mz-health/OMOP
mz-health
/
OMOP
mirror of https://github.com/OHDSI/CommonDataModel.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity
OMOP/rmd/cdm54ToolingSupport.RMD

111 lines
17 KiB
Plaintext
Raw Normal View History

initial tooling support page
2023-02-23 07:21:52 +00:00
---
title: "**OMOP CDM v5.4 Detailed Tooling Support**"
output:
html_document:
toc: TRUE
toc_float: TRUE
---
# Introduction
This tables below contain an overview of which standard OHDSI tools make use of which OMOP CDM fields.
The goal is to inform ETL developers, tooling developers and CDM extensions.
[DATALAD RUNCMD] Fix fieds typo === Do not change lines below === { "chain": [], "cmd": "git-sedi fieds fields", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^
2024-03-28 19:31:21 +00:00
- For ETL developers it helps to have guidance on which fields to prioritise in the mapping. Most value will be gained from populating fields support across the OHDSI tooling.
initial tooling support page
2023-02-23 07:21:52 +00:00
- For OHDSI tooling developers, this page provides insight in the gaps of support and can drive future development efforts.
[DATALAD RUNCMD] run codespell throughout fixing typos automagically === Do not change lines below === { "chain": [], "cmd": "codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^
2024-03-28 19:31:24 +00:00
- For CDM extensions, it helps to known what it means for an OMOP CDM table/field to be part of the standard. In other words: what OHDSI tooling do we at least expect to support the new extensions?
initial tooling support page
2023-02-23 07:21:52 +00:00
Currently four OHDSI tools have been evaluated: DataQualityDashboard, Achilles, Atlas (Data Sources and Cohort creation) and Feature Extraction.
## Criteria
Tool | Supports CDM Field if | Link to resource used
--- | --- | ---
DataQualityDashboard | Part of Field Level checks | https://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv
Achilles | Covered by at least one Achilles analysis | https://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv
Atlas Data Sources | A statistic based on the field is shown in a 'Data Sources' visualisation | https://atlas-demo.ohdsi.org/
Atlas Cohort | Used in te Atlas User Interface for cohort definition criteria (directly, or via 'Add attribute') | https://atlas-demo.ohdsi.org/
Feature Extraction | Used in one of the Feature Extraction analyses | https://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/
General criteria:
Full website, ddl, indices, and primary key updates
2024-03-28 19:09:22 +00:00
- `r emoji::emoji("heavy_check_mark")` if the field essential for OMOP CDM definition (Primary Key, Foreign Key) e.g. person_id not explicitly used, but essential. (if the PK is marked as False, it typically means the whole table is not used in the tool e.g. `_source_value` fields that are used for traceability in ETL)
- `r emoji::emoji("exclamation")` if field is used by the tool, but not in a meaningful way. e.g. `provider_id` in Achilles only checked for a valid foreign key to the provider table.
initial tooling support page
2023-02-23 07:21:52 +00:00
# Tooling Support for OMOP fields
[DATALAD RUNCMD] run codespell throughout fixing typos automagically === Do not change lines below === { "chain": [], "cmd": "codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^
2024-03-28 19:31:24 +00:00
**Abbreviations** |  
initial tooling support page
2023-02-23 07:21:52 +00:00
--- | ---
**PK** | Primary Key
**SV** | Source Value (for data quality / etl validation)
**BC** | Backwards Compatibility, to support CDM <v5.4
**FC** | Forwards Compatibility, to easy support for CDM v6 in the future.
## Person
cdmTableName | cdmFieldName | Special Fields | DQD (v1.0) | Achilles (v1.7) | Atlas Cohort (v2.10) | Atlas Cohort (v2.12) | Atlas Data Sources (v2.12) | Feature Extraction (v3.2) | Comment
--- | --- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | ---
Full website, ddl, indices, and primary key updates
2024-03-28 19:09:22 +00:00
PERSON | person_id | PK | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
PERSON | gender_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
PERSON | year_of_birth | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
PERSON | month_of_birth | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
PERSON | day_of_birth | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
PERSON | birth_datetime | FC | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
PERSON | race_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
PERSON | ethnicity_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
PERSON | location_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | Achilles only does FK check
PERSON | provider_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | Achilles only does FK check
PERSON | care_site_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | Achilles only does FK check
PERSON | person_source_value | SV | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
PERSON | gender_source_value | SV | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
PERSON | gender_source_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
PERSON | race_source_value | SV | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
PERSON | race_source_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
PERSON | ethnicity_source_value | SV | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
PERSON | ethnicity_source_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
initial tooling support page
2023-02-23 07:21:52 +00:00
## Observation Period
cdmTableName | cdmFieldName | Special Fields | DQD (v1.0) | Achilles (v1.7) | Atlas Cohort (v2.10) | Atlas Cohort (v2.12) | Atlas Data Sources (v2.12) | Feature Extraction (v3.2) | Comment
--- | --- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | ---
Full website, ddl, indices, and primary key updates
2024-03-28 19:09:22 +00:00
OBSERVATION_PERIOD | observation_period_id | PK | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
OBSERVATION_PERIOD | person_id | Pid | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
OBSERVATION_PERIOD | observation_period_start_date | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
OBSERVATION_PERIOD | observation_period_end_date | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
OBSERVATION_PERIOD | period_type_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
initial tooling support page
2023-02-23 07:21:52 +00:00
## Visit Occurrence
cdmTableName | cdmFieldName | Special Fields | DQD (v1.0) | Achilles (v1.7) | Atlas Cohort (v2.10) | Atlas Cohort (v2.12) | Atlas Data Sources (v2.12) | Feature Extraction (v3.2) | Comment
--- | --- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | ---
Full website, ddl, indices, and primary key updates
2024-03-28 19:09:22 +00:00
VISIT_OCCURRENCE | visit_occurrence_id | PK | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
VISIT_OCCURRENCE | person_id | Pid | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
VISIT_OCCURRENCE | visit_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` |
VISIT_OCCURRENCE | visit_source_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
VISIT_OCCURRENCE | visit_source_value | SV | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
VISIT_OCCURRENCE | visit_start_date | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | Achilles check 1900
VISIT_OCCURRENCE | visit_start_datetime | FC | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
VISIT_OCCURRENCE | visit_end_date | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("heavy_check_mark")` |
VISIT_OCCURRENCE | visit_end_datetime | FC | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
VISIT_OCCURRENCE | visit_type_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
VISIT_OCCURRENCE | provider_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | Atlas uses provider.specialty_concept_id
VISIT_OCCURRENCE | care_site_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | Achilles only does FK check, Atlas uses care_site.place_of_service_concept_id
VISIT_OCCURRENCE | admitted_from_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
VISIT_OCCURRENCE | admitted_from_source_value | SV | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | Achilles check 1900
VISIT_OCCURRENCE | discharged_to_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
VISIT_OCCURRENCE | discharged_to_source_value | SV | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | Achilles check 1900
VISIT_OCCURRENCE | preceding_visit_occurrence_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
initial tooling support page
2023-02-23 07:21:52 +00:00
## Episode
cdmTableName | cdmFieldName | Special Fields | DQD (v1.0) | Achilles (v1.7) | Atlas Cohort (v2.10) | Atlas Cohort (v2.12) | Atlas Data Sources (v2.12) | Feature Extraction (v3.2) | Comment
--- | --- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | ---
Full website, ddl, indices, and primary key updates
2024-03-28 19:09:22 +00:00
EPISODE | episode_id | PK | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | person_id | Pid | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_start_date | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_start_datetime | FC | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_end_date | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_end_datetime | FC | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_parent_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_number | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_object_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_type_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_source_value | SV | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
EPISODE | episode_source_concept_id | | `r emoji::emoji("heavy_check_mark")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` | `r emoji::emoji("exclamation")` |
initial tooling support page
2023-02-23 07:21:52 +00:00
This was an effort by the CDM Working Group in 2022.
*Credits: Clair Blacketer, Maxim Moinat, Nitin Park