111 lines
16 KiB
Plaintext
111 lines
16 KiB
Plaintext
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---
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title: "**OMOP CDM v5.4 Detailed Tooling Support**"
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output:
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html_document:
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toc: TRUE
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toc_float: TRUE
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---
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# Introduction
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This tables below contain an overview of which standard OHDSI tools make use of which OMOP CDM fields.
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The goal is to inform ETL developers, tooling developers and CDM extensions.
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- For ETL developers it helps to have guidance on which fieds to prioritise in the mapping. Most value will be gained from populating fields support across the OHDSI tooling.
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- For OHDSI tooling developers, this page provides insight in the gaps of support and can drive future development efforts.
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- For CDM extenstions, 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?
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Currently four OHDSI tools have been evaluated: DataQualityDashboard, Achilles, Atlas (Data Sources and Cohort creation) and Feature Extraction.
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## Criteria
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Tool | Supports CDM Field if | Link to resource used
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--- | --- | ---
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DataQualityDashboard | Part of Field Level checks | https://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv
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Achilles | Covered by at least one Achilles analysis | https://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv
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Atlas Data Sources | A statistic based on the field is shown in a 'Data Sources' visualisation | https://atlas-demo.ohdsi.org/
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Atlas Cohort | Used in te Atlas User Interface for cohort definition criteria (directly, or via 'Add attribute') | https://atlas-demo.ohdsi.org/
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Feature Extraction | Used in one of the Feature Extraction analyses | https://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/
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General criteria:
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- `r emo::ji("white 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)
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- `r emo::ji("warning")` 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.
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# Tooling Support for OMOP fields
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**Abbrevations** |
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--- | ---
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**PK** | Primary Key
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**SV** | Source Value (for data quality / etl validation)
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**BC** | Backwards Compatibility, to support CDM <v5.4
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**FC** | Forwards Compatibility, to easy support for CDM v6 in the future.
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## Person
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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
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--- | --- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | ---
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PERSON | person_id | PK | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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PERSON | gender_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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PERSON | year_of_birth | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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PERSON | month_of_birth | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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PERSON | day_of_birth | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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PERSON | birth_datetime | FC | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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PERSON | race_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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PERSON | ethnicity_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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PERSON | location_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("warning")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | Achilles only does FK check
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PERSON | provider_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("warning")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | Achilles only does FK check
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PERSON | care_site_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("warning")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | Achilles only does FK check
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PERSON | person_source_value | SV | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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PERSON | gender_source_value | SV | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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PERSON | gender_source_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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PERSON | race_source_value | SV | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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PERSON | race_source_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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PERSON | ethnicity_source_value | SV | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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PERSON | ethnicity_source_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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## Observation Period
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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
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--- | --- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | ---
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OBSERVATION_PERIOD | observation_period_id | PK | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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OBSERVATION_PERIOD | person_id | Pid | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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OBSERVATION_PERIOD | observation_period_start_date | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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OBSERVATION_PERIOD | observation_period_end_date | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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OBSERVATION_PERIOD | period_type_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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## Visit Occurrence
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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
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--- | --- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | ---
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VISIT_OCCURRENCE | visit_occurrence_id | PK | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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VISIT_OCCURRENCE | person_id | Pid | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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VISIT_OCCURRENCE | visit_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` |
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VISIT_OCCURRENCE | visit_source_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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VISIT_OCCURRENCE | visit_source_value | SV | `r emo::ji("white heavy check mark")` | `r emo::ji("warning")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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VISIT_OCCURRENCE | visit_start_date | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | Achilles check 1900
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VISIT_OCCURRENCE | visit_start_datetime | FC | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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VISIT_OCCURRENCE | visit_end_date | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("white heavy check mark")` |
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VISIT_OCCURRENCE | visit_end_datetime | FC | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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VISIT_OCCURRENCE | visit_type_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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VISIT_OCCURRENCE | provider_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | Atlas uses provider.specialty_concept_id
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VISIT_OCCURRENCE | care_site_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("warning")` | `r emo::ji("white heavy check mark")` | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | Achilles only does FK check, Atlas uses care_site.place_of_service_concept_id
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VISIT_OCCURRENCE | admitted_from_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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VISIT_OCCURRENCE | admitted_from_source_value | SV | `r emo::ji("white heavy check mark")` | `r emo::ji("warning")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | Achilles check 1900
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VISIT_OCCURRENCE | discharged_to_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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VISIT_OCCURRENCE | discharged_to_source_value | SV | `r emo::ji("white heavy check mark")` | `r emo::ji("warning")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | Achilles check 1900
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VISIT_OCCURRENCE | preceding_visit_occurrence_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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## Episode
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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
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--- | --- | :---: | :---: | :---: | :---: | :---: | :---: | :---: | ---
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EPISODE | episode_id | PK | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | person_id | Pid | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_start_date | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_start_datetime | FC | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_end_date | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_end_datetime | FC | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_parent_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_number | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_object_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_type_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_source_value | SV | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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EPISODE | episode_source_concept_id | | `r emo::ji("white heavy check mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` | `r emo::ji("cross_mark")` |
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This was an effort by the CDM Working Group in 2022.
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*Credits: Clair Blacketer, Maxim Moinat, Nitin Park
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