From ce6499e0f841707ec972859e95fe9f760f72157e Mon Sep 17 00:00:00 2001 From: Clair Blacketer Date: Tue, 30 Apr 2024 12:03:05 -0400 Subject: [PATCH] Create cdm54ToolingSupport.html --- docs/cdm54ToolingSupport.html | 1462 +++++++++++++++++++++++++++++++++ 1 file changed, 1462 insertions(+) create mode 100644 docs/cdm54ToolingSupport.html diff --git a/docs/cdm54ToolingSupport.html b/docs/cdm54ToolingSupport.html new file mode 100644 index 0000000..cb33a3e --- /dev/null +++ b/docs/cdm54ToolingSupport.html @@ -0,0 +1,1462 @@ + + + + + + + + + + + + + +OMOP CDM v5.4 Detailed Tooling Support + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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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. 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 fields 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 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?
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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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ToolSupports CDM Field ifLink to resource used
DataQualityDashboardPart of Field Level checkshttps://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv
AchillesCovered by at least one Achilles analysishttps://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv
Atlas Data SourcesA statistic based on the field is shown in a ‘Data Sources’ +visualisationhttps://atlas-demo.ohdsi.org/
Atlas CohortUsed in te Atlas User Interface for cohort definition criteria +(directly, or via ‘Add attribute’)https://atlas-demo.ohdsi.org/
Feature ExtractionUsed in one of the Feature Extraction analyseshttps://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/
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General criteria: - ✔️ 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) - ❗ 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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Abbreviations 
PKPrimary Key
SVSource Value (for data quality / etl validation)
BCBackwards Compatibility, to support CDM <v5.4
FCForwards Compatibility, to easy support for CDM v6 in the +future.
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Person

+ ++++++++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
cdmTableNamecdmFieldNameSpecial FieldsDQD (v1.0)Achilles (v1.7)Atlas Cohort (v2.10)Atlas Cohort (v2.12)Atlas Data Sources (v2.12)Feature Extraction (v3.2)Comment
PERSONperson_idPK✔️✔️✔️✔️✔️✔️
PERSONgender_concept_id✔️✔️✔️✔️✔️✔️
PERSONyear_of_birth✔️✔️✔️✔️✔️✔️
PERSONmonth_of_birth✔️✔️❗❗❗❗
PERSONday_of_birth✔️❗❗❗❗❗
PERSONbirth_datetimeFC✔️❗❗❗❗❗
PERSONrace_concept_id✔️✔️✔️✔️✔️✔️
PERSONethnicity_concept_id✔️✔️✔️✔️✔️✔️
PERSONlocation_id✔️❗❗❗❗❗Achilles only does FK check
PERSONprovider_id✔️❗❗❗❗❗Achilles only does FK check
PERSONcare_site_id✔️❗❗❗❗❗Achilles only does FK check
PERSONperson_source_valueSV✔️❗❗❗❗❗
PERSONgender_source_valueSV✔️❗❗❗❗❗
PERSONgender_source_concept_id✔️❗❗❗❗❗
PERSONrace_source_valueSV✔️❗❗❗❗❗
PERSONrace_source_concept_id✔️❗❗❗❗❗
PERSONethnicity_source_valueSV✔️❗❗❗❗❗
PERSONethnicity_source_concept_id✔️❗❗❗❗❗
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Observation Period

+ ++++++++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
cdmTableNamecdmFieldNameSpecial FieldsDQD (v1.0)Achilles (v1.7)Atlas Cohort (v2.10)Atlas Cohort (v2.12)Atlas Data Sources (v2.12)Feature Extraction (v3.2)Comment
OBSERVATION_PERIODobservation_period_idPK✔️✔️✔️✔️✔️✔️
OBSERVATION_PERIODperson_idPid✔️✔️✔️✔️✔️✔️
OBSERVATION_PERIODobservation_period_start_date✔️✔️✔️✔️✔️✔️
OBSERVATION_PERIODobservation_period_end_date✔️✔️✔️✔️✔️✔️
OBSERVATION_PERIODperiod_type_concept_id✔️✔️✔️✔️❗❗
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Visit Occurrence

+ ++++++++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
cdmTableNamecdmFieldNameSpecial FieldsDQD (v1.0)Achilles (v1.7)Atlas Cohort (v2.10)Atlas Cohort (v2.12)Atlas Data Sources (v2.12)Feature Extraction (v3.2)Comment
VISIT_OCCURRENCEvisit_occurrence_idPK✔️✔️✔️✔️✔️✔️
VISIT_OCCURRENCEperson_idPid✔️✔️✔️✔️✔️✔️
VISIT_OCCURRENCEvisit_concept_id✔️✔️✔️✔️✔️✔️
VISIT_OCCURRENCEvisit_source_concept_id✔️✔️✔️✔️❗❗
VISIT_OCCURRENCEvisit_source_valueSV✔️❗❗❗❗❗
VISIT_OCCURRENCEvisit_start_date✔️✔️✔️✔️✔️✔️Achilles check 1900
VISIT_OCCURRENCEvisit_start_datetimeFC✔️❗❗❗❗❗
VISIT_OCCURRENCEvisit_end_date✔️✔️✔️✔️❗✔️
VISIT_OCCURRENCEvisit_end_datetimeFC✔️❗❗❗❗❗
VISIT_OCCURRENCEvisit_type_concept_id✔️✔️✔️✔️❗❗
VISIT_OCCURRENCEprovider_id✔️❗✔️✔️❗❗Atlas uses provider.specialty_concept_id
VISIT_OCCURRENCEcare_site_id✔️❗✔️✔️❗❗Achilles only does FK check, Atlas uses +care_site.place_of_service_concept_id
VISIT_OCCURRENCEadmitted_from_concept_id✔️❗❗❗❗❗
VISIT_OCCURRENCEadmitted_from_source_valueSV✔️❗❗❗❗❗Achilles check 1900
VISIT_OCCURRENCEdischarged_to_concept_id✔️❗❗❗❗❗
VISIT_OCCURRENCEdischarged_to_source_valueSV✔️❗❗❗❗❗Achilles check 1900
VISIT_OCCURRENCEpreceding_visit_occurrence_id✔️❗❗❗❗❗
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Episode

+ ++++++++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
cdmTableNamecdmFieldNameSpecial FieldsDQD (v1.0)Achilles (v1.7)Atlas Cohort (v2.10)Atlas Cohort (v2.12)Atlas Data Sources (v2.12)Feature Extraction (v3.2)Comment
EPISODEepisode_idPK✔️❗❗❗❗❗
EPISODEperson_idPid✔️❗❗❗❗❗
EPISODEepisode_concept_id✔️❗❗❗❗❗
EPISODEepisode_start_date✔️❗❗❗❗❗
EPISODEepisode_start_datetimeFC✔️❗❗❗❗❗
EPISODEepisode_end_date✔️❗❗❗❗❗
EPISODEepisode_end_datetimeFC✔️❗❗❗❗❗
EPISODEepisode_parent_id✔️❗❗❗❗❗
EPISODEepisode_number✔️❗❗❗❗❗
EPISODEepisode_object_concept_id✔️❗❗❗❗❗
EPISODEepisode_type_concept_id✔️❗❗❗❗❗
EPISODEepisode_source_valueSV✔️❗❗❗❗❗
EPISODEepisode_source_concept_id✔️❗❗❗❗❗
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This was an effort by the CDM Working Group in 2022. *Credits: Clair +Blacketer, Maxim Moinat, Nitin Park

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