MCHC [Entitic Mass/volume] in Red Blood Cells by Automated count semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1671 lbscat_mchc Question 3009744 Measurement LOINC Lab Test 786-4 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_rdw RDW - % skos:exactMatch OMOP:3019897 Erythrocyte [DistWidth] in Red Blood Cells by Automated count semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1672 lbscat_rdw Question 3019897 Measurement LOINC Lab Test 788-0 S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_plt Platelets - x10E3/µL skos:exactMatch OMOP:3024929 Platelets [#/volume] in Blood by Automated count semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text 1673 lbscat_plt Question 3024929 Measurement LOINC Lab Test 777-3 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 AIREADI_REDCAP:meds_assessment.cm_act Have you taken acetaminophen medicines, such as Tylenol, in the past 2 weeks? skos:exactMatch OMOP:2005200146 Have you taken acetaminophen medicines, such as Tylenol, in the past 2 weeks? semapv:ManualMappingCuration 1 AI-READI REDCap AIREADI AI-READI manual_curation meds_assessment radio 1462 cm_act Question 2005200146 2005200146 Observation AIREADI Survey S Yes open-source Yes @@ -2002,3 +2002,51 @@ AIREADI_REDCAP:imported.score.moca_total_score_u score skos:exactMatch OMOP:4477 AIREADI_REDCAP:imported.ratio.import_ag_ratio_u ratio skos:exactMatch OMOP:8523 ratio semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation fixed unit; no REDCap unit field imported text import_ag_ratio_u ratio import_ag_ratio_u Unit 8523 Unit UCUM Unit {ratio} S No open-source Yes AIREADI_REDCAP:physical_assessment.ratio.whr_vsorres_u ratio skos:exactMatch OMOP:8523 ratio semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation fixed unit; no REDCap unit field physical_assessment text whr_vsorres_u ratio whr_vsorres_u Unit 8523 Unit UCUM Unit {ratio} S No open-source Yes AIREADI_REDCAP:imported.ratio.import_buncreatinineratio_u ratio skos:exactMatch OMOP:8523 ratio semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation fixed unit; no REDCap unit field imported text import_buncreatinineratio_u ratio import_buncreatinineratio_u Unit 8523 Unit UCUM Unit {ratio} S No open-source Yes +AIREADI_REDCAP:retinal_imaging_v2.1.rtop_odd_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtop_odd 1 rtop_odd_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtop_odm_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtop_odm 1 rtop_odm_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtei_odir_1 Yes skos:closeMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtei_odir 1 rtei_odir_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtei_odfaf_1 Yes skos:closeMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtei_odfaf 1 rtei_odfaf_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtsm_odc_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtsm_odc 1 rtsm_odc_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtsm_odn_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtsm_odn 1 rtsm_odn_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtsm_odt_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtsm_odt 1 rtsm_odt_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtsm_odm_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtsm_odm 1 rtsm_odm_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtso_odo_1 Yes skos:closeMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtso_odo 1 rtso_odo_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtso_odp_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtso_odp 1 rtso_odp_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtso_odm_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtso_odm 1 rtso_odm_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtci_odm1_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtci_odm1 1 rtci_odm1_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtci_odd1_1 Yes skos:closeMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtci_odd1 1 rtci_odd1_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtci_odm2_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtci_odm2 1 rtci_odm2_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtci_odd2_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 0.75 AI-READI REDCap CPT4 AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtci_odd2 1 rtci_odd2_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtma_odw_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtma_odw 1 rtma_odw_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtma_odm_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtma_odm 1 rtma_odm_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtma_odm1_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtma_odm1 1 rtma_odm1_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rttr_odr_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rttr_odr 1 rttr_odr_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rttr_odm1_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rttr_odm1 1 rttr_odm1_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rttr_odm2_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rttr_odm2 1 rttr_odm2_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtfl_od_1 Yes skos:closeMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation right eye|45888271 retinal_imaging_v2 yesno rtfl_od 1 rtfl_od_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888271 Right eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtop_osd_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtop_osd 1 rtop_osd_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtop_osm_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtop_osm 1 rtop_osm_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtei_osir_1 Yes skos:closeMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtei_osir 1 rtei_osir_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtei_osfaf_1 Yes skos:closeMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtei_osfaf 1 rtei_osfaf_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtsm_osc_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtsm_osc 1 rtsm_osc_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtsm_osn_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtsm_osn 1 rtsm_osn_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtsm_ost_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtsm_ost 1 rtsm_ost_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtsm_osm_1 Yes skos:exactMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtsm_osm 1 rtsm_osm_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtso_oso_1 Yes skos:closeMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtso_oso 1 rtso_oso_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtso_osp_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtso_osp 1 rtso_osp_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtso_osm_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtso_osm 1 rtso_osm_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtci_osm1_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtci_osm1 1 rtci_osm1_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtci_osd1_1 Yes skos:closeMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtci_osd1 1 rtci_osd1_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtci_osm2_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtci_osm2 1 rtci_osm2_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtci_osd2_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 0.75 AI-READI REDCap CPT4 AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtci_osd2 1 rtci_osd2_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtma_osw_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtma_osw 1 rtma_osw_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtma_osm_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtma_osm 1 rtma_osm_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtma_osm1_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtma_osm1 1 rtma_osm1_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rttr_osr_1 Yes skos:exactMatch OMOP:1073298 Optical coherence tomography of posterior segment of eye semapv:ManualMappingCuration 1 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rttr_osr 1 rttr_osr_1 Answer 1073298 Procedure SNOMED Procedure 1303746000 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rttr_osm1_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rttr_osm1 1 rttr_osm1_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rttr_osm2_1 Yes skos:closeMatch OMOP:745759 Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography semapv:ManualMappingCuration 1 AI-READI REDCap CPT4 AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rttr_osm2 1 rttr_osm2_1 Answer 745759 Procedure CPT4 CPT4 92137 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:retinal_imaging_v2.1.rtfl_os_1 Yes skos:closeMatch OMOP:4063911 Ocular fundus photography semapv:ManualMappingCuration 0.75 AI-READI REDCap SNOMED AI-READI manual_curation left eye|45888270 retinal_imaging_v2 yesno rtfl_os 1 rtfl_os_1 Answer 4063911 Procedure SNOMED Procedure 20067007 S No open-source Yes 45888270 Left eye +AIREADI_REDCAP:imported.31045-8.Creatinine_BUN_ratio Creatinine/BUN ratio skos:exactMatch OMOP:3033837 Creatinine/Urea nitrogen [Mass Ratio] in Serum or Plasma semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation imported text import_bun_creatinine_ratio 31045-8 Creatinine/BUN ratio Question 3033837 Measurement LOINC Lab Test 31045-8 S No open-source Yes +AIREADI_REDCAP:imported.ratio.import_bun_creatinine_ratio_u ratio skos:exactMatch OMOP:8523 ratio semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation fixed unit; no REDCap unit field imported text import_bun_creatinine_ratio_u ratio import_bun_creatinine_ratio_u Unit 8523 Unit UCUM Unit {ratio} S No open-source Yes +AIREADI_REDCAP:lab_results.lbscat_nrbc NRBC - % skos:exactMatch OMOP:40761514 Nucleated erythrocytes/Leukocytes [Ratio] in Blood by Automated count semapv:ManualMappingCuration 1 AI-READI REDCap LOINC AI-READI manual_curation lab_results text lbscat_nrbc Question 40761514 Measurement LOINC Lab Test 58413-6 S No open-source Yes +AIREADI_REDCAP:lab_results.missing.lbscat_nrbc_u percent skos:exactMatch OMOP:8554 percent semapv:ManualMappingCuration 1 AI-READI REDCap UCUM AI-READI manual_curation fixed unit; no REDCap unit field lab_results text lbscat_nrbc_u % lbscat_nrbc_u Unit 8554 Unit UCUM Unit % S No open-source Yes diff --git a/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.yaml b/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.yaml index 875914b..84710b9 100644 --- a/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.yaml +++ b/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping.sssom.yaml @@ -15,4 +15,4 @@ curie_map: semapv: https://w3id.org/semapv/vocab/ subject_source: AI-READI REDCap object_source: OMOP Standardized Vocabularies -mapping_date: '2026-10-22' +mapping_date: '2026-10-24' diff --git a/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping_sssom_README.md b/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping_sssom_README.md index 557835c..6a02338 100644 --- a/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping_sssom_README.md +++ b/redCapDataDictionaryWithExtension/sssom/ai_readi_redcap_value_set_mapping_sssom_README.md @@ -10,8 +10,8 @@ Generated from `_ai_readi_redcap_value_set_mapping_common.csv` with `generate_li ## Row counts -- Source rows: 2,079 -- Rows included in SSSOM TSV: 2,003 +- Source rows: 2,127 +- Rows included in SSSOM TSV: 2,051 - Rows excluded as incomplete for SSSOM: 76 ## Identifier conventions diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common.csv b/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common.csv index 5223564..c5d25ba 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common.csv +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/_ai_readi_redcap_value_set_mapping_common.csv @@ -645,26 +645,26 @@ Yes,Yes,open-source,Yes,imported,text,moca_combined_mis_score,,Question,moca_com Yes,Yes,open-source,No,imported,text,moca_total_score_time,,Question,moca_total_score_time,,Total Score (Time),1988422,,Time to complete survey,Observation,LOINC,Survey,99423-6,S,skos:closeMatch,0.75,,,, Yes,Yes,open-source,Yes,imported,text,age_years_at_interview,,Question,age_years_at_interview,,"pull down menu of 3-4 year age spans, age in years",2005200372,2005200372,Age in years (3-4 year span),Observation,AIREADI-MOCA,Observable Entity,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,moca_total_score,,Question,moca_total_score,,Total Score,606671,,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scale,1148423001,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,trails_time_unit,,,trails_time_unit,,Time taken to do trails in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,trails_score_unit,,,trails_score_unit,,Trail drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,cube_time_unit,,,cube_time_unit,,Time taken to do cube in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,cube_score_unit,,,cube_score_unit,,Cube drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,clock_time_unit,,,clock_time_unit,,Time taken to do clock in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,clock_score_unit,,,clock_score_unit,,Clock drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,naming_time_unit,,,naming_time_unit,,time in seconds to perform the animal name recall task (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,memorytrial1_time_unit,,,memorytrial1_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,memorytrial2_time_unit,,,memorytrial2_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,digitspan_time_unit,,,digitspan_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,lettera_time_unit,,,lettera_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,lettera_score_unit,,,lettera_score_unit,,Letter tapping score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,subtraction_time_unit,,,subtraction_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,repetition_time_unit,,,repetition_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,fluency_language_time_unit,,,fluency_language_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,abstraction_time_unit,,,abstraction_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,delayedrecall_time_unit,,,delayedrecall_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,orientation_time_unit,,,orientation_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,moca_combined_mis_score_unit,,,moca_combined_mis_score_unit,,"combined score of MOCA delayed recall with no cue, MOCA delayed recall category cue (not included in total score), MOCA delayed recall multiple choice cue (not included in total score) (Unit)",44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,moca_total_score_unit,,,moca_total_score_unit,,Montreal Cognitive Assessment Total Score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,trails_time_unit,,,trails_time_unit,,Time taken to do trails in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,trails_score_unit,,,trails_score_unit,,Trail drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,cube_time_unit,,,cube_time_unit,,Time taken to do cube in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,cube_score_unit,,,cube_score_unit,,Cube drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,clock_time_unit,,,clock_time_unit,,Time taken to do clock in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,clock_score_unit,,,clock_score_unit,,Clock drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,naming_time_unit,,,naming_time_unit,,time in seconds to perform the animal name recall task (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,memorytrial1_time_unit,,,memorytrial1_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,memorytrial2_time_unit,,,memorytrial2_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,digitspan_time_unit,,,digitspan_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,lettera_time_unit,,,lettera_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,lettera_score_unit,,,lettera_score_unit,,Letter tapping score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,subtraction_time_unit,,,subtraction_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,repetition_time_unit,,,repetition_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,fluency_language_time_unit,,,fluency_language_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,abstraction_time_unit,,,abstraction_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,delayedrecall_time_unit,,,delayedrecall_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,orientation_time_unit,,,orientation_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,moca_combined_mis_score_unit,,,moca_combined_mis_score_unit,,"combined score of MOCA delayed recall with no cue, MOCA delayed recall category cue (not included in total score), MOCA delayed recall multiple choice cue (not included in total score) (Unit)",44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, +No,Yes,open-source,No,imported,text,moca_total_score_unit,,,moca_total_score_unit,,Montreal Cognitive Assessment Total Score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,s,,,s,,second,8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, 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,,,, @@ -672,12 +672,12 @@ Yes,Yes,open-source,No,lab_results,text,,1661,Question,lbdattim1,,Date & time cl 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,,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,,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,lab_results,text,,1668,Question,lbscat_hct,,Hematocrit - %,3023314,,Hematocrit [Volume Fraction] of Blood by Automated count,Measurement,LOINC,Lab Test,4544-3,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1669,Question,lbscat_mcv,,MCV - fL,3023599,,MCV [Entitic mean volume] in Red Blood Cells by Automated count,Measurement,LOINC,Lab Test,787-2,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1670,Question,lbscat_mch,,MCH - pg,3012030,,MCH [Entitic mass] by Automated count,Measurement,LOINC,Lab Test,785-6,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1671,Question,lbscat_mchc,,MCHC - g/dL,3009744,,MCHC [Entitic Mass/volume] in Red Blood Cells by Automated count,Measurement,LOINC,Lab Test,786-4,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1672,Question,lbscat_rdw,,RDW - %,3019897,,Erythrocyte [DistWidth] in Red Blood Cells by Automated count,Measurement,LOINC,Lab Test,788-0,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1673,Question,lbscat_plt,,Platelets - x10E3/µL,3024929,,Platelets [#/volume] in Blood by Automated count,Measurement,LOINC,Lab Test,777-3,S,skos:exactMatch,1,,,, 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,,,, Yes,Yes,open-source,Yes,meds_assessment,radio,,1462,Question,cm_act,,"Have you taken acetaminophen medicines, such as Tylenol, in the past 2 weeks?",2005200146,2005200146,"Have you taken acetaminophen medicines, such as Tylenol, in the past 2 weeks?",Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, @@ -2078,3 +2078,51 @@ Yes,Yes,open-source,No,imported,text,moca_total_score_u,,Unit,score,moca_total_s Yes,Yes,open-source,No,imported,text,import_ag_ratio_u,,Unit,ratio,import_ag_ratio_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, Yes,Yes,open-source,No,physical_assessment,text,whr_vsorres_u,,Unit,ratio,whr_vsorres_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, Yes,Yes,open-source,No,imported,text,import_buncreatinineratio_u,,Unit,ratio,import_buncreatinineratio_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_odd,,Answer,1,rtop_odd_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_odm,,Answer,1,rtop_odm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_odir,,Answer,1,rtei_odir_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_odfaf,,Answer,1,rtei_odfaf_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odc,,Answer,1,rtsm_odc_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odn,,Answer,1,rtsm_odn_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odt,,Answer,1,rtsm_odt_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odm,,Answer,1,rtsm_odm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_odo,,Answer,1,rtso_odo_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_odp,,Answer,1,rtso_odp_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_odm,,Answer,1,rtso_odm_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odm1,,Answer,1,rtci_odm1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odd1,,Answer,1,rtci_odd1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odm2,,Answer,1,rtci_odm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odd2,,Answer,1,rtci_odd2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_odw,,Answer,1,rtma_odw_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_odm,,Answer,1,rtma_odm_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_odm1,,Answer,1,rtma_odm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_odr,,Answer,1,rttr_odr_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_odm1,,Answer,1,rttr_odm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_odm2,,Answer,1,rttr_odm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtfl_od,,Answer,1,rtfl_od_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_osd,,Answer,1,rtop_osd_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_osm,,Answer,1,rtop_osm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_osir,,Answer,1,rtei_osir_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_osfaf,,Answer,1,rtei_osfaf_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_osc,,Answer,1,rtsm_osc_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_osn,,Answer,1,rtsm_osn_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_ost,,Answer,1,rtsm_ost_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_osm,,Answer,1,rtsm_osm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_oso,,Answer,1,rtso_oso_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_osp,,Answer,1,rtso_osp_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_osm,,Answer,1,rtso_osm_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osm1,,Answer,1,rtci_osm1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osd1,,Answer,1,rtci_osd1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osm2,,Answer,1,rtci_osm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osd2,,Answer,1,rtci_osd2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_osw,,Answer,1,rtma_osw_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_osm,,Answer,1,rtma_osm_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_osm1,,Answer,1,rtma_osm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_osr,,Answer,1,rttr_osr_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_osm1,,Answer,1,rttr_osm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_osm2,,Answer,1,rttr_osm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtfl_os,,Answer,1,rtfl_os_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,imported,text,import_bun_creatinine_ratio,,Question,31045-8,Creatinine/BUN ratio,Creatinine/BUN ratio,3033837,,Creatinine/Urea nitrogen [Mass Ratio] in Serum or Plasma,Measurement,LOINC,Lab Test,31045-8,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,imported,text,import_bun_creatinine_ratio_u,,Unit,ratio,import_bun_creatinine_ratio_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, +Yes,Yes,open-source,No,lab_results,text,,,Question,lbscat_nrbc,,NRBC - %,40761514,,Nucleated erythrocytes/Leukocytes [Ratio] in Blood by Automated count,Measurement,LOINC,Lab Test,58413-6,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,lbscat_nrbc_u,,Unit,%,lbscat_nrbc_u,percent,8554,,percent,Unit,UCUM,Unit,%,S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, 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 7483d0f..adc43c7 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 @@ -643,26 +643,6 @@ Yes,Yes,open-source,Yes,imported,text,moca_combined_mis_score,,Question,moca_com Yes,Yes,open-source,No,imported,text,moca_total_score_time,,Question,moca_total_score_time,,Total Score (Time),1988422,,Time to complete survey,Observation,LOINC,Survey,99423-6,S,skos:closeMatch,0.75,,,, Yes,Yes,open-source,Yes,imported,text,age_years_at_interview,,Question,age_years_at_interview,,"pull down menu of 3-4 year age spans, age in years",2005200372,2005200372,Age in years (3-4 year span),Observation,AIREADI-MOCA,Observable Entity,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,moca_total_score,,Question,moca_total_score,,Total Score,606671,,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scale,1148423001,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,trails_time_unit,,,trails_time_unit,,Time taken to do trails in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,trails_score_unit,,,trails_score_unit,,Trail drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,cube_time_unit,,,cube_time_unit,,Time taken to do cube in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,cube_score_unit,,,cube_score_unit,,Cube drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,clock_time_unit,,,clock_time_unit,,Time taken to do clock in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,clock_score_unit,,,clock_score_unit,,Clock drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,naming_time_unit,,,naming_time_unit,,time in seconds to perform the animal name recall task (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,memorytrial1_time_unit,,,memorytrial1_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,memorytrial2_time_unit,,,memorytrial2_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,digitspan_time_unit,,,digitspan_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,lettera_time_unit,,,lettera_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,lettera_score_unit,,,lettera_score_unit,,Letter tapping score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,subtraction_time_unit,,,subtraction_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,repetition_time_unit,,,repetition_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,fluency_language_time_unit,,,fluency_language_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,abstraction_time_unit,,,abstraction_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,delayedrecall_time_unit,,,delayedrecall_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,orientation_time_unit,,,orientation_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,moca_combined_mis_score_unit,,,moca_combined_mis_score_unit,,"combined score of MOCA delayed recall with no cue, MOCA delayed recall category cue (not included in total score), MOCA delayed recall multiple choice cue (not included in total score) (Unit)",44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,moca_total_score_unit,,,moca_total_score_unit,,Montreal Cognitive Assessment Total Score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,s,,,s,,second,8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, 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,,,, @@ -670,12 +650,12 @@ Yes,Yes,open-source,No,lab_results,text,,1661,Question,lbdattim1,,Date & time cl 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,,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,,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,lab_results,text,,1668,Question,lbscat_hct,,Hematocrit - %,3023314,,Hematocrit [Volume Fraction] of Blood by Automated count,Measurement,LOINC,Lab Test,4544-3,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1669,Question,lbscat_mcv,,MCV - fL,3023599,,MCV [Entitic mean volume] in Red Blood Cells by Automated count,Measurement,LOINC,Lab Test,787-2,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1670,Question,lbscat_mch,,MCH - pg,3012030,,MCH [Entitic mass] by Automated count,Measurement,LOINC,Lab Test,785-6,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1671,Question,lbscat_mchc,,MCHC - g/dL,3009744,,MCHC [Entitic Mass/volume] in Red Blood Cells by Automated count,Measurement,LOINC,Lab Test,786-4,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1672,Question,lbscat_rdw,,RDW - %,3019897,,Erythrocyte [DistWidth] in Red Blood Cells by Automated count,Measurement,LOINC,Lab Test,788-0,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1673,Question,lbscat_plt,,Platelets - x10E3/µL,3024929,,Platelets [#/volume] in Blood by Automated count,Measurement,LOINC,Lab Test,777-3,S,skos:exactMatch,1,,,, 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,,,, Yes,Yes,open-source,Yes,meds_assessment,radio,,1462,Question,cm_act,,"Have you taken acetaminophen medicines, such as Tylenol, in the past 2 weeks?",2005200146,2005200146,"Have you taken acetaminophen medicines, such as Tylenol, in the past 2 weeks?",Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, @@ -2073,3 +2053,51 @@ Yes,Yes,open-source,No,imported,text,moca_total_score_u,,Unit,score,moca_total_s Yes,Yes,open-source,No,imported,text,import_ag_ratio_u,,Unit,ratio,import_ag_ratio_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, Yes,Yes,open-source,No,physical_assessment,text,whr_vsorres_u,,Unit,ratio,whr_vsorres_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, Yes,Yes,open-source,No,imported,text,import_buncreatinineratio_u,,Unit,ratio,import_buncreatinineratio_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_odd,,Answer,1,rtop_odd_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_odm,,Answer,1,rtop_odm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_odir,,Answer,1,rtei_odir_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_odfaf,,Answer,1,rtei_odfaf_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odc,,Answer,1,rtsm_odc_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odn,,Answer,1,rtsm_odn_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odt,,Answer,1,rtsm_odt_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odm,,Answer,1,rtsm_odm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_odo,,Answer,1,rtso_odo_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_odp,,Answer,1,rtso_odp_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_odm,,Answer,1,rtso_odm_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odm1,,Answer,1,rtci_odm1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odd1,,Answer,1,rtci_odd1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odm2,,Answer,1,rtci_odm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odd2,,Answer,1,rtci_odd2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_odw,,Answer,1,rtma_odw_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_odm,,Answer,1,rtma_odm_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_odm1,,Answer,1,rtma_odm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_odr,,Answer,1,rttr_odr_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_odm1,,Answer,1,rttr_odm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_odm2,,Answer,1,rttr_odm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtfl_od,,Answer,1,rtfl_od_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_osd,,Answer,1,rtop_osd_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_osm,,Answer,1,rtop_osm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_osir,,Answer,1,rtei_osir_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_osfaf,,Answer,1,rtei_osfaf_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_osc,,Answer,1,rtsm_osc_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_osn,,Answer,1,rtsm_osn_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_ost,,Answer,1,rtsm_ost_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_osm,,Answer,1,rtsm_osm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_oso,,Answer,1,rtso_oso_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_osp,,Answer,1,rtso_osp_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_osm,,Answer,1,rtso_osm_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osm1,,Answer,1,rtci_osm1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osd1,,Answer,1,rtci_osd1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osm2,,Answer,1,rtci_osm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osd2,,Answer,1,rtci_osd2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_osw,,Answer,1,rtma_osw_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_osm,,Answer,1,rtma_osm_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_osm1,,Answer,1,rtma_osm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_osr,,Answer,1,rttr_osr_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_osm1,,Answer,1,rttr_osm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_osm2,,Answer,1,rttr_osm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtfl_os,,Answer,1,rtfl_os_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,imported,text,import_bun_creatinine_ratio,,Question,31045-8,Creatinine/BUN ratio,Creatinine/BUN ratio,3033837,,Creatinine/Urea nitrogen [Mass Ratio] in Serum or Plasma,Measurement,LOINC,Lab Test,31045-8,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,imported,text,import_bun_creatinine_ratio_u,,Unit,ratio,import_bun_creatinine_ratio_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, +Yes,Yes,open-source,No,lab_results,text,,,Question,lbscat_nrbc,,NRBC - %,40761514,,Nucleated erythrocytes/Leukocytes [Ratio] in Blood by Automated count,Measurement,LOINC,Lab Test,58413-6,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,lbscat_nrbc_u,,Unit,%,lbscat_nrbc_u,percent,8554,,percent,Unit,UCUM,Unit,%,S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, 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 ba01780..fd27c6e 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 @@ -585,26 +585,6 @@ Yes,Yes,open-source,Yes,imported,text,moca_combined_mis_score,,Question,moca_com Yes,Yes,open-source,No,imported,text,moca_total_score_time,,Question,moca_total_score_time,,Total Score (Time),1988422,,Time to complete survey,Observation,LOINC,Survey,99423-6,S,skos:closeMatch,0.75,,,, Yes,Yes,open-source,Yes,imported,text,age_years_at_interview,,Question,age_years_at_interview,,"pull down menu of 3-4 year age spans, age in years",2005200372,2005200372,Age in years (3-4 year span),Observation,AIREADI-MOCA,Observable Entity,,S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,moca_total_score,,Question,moca_total_score,,Total Score,606671,,Montreal Cognitive Assessment version 8.1,Measurement,SNOMED,Staging / Scale,1148423001,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,trails_time_unit,,,trails_time_unit,,Time taken to do trails in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,trails_score_unit,,,trails_score_unit,,Trail drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,cube_time_unit,,,cube_time_unit,,Time taken to do cube in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,cube_score_unit,,,cube_score_unit,,Cube drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,clock_time_unit,,,clock_time_unit,,Time taken to do clock in seconds (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,clock_score_unit,,,clock_score_unit,,Clock drawings score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,naming_time_unit,,,naming_time_unit,,time in seconds to perform the animal name recall task (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,memorytrial1_time_unit,,,memorytrial1_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,memorytrial2_time_unit,,,memorytrial2_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,digitspan_time_unit,,,digitspan_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,lettera_time_unit,,,lettera_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,lettera_score_unit,,,lettera_score_unit,,Letter tapping score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,subtraction_time_unit,,,subtraction_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,repetition_time_unit,,,repetition_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,fluency_language_time_unit,,,fluency_language_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,abstraction_time_unit,,,abstraction_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,delayedrecall_time_unit,,,delayedrecall_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,orientation_time_unit,,,orientation_time_unit,,Time in seconds to perform the above task. (Unit),8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,moca_combined_mis_score_unit,,,moca_combined_mis_score_unit,,"combined score of MOCA delayed recall with no cue, MOCA delayed recall category cue (not included in total score), MOCA delayed recall multiple choice cue (not included in total score) (Unit)",44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, -Yes,Yes,open-source,No,imported,text,moca_total_score_unit,,,moca_total_score_unit,,Montreal Cognitive Assessment Total Score (Unit),44777566,,score,Unit,UCUM,Unit,[score],S,skos:exactMatch,1,,,, Yes,Yes,open-source,No,imported,text,s,,,s,,second,8555,,second,Unit,UCUM,Unit,s,S,skos:exactMatch,1,,,, 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,,,, @@ -612,12 +592,12 @@ Yes,Yes,open-source,No,lab_results,text,,1661,Question,lbdattim1,,Date & time cl 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,,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,,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,lab_results,text,,1668,Question,lbscat_hct,,Hematocrit - %,3023314,,Hematocrit [Volume Fraction] of Blood by Automated count,Measurement,LOINC,Lab Test,4544-3,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1669,Question,lbscat_mcv,,MCV - fL,3023599,,MCV [Entitic mean volume] in Red Blood Cells by Automated count,Measurement,LOINC,Lab Test,787-2,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1670,Question,lbscat_mch,,MCH - pg,3012030,,MCH [Entitic mass] by Automated count,Measurement,LOINC,Lab Test,785-6,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1671,Question,lbscat_mchc,,MCHC - g/dL,3009744,,MCHC [Entitic Mass/volume] in Red Blood Cells by Automated count,Measurement,LOINC,Lab Test,786-4,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1672,Question,lbscat_rdw,,RDW - %,3019897,,Erythrocyte [DistWidth] in Red Blood Cells by Automated count,Measurement,LOINC,Lab Test,788-0,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,,1673,Question,lbscat_plt,,Platelets - x10E3/µL,3024929,,Platelets [#/volume] in Blood by Automated count,Measurement,LOINC,Lab Test,777-3,S,skos:exactMatch,1,,,, 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,,,, Yes,Yes,open-source,Yes,meds_assessment,radio,,1462,Question,cm_act,,"Have you taken acetaminophen medicines, such as Tylenol, in the past 2 weeks?",2005200146,2005200146,"Have you taken acetaminophen medicines, such as Tylenol, in the past 2 weeks?",Observation,AIREADI,Survey,,S,skos:exactMatch,1,,,, @@ -1964,3 +1944,51 @@ Yes,Yes,open-source,No,imported,text,moca_total_score_u,,Unit,score,moca_total_s Yes,Yes,open-source,No,imported,text,import_ag_ratio_u,,Unit,ratio,import_ag_ratio_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, Yes,Yes,open-source,No,physical_assessment,text,whr_vsorres_u,,Unit,ratio,whr_vsorres_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, Yes,Yes,open-source,No,imported,text,import_buncreatinineratio_u,,Unit,ratio,import_buncreatinineratio_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_odd,,Answer,1,rtop_odd_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_odm,,Answer,1,rtop_odm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_odir,,Answer,1,rtei_odir_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_odfaf,,Answer,1,rtei_odfaf_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odc,,Answer,1,rtsm_odc_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odn,,Answer,1,rtsm_odn_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odt,,Answer,1,rtsm_odt_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_odm,,Answer,1,rtsm_odm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_odo,,Answer,1,rtso_odo_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_odp,,Answer,1,rtso_odp_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_odm,,Answer,1,rtso_odm_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odm1,,Answer,1,rtci_odm1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odd1,,Answer,1,rtci_odd1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odm2,,Answer,1,rtci_odm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_odd2,,Answer,1,rtci_odd2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_odw,,Answer,1,rtma_odw_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_odm,,Answer,1,rtma_odm_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_odm1,,Answer,1,rtma_odm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_odr,,Answer,1,rttr_odr_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_odm1,,Answer,1,rttr_odm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_odm2,,Answer,1,rttr_odm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtfl_od,,Answer,1,rtfl_od_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,right eye|45888271,,45888271,Right eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_osd,,Answer,1,rtop_osd_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtop_osm,,Answer,1,rtop_osm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_osir,,Answer,1,rtei_osir_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtei_osfaf,,Answer,1,rtei_osfaf_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_osc,,Answer,1,rtsm_osc_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_osn,,Answer,1,rtsm_osn_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_ost,,Answer,1,rtsm_ost_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtsm_osm,,Answer,1,rtsm_osm_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_oso,,Answer,1,rtso_oso_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_osp,,Answer,1,rtso_osp_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtso_osm,,Answer,1,rtso_osm_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osm1,,Answer,1,rtci_osm1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osd1,,Answer,1,rtci_osd1_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osm2,,Answer,1,rtci_osm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtci_osd2,,Answer,1,rtci_osd2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_osw,,Answer,1,rtma_osw_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_osm,,Answer,1,rtma_osm_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtma_osm1,,Answer,1,rtma_osm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_osr,,Answer,1,rttr_osr_1,Yes,1073298,,Optical coherence tomography of posterior segment of eye,Procedure,SNOMED,Procedure,1303746000,S,skos:exactMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_osm1,,Answer,1,rttr_osm1_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rttr_osm2,,Answer,1,rttr_osm2_1,Yes,745759,,"Computerized ophthalmic diagnostic imaging (eg, optical coherence tomography [OCT]), posterior segment, with interpretation and report, unilateral or bilateral; retina, including OCT angiography",Procedure,CPT4,CPT4,92137,S,skos:closeMatch,1,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,retinal_imaging_v2,yesno,rtfl_os,,Answer,1,rtfl_os_1,Yes,4063911,,Ocular fundus photography,Procedure,SNOMED,Procedure,20067007,S,skos:closeMatch,0.75,left eye|45888270,,45888270,Left eye +Yes,Yes,open-source,No,imported,text,import_bun_creatinine_ratio,,Question,31045-8,Creatinine/BUN ratio,Creatinine/BUN ratio,3033837,,Creatinine/Urea nitrogen [Mass Ratio] in Serum or Plasma,Measurement,LOINC,Lab Test,31045-8,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,imported,text,import_bun_creatinine_ratio_u,,Unit,ratio,import_bun_creatinine_ratio_u,ratio,8523,,ratio,Unit,UCUM,Unit,{ratio},S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, +Yes,Yes,open-source,No,lab_results,text,,,Question,lbscat_nrbc,,NRBC - %,40761514,,Nucleated erythrocytes/Leukocytes [Ratio] in Blood by Automated count,Measurement,LOINC,Lab Test,58413-6,S,skos:exactMatch,1,,,, +Yes,Yes,open-source,No,lab_results,text,lbscat_nrbc_u,,Unit,%,lbscat_nrbc_u,percent,8554,,percent,Unit,UCUM,Unit,%,S,skos:exactMatch,1,fixed unit; no REDCap unit field,,, diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/01_create_unit_lookup.sql b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/01_create_unit_lookup.sql index 42b7b6d..1db268f 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/01_create_unit_lookup.sql +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/01_create_unit_lookup.sql @@ -3,9 +3,9 @@ -- AI-READI concept map: create the unit_lookup table (one query) -- -- unit_lookup has one row per (key_type, lookup_key): --- key_type = 'field' : lookup_key = measurement field name (e.g. lbscat_rbc) -> 88 rows +-- key_type = 'field' : lookup_key = measurement field name (e.g. lbscat_rbc) -> 90 rows -- key_type = 'string' : lookup_key = unit text (e.g. 'mEq/L') -> 25 rows --- v1.6: 113 rows (v1.4 and v1.5: 110). Same content as unit_concept_lookup.csv (option A: 01a_load_unit_concept_lookup_csv.sql). +-- v1.7: 115 rows (v1.6: 113; v1.4 and v1.5: 110). Same content as unit_concept_lookup.csv (option A: 01a_load_unit_concept_lookup_csv.sql). -- -- Requires the concept map as a table or view named concept_map (see 00_load_concept_map.sql). -- Dialect: Databricks / Spark SQL. diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/01a_load_unit_concept_lookup_csv.sql b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/01a_load_unit_concept_lookup_csv.sql index c9ab0ab..3c8acc6 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/01a_load_unit_concept_lookup_csv.sql +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/01a_load_unit_concept_lookup_csv.sql @@ -6,7 +6,7 @@ -- 01_create_unit_lookup.sql (option B), without loading the concept map. -- -- unit_concept_lookup.csv columns: key_type, lookup_key, unit_concept_id, unit_source_value --- v1.6: 113 rows (field 88, string 25), one row per (key_type, lookup_key). +-- v1.7: 115 rows (field 90, string 25), one row per (key_type, lookup_key). -- The file is UTF-8 (x10E3/µL and x10E6/µL use the micro sign U+00B5). -- -- Set the path to your copy of unit_concept_lookup.csv, then run. @@ -28,5 +28,5 @@ SELECT TRIM(key_type) AS key_type, TRIM(unit_source_value) AS unit_source_value FROM unit_concept_lookup_csv; --- Check: 113 rows; field 88, string 25. +-- Check: 115 rows; field 90, string 25. SELECT key_type, COUNT(*) AS n FROM unit_lookup GROUP BY key_type ORDER BY key_type; diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/02_view_unit_lookup.sql b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/02_view_unit_lookup.sql index 424ede9..55fc774 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/02_view_unit_lookup.sql +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/02_view_unit_lookup.sql @@ -5,13 +5,13 @@ -- Requires unit_lookup (01_create_unit_lookup.sql). Dialect: Databricks / Spark SQL. -- ============================================================================= --- Row counts by key type. v1.6: field 88, string 25. +-- Row counts by key type. v1.7: field 90, string 25. SELECT key_type, COUNT(*) AS n FROM unit_lookup GROUP BY key_type ORDER BY key_type; --- Lookup by measurement field name (88 rows). +-- Lookup by measurement field name (90 rows). SELECT lookup_key AS field_name, unit_concept_id, unit_source_value FROM unit_lookup WHERE key_type = 'field' diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/03_left_join_unit_lookup_template.sql b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/03_left_join_unit_lookup_template.sql index 8506210..a6374f4 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/03_left_join_unit_lookup_template.sql +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/03_left_join_unit_lookup_template.sql @@ -8,6 +8,7 @@ -- : the unit text on the record, if any, e.g. 'mEq/L' (may be NULL) -- -- Rule: unit by field name first, then by unit text, otherwise 0 (no matching concept). +-- Unit text is trimmed, and blank text (e.g. ' ') is written as NULL (v1.7 ETL rule 5). -- unit_lookup has one row per key, so the LEFT JOINs never add rows. -- Requires unit_lookup (01_create_unit_lookup.sql). Dialect: Databricks / Spark SQL. -- This file contains placeholders and does not run until they are replaced. @@ -15,7 +16,7 @@ SELECT m.*, COALESCE(f.unit_concept_id, u.unit_concept_id, 0) AS unit_concept_id, - COALESCE(f.unit_source_value, m.) AS unit_source_value + COALESCE(f.unit_source_value, NULLIF(TRIM(m.), '')) AS unit_source_value FROM m LEFT JOIN unit_lookup f ON f.key_type = 'field' AND f.lookup_key = TRIM(m.) diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/04_example_omop_survey_measurement.sql b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/04_example_omop_survey_measurement.sql index dcc0b2d..f9bdaea 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/04_example_omop_survey_measurement.sql +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/04_example_omop_survey_measurement.sql @@ -13,7 +13,7 @@ SELECT m.measurement_id, m.value_as_number, m.unit_concept_id AS unit_concept_id_current, COALESCE(f.unit_concept_id, u.unit_concept_id, 0) AS unit_concept_id, - COALESCE(f.unit_source_value, m.unit_source_value) AS unit_source_value + COALESCE(f.unit_source_value, NULLIF(TRIM(m.unit_source_value), '')) AS unit_source_value FROM omop_survey.measurement m LEFT JOIN unit_lookup f ON f.key_type = 'field' AND f.lookup_key = TRIM(SPLIT_PART(m.measurement_source_value, ',', 1)) @@ -24,7 +24,7 @@ LEFT JOIN unit_lookup u SELECT TRIM(SPLIT_PART(m.measurement_source_value, ',', 1)) AS field_name, m.unit_concept_id AS unit_concept_id_current, COALESCE(f.unit_concept_id, u.unit_concept_id, 0) AS unit_concept_id, - COALESCE(f.unit_source_value, m.unit_source_value) AS unit_source_value, + COALESCE(f.unit_source_value, NULLIF(TRIM(m.unit_source_value), '')) AS unit_source_value, COUNT(*) AS n FROM omop_survey.measurement m LEFT JOIN unit_lookup f diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/README.md b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/README.md index bd28053..23505e7 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/README.md +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/README.md @@ -6,9 +6,9 @@ Scripts to fill `MEASUREMENT.unit_concept_id` from the AI-READI concept map (`.. |---|---| | `USAGE.md` | **Step-by-step usage** | | `00_load_concept_map.sql` | Loads the mapping file as `concept_map` (only needed for option B; set the file path) | -| `unit_concept_lookup.csv` | **The ready-made lookup table** (113 rows): load it and skip building it | +| `unit_concept_lookup.csv` | **The ready-made lookup table** (115 rows): load it and skip building it | | `01a_load_unit_concept_lookup_csv.sql` | Option A: creates `unit_lookup` from `unit_concept_lookup.csv` | -| `01_create_unit_lookup.sql` | Option B: **one query** that builds `unit_lookup` from the concept map (same 113 rows) | +| `01_create_unit_lookup.sql` | Option B: **one query** that builds `unit_lookup` from the concept map (same 115 rows) | | `02_view_unit_lookup.sql` | Review `unit_lookup`: counts, field and unit-text lists, duplicate check | | `03_left_join_unit_lookup_template.sql` | **The LEFT JOIN** to add to the ETL (replace the placeholders) | | `04_example_omop_survey_measurement.sql` | The same join, ready to run on `omop_survey.measurement` | @@ -21,7 +21,7 @@ Scripts to fill `MEASUREMENT.unit_concept_id` from the AI-READI concept map (`.. ```sql SELECT m.*, COALESCE(f.unit_concept_id, u.unit_concept_id, 0) AS unit_concept_id, - COALESCE(f.unit_source_value, m.) AS unit_source_value + COALESCE(f.unit_source_value, NULLIF(TRIM(m.), '')) AS unit_source_value FROM m LEFT JOIN unit_lookup f ON f.key_type = 'field' AND f.lookup_key = TRIM(m.) @@ -38,7 +38,7 @@ LEFT JOIN unit_lookup u | key_type | lookup_key | Rows | Source in the concept map | |---|---|---|---| -| `field` | measurement field name | 88 | Unit rows named `_u`: the imported-lab unit fields (e.g. `import_potassium_u`) and the v1.4 fixed-unit rows for fields with no unit field (CBC, physical assessment, autorefractor, globulin, bilirubin, urine albumin/creatinine, MoCA scores and times; v1.6: the BUN/creatinine, A/G and waist/hip ratios). Plus `import_ldl_cholesterol_calculation`, whose unit field has a different name (`import_ldl_cholesterol_u`). | +| `field` | measurement field name | 90 | Unit rows named `_u`: the imported-lab unit fields (e.g. `import_potassium_u`) and the v1.4 fixed-unit rows for fields with no unit field (CBC, physical assessment, autorefractor, globulin, bilirubin, urine albumin/creatinine, MoCA scores and times; v1.6: the BUN/creatinine, A/G and waist/hip ratios; v1.7: `import_bun_creatinine_ratio` and the proposed `lbscat_nrbc`). Plus `import_ldl_cholesterol_calculation`, whose unit field has a different name (`import_ldl_cholesterol_u`). | | `string` | unit text | 25 | Generic Unit rows (blank `FIELD_ID`) plus `s`, `second`, `score` | Notes: @@ -46,7 +46,7 @@ Notes: - MoCA: score fields → 44777566 (score), time fields → 8555 (second). - Do not join on all Unit rows of the concept map by `SRC_CODE`: the same text appears in several rows (e.g. `g/dL` in 6), which would multiply measurement rows. `unit_lookup` avoids this. -### key_type = 'field' (88 rows) +### key_type = 'field' (90 rows) | lookup_key | unit_concept_id | unit_source_value | |---|---|---| @@ -74,6 +74,7 @@ Notes: | `import_ast_got` | 8923 | IU/L | | `import_bilirubin_total` | 8840 | mg/dL | | `import_bun` | 8840 | mg/dL | +| `import_bun_creatinine_ratio` | 8523 | ratio | | `import_buncreatinineratio` | 8523 | ratio | | `import_c_peptide` | 8725 | ng/L | | `import_calcium` | 8840 | mg/dL | @@ -103,6 +104,7 @@ Notes: | `lbscat_mch` | 8564 | pg | | `lbscat_mchc` | 8713 | g/dL | | `lbscat_mcv` | 8583 | fL | +| `lbscat_nrbc` | 8554 | % | | `lbscat_plt` | 8848 | x10E3/µL | | `lbscat_rbc` | 8815 | x10E6/µL | | `lbscat_rdw` | 8554 | % | diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/USAGE.md b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/USAGE.md index 317569a..405a3e6 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/USAGE.md +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/USAGE.md @@ -4,7 +4,7 @@ How to fill `MEASUREMENT.unit_concept_id` from the AI-READI concept map: create ## Step 1. Create the unit_lookup table (choose one) -**Option A: load the ready-made file (simplest).** `unit_concept_lookup.csv` (in this folder) is the complete lookup table, 113 rows: +**Option A: load the ready-made file (simplest).** `unit_concept_lookup.csv` (in this folder) is the complete lookup table, 115 rows: | Column | Meaning | |---|---| @@ -19,7 +19,7 @@ Upload it, set the path in `01a_load_unit_concept_lookup_csv.sql`, and run it. T | key_type | lookup_key | Rows | Example | |---|---|---|---| -| `field` | measurement field name | 88 | `lbscat_rbc` → 8815 (`x10E6/µL`) | +| `field` | measurement field name | 90 | `lbscat_rbc` → 8815 (`x10E6/µL`) | | `string` | unit text | 25 | `mEq/L` → 9557 | Each key appears once. @@ -35,7 +35,7 @@ Copy the query in `03_left_join_unit_lookup_template.sql` and replace the placeh ```sql SELECT m.*, COALESCE(f.unit_concept_id, u.unit_concept_id, 0) AS unit_concept_id, - COALESCE(f.unit_source_value, m.) AS unit_source_value + COALESCE(f.unit_source_value, NULLIF(TRIM(m.), '')) AS unit_source_value FROM m LEFT JOIN unit_lookup f ON f.key_type = 'field' AND f.lookup_key = TRIM(m.) @@ -49,7 +49,7 @@ LEFT JOIN unit_lookup u | `` | the REDCap field name | `lbscat_rbc` | | `` | the unit text on the record, if any (can be NULL) | `mEq/L` | -How it decides: the unit for the field first; if the field is not in `unit_lookup`, the unit text on the record; otherwise 0 (OMOP: no matching concept). `unit_source_value` is the unit text that goes with the concept chosen. +How it decides: the unit for the field first; if the field is not in `unit_lookup`, the unit text on the record; otherwise 0 (OMOP: no matching concept). `unit_source_value` is the unit text that goes with the concept chosen; when nothing matches, the record's own unit text is kept, trimmed, and blank text (e.g. a single space) becomes NULL. `04_example_omop_survey_measurement.sql` is the same join, ready to run on `omop_survey.measurement`, where the field name is the text before the first comma of `measurement_source_value`: ```sql @@ -85,7 +85,9 @@ f.lookup_key = TRIM(SPLIT_PART(m.measurement_source_value, ',', 1)) - **Exact text:** `x10E3/µL` and `x10E6/µL` use the micro sign µ (U+00B5). If your data uses the Greek letter μ (U+03BC), use `REPLACE(TRIM(m.), 'μ', 'µ')` in the second join. - **Missing values:** text such as "NA", "N/A" or "nan" in the unit column does not match anything, so those records get the field's unit (or 0). It is still best to load missing values as NULL. - **LDL:** the field `import_ldl_cholesterol_calculation` has its unit in the REDCap field `import_ldl_cholesterol_u`; `unit_lookup` includes this pair. -- **MoCA:** score fields get 44777566 (score) and time fields 8555 (second). +- **MoCA:** score fields get 44777566 (score) and time fields 8555 (second), through the `field` keys built from the v1.4 `_u` rows (concept map lines 2048–2077), one per MoCA measurement field. The original MoCA unit rows (`trails_time_unit`, `lettera_score_unit`, … lines 648–667) are not named after the fields and were never used; since v1.7 they have `Map_to_OMOP` = No and are not in `unit_lookup`. +- **Generic unit text:** the `string` keys `s`, `second` → 8555 and `score` → 44777566 (lines 668–670), like `mg/dL` or `mEq/L`, match on the unit text on the record. They are the fallback for records whose field has no `field` key. +- **Blank unit text:** the current OMOP data has `unit_source_value` = " " (a single space) on the MoCA records and a leading space on lab units (" mg/dL"). The joins trim the text, and the output writes blank text as NULL (v1.7 ETL rule 5). - **After a new concept map release:** reload the new `unit_concept_lookup.csv` (option A) or rerun `01_create_unit_lookup.sql` (option B). The CSV is regenerated with every release. ## Medication route (DRUG_EXPOSURE.route_concept_id) diff --git a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup.csv b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup.csv index f4d9530..d6c4060 100644 --- a/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup.csv +++ b/redCapDataDictionaryWithExtension/value-set-mapping-common/scripts/unit_concept_lookup.csv @@ -23,6 +23,7 @@ field,import_alt_got,8923,IU/L field,import_ast_got,8923,IU/L field,import_bilirubin_total,8840,mg/dL field,import_bun,8840,mg/dL +field,import_bun_creatinine_ratio,8523,ratio field,import_buncreatinineratio,8523,ratio field,import_c_peptide,8725,ng/L field,import_calcium,8840,mg/dL @@ -52,6 +53,7 @@ field,lbscat_hct,8554,% field,lbscat_mch,8564,pg field,lbscat_mchc,8713,g/dL field,lbscat_mcv,8583,fL +field,lbscat_nrbc,8554,% field,lbscat_plt,8848,x10E3/µL field,lbscat_rbc,8815,x10E6/µL field,lbscat_rdw,8554,%