From 1364d6b7fe696a29d71ecf43aec944bffe4a84ba Mon Sep 17 00:00:00 2001 From: Clair Blacketer Date: Fri, 12 Apr 2024 13:26:05 -0400 Subject: [PATCH] adding custom concept page --- docs/background.html | 3 + docs/cdm30.html | 3 + docs/cdm53.html | 3 + docs/cdm531.html | 3 + docs/cdm54.html | 3 + docs/cdm54Changes.html | 3 + docs/cdm54ToolingSupport.html | 1459 --- docs/cdm54erd.html | 3 + docs/cdm60.html | 13734 +--------------------------- docs/cdmDecisionTree.html | 3 + docs/cdmPrivacy.html | 3 + docs/cdmRPackage.html | 3 + docs/cdmRefreshProcess.html | 3 + docs/cdmRequestProcess.html | 3 + docs/contactVocab.html | 3 + docs/contribute.html | 3 + docs/customConcepts.html | 748 ++ docs/dataModelConventions.html | 3 + docs/download.html | 3 + docs/drug_dose.html | 3 + docs/ehrObsPeriods.html | 3 + docs/faq.html | 3 + docs/index.html | 19 +- docs/indices-primary-foreign.html | 3 + docs/leaveAsIs.html | 3 + docs/localChange.html | 3 + docs/networkUseCase.html | 3 + docs/oncology.html | 3 + docs/queries.html | 3 + docs/reviewProposals.html | 3 + docs/sqlScripts.html | 5 +- docs/useCaseN.html | 3 + docs/useCaseY.html | 3 + docs/vocabN.html | 3 + docs/vocabRequest.html | 3 + docs/vocabY.html | 3 + docs/vocabulary.html | 3 + rmd/_site.yml | 2 + rmd/customConcepts.Rmd | 99 + 39 files changed, 963 insertions(+), 15199 deletions(-) delete mode 100644 docs/cdm54ToolingSupport.html create mode 100644 docs/customConcepts.html create mode 100644 rmd/customConcepts.Rmd diff --git a/docs/background.html b/docs/background.html index 936c4136..99117cdb 100644 --- a/docs/background.html +++ b/docs/background.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
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  • + Custom Concepts +
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  • Patient Privacy and OMOP
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  • Patient Privacy and OMOP
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  • Patient Privacy and OMOP
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  • diff --git a/docs/cdm54.html b/docs/cdm54.html index 96aa17e8..f6c2729a 100644 --- a/docs/cdm54.html +++ b/docs/cdm54.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
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  • diff --git a/docs/cdm54Changes.html b/docs/cdm54Changes.html index bd2d2af2..5c52c676 100644 --- a/docs/cdm54Changes.html +++ b/docs/cdm54Changes.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
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  • + Custom Concepts +
  • diff --git a/docs/cdm54ToolingSupport.html b/docs/cdm54ToolingSupport.html deleted file mode 100644 index 021f2a29..00000000 --- a/docs/cdm54ToolingSupport.html +++ /dev/null @@ -1,1459 +0,0 @@ - - - - - - - - - - - - - -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✔️❗❗❗❗❗
    -

    This was an effort by the CDM Working Group in 2022. *Credits: Clair -Blacketer, Maxim Moinat, Nitin Park

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  • Patient Privacy and OMOP
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  • Patient Privacy and OMOP
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    person

    CONDITION_STATUS_CONCEPT_ID 32891 for ‘Cause of death’.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -person_id - -It is assumed that every person with a different unique identifier is in -fact a different person and should be treated independently. - -Any person linkage that needs to occur to uniquely identify Persons -ought to be done prior to writing this table. This identifier can be the -original id from the source data provided if it is an integer, otherwise -it can be an autogenerated number. - -bigint - -Yes - -Yes - -No - - -
    -gender_concept_id - -This field is meant to capture the biological sex at birth of the -Person. This field should not be used to study gender identity issues. - -Use the gender or sex value present in the data under the assumption -that it is the biological sex at birth. If the source data captures -gender identity it should be stored in the OBSERVATION -table. Accepted -gender concepts - -integer - -Yes - -No - -Yes - -CONCEPT - -Gender -
    -year_of_birth - -Compute age using year_of_birth. - -For data sources with date of birth, the year should be extracted. For -data sources where the year of birth is not available, the approximate -year of birth could be derived based on age group categorization, if -available. If no year of birth is available all the person’s data should -be dropped from the CDM instance. - -integer - -Yes - -No - -No - - -
    -month_of_birth - - -For data sources that provide the precise date of birth, the month -should be extracted and stored in this field. - -integer - -No - -No - -No - - -
    -day_of_birth - - -For data sources that provide the precise date of birth, the day should -be extracted and stored in this field. - -integer - -No - -No - -No - - -
    -birth_datetime - - -This field is not required but highly encouraged. For data sources that -provide the precise datetime of birth, that value should be stored in -this field. If birth_datetime is not provided in the source, use the -following logic to infer the date: If day_of_birth is null and -month_of_birth is not null then use the first of the month in that year. -If month_of_birth is null or if day_of_birth AND month_of_birth are both -null and the person has records during their year of birth then use the -date of the earliest record, otherwise use the 15th of June of that -year. If time of birth is not given use midnight (00:00:0000). - -datetime - -No - -No - -No - - -
    -death_datetime - -This field is the death date to be used in analysis, as determined by -the ETL logic. Any additional information about a Person’s death is -stored in the OBSERVATION -table with the concept_id 4306655 -or in the CONDITION_OCCURRENCE . - -If there are multiple dates of death given for a Person, choose the one -that is deemed most reliable. This may be a discharge from the hospital -where the Person is listed as deceased or it could be latest death date -provided. If a patient has clinical activity more than 60 days after the -death date given in the source, it is a viable option to drop the death -record as it may have been falsely reported. Similarly, if the death -record is from a reputable source (e.g. government provided information) -it is also a viable option to remove event records that occur in the -data > 60 days after death. - -datetime - -No - - - - -
    -race_concept_id - -This field captures race or ethnic background of the person. - -Only use this field if you have information about race or ethnic -background. The Vocabulary contains Concepts about the main races and -ethnic backgrounds in a hierarchical system. Due to the imprecise nature -of human races and ethnic backgrounds, this is not a perfect system. -Mixed races are not supported. If a clear race or ethnic background -cannot be established, use Concept_Id 0. Accepted -Race Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Race -
    -ethnicity_concept_id - -This field captures Ethnicity as defined by the Office of Management and -Budget (OMB) of the US Government: it distinguishes only between -“Hispanic” and “Not Hispanic”. Races and ethnic backgrounds are not -stored here. - -Only use this field if you have US-based data and a source of this -information. Do not attempt to infer Ethnicity from the race or ethnic -background of the Person. Accepted -ethnicity concepts - -integer - -Yes - -No - -Yes - -CONCEPT - -Ethnicity -
    -location_id - -The location refers to the physical address of the person. This field -should capture the last known location of the person. Any prior -locations are captured in the LOCATION_HISTORY -table. - -Put the location_id from the LOCATION table here that represents the -most granular location information for the person. This could represent -anything from postal code or parts thereof, state, or county for -example. Since many databases contain deidentified data, it is common -that the precision of the location is reduced to prevent -re-identification. This field should capture the last known location. -Any prior locations are captured in the LOCATION_HISTORY -table. - -bigint - -No - -No - -Yes - -LOCATION - -
    -provider_id - -The Provider refers to the last known primary care provider (General -Practitioner). - -Put the provider_id from the PROVIDER table of the last known general -practitioner of the person. If there are multiple providers, it is up to -the ETL to decide which to put here. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -care_site_id - -The Care Site refers to where the Provider typically provides the -primary care. - - -bigint - -No - -No - -Yes - -CARE_SITE - -
    -person_source_value - -Use this field to link back to persons in the source data. This is -typically used for error checking of ETL logic. - -Some use cases require the ability to link back to persons in the source -data. This field allows for the storing of the person value as it -appears in the source. This field is not required but strongly -recommended. - -varchar(50) - -No - -No - -No - - -
    -gender_source_value - -This field is used to store the biological sex of the person from the -source data. It is not intended for use in standard analytics but for -reference only. - -Put the biological sex of the person as it appears in the source data. - -varchar(50) - -No - -No - -No - - -
    -gender_source_concept_id - -Due to the small number of options, this tends to be zero. - -If the source data codes biological sex in a non-standard vocabulary, -store the concept_id here, otherwise set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -race_source_value - -This field is used to store the race of the person from the source data. -It is not intended for use in standard analytics but for reference only. - -Put the race of the person as it appears in the source data. - -varchar(50) - -No - -No - -No - - -
    -race_source_concept_id - -Due to the small number of options, this tends to be zero. - -If the source data codes race in an OMOP supported vocabulary store the -concept_id here, otherwise set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -ethnicity_source_value - -This field is used to store the ethnicity of the person from the source -data. It is not intended for use in standard analytics but for reference -only. - -If the person has an ethnicity other than the OMB standard of “Hispanic” -or “Not Hispanic” store that value from the source data here. - -varchar(50) - -No - -No - -No - - -
    -ethnicity_source_concept_id - -Due to the small number of options, this tends to be zero. - -If the source data codes ethnicity in an OMOP supported vocabulary, -store the concept_id here, otherwise set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -

    observation_period

    @@ -1255,198 +622,6 @@

    observation_period

    of Clinical Events generally are not used to generate OBSERVATION_PERIOD records around the time they are referring to. Any two overlapping or adjacent OBSERVATION_PERIOD records have to be merged into one.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -observation_period_id - -A Person can have multiple discrete Observation Periods which are -identified by the Observation_Period_Id. - -Assign a unique observation_period_id to each discrete Observation -Period for a Person. - -bigint - -Yes - -Yes - -No - - -
    -person_id - -The Person ID of the PERSON record for which the Observation Period is -recorded. - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -observation_period_start_date - -Use this date to determine the start date of the Observation Period - -It is often the case that the idea of Observation Periods does not exist -in source data. In those cases, the observation_period_start_date can be -inferred as the earliest Event date available for the Person. In -insurance claim data, the Observation Period can be considered as the -time period the Person is enrolled with a payer. If a Person switches -plans but stays with the same payer, and therefore capturing of data -continues, that change would be captured in PAYER_PLAN_PERIOD. - -date - -Yes - -No - -No - - -
    -observation_period_end_date - -Use this date to determine the end date of the period for which we can -assume that all events for a Person are recorded. - -It is often the case that the idea of Observation Periods does not exist -in source data. In those cases, the observation_period_end_date can be -inferred as the last Event date available for the Person. In insurance -claim data, the Observation Period can be considered as the time period -the Person is enrolled with a payer. - -date - -Yes - -No - -No - - -
    -period_type_concept_id - -This field can be used to determine the provenance of the Observation -Period as in whether the period was determined from an insurance -enrollment file, EHR healthcare encounters, or other sources. - -Choose the observation_period_type_concept_id that best represents how -the period was determined. Accepted -Concepts. - -Integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -

    visit_occurrence

    @@ -1545,571 +720,6 @@

    visit_occurrence

    can be associated with a Visit through the PROVIDER_ID field, or indirectly through PROCEDURE_OCCURRENCE records linked both to the VISIT and PROVIDER tables.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -visit_occurrence_id - -Use this to identify unique interactions between a person and the health -care system. This identifier links across the other CDM event tables to -associate events with a visit. - -This should be populated by creating a unique identifier for each unique -interaction between a person and the healthcare system where the person -receives a medical good or service over a span of time. - -bigint - -Yes - -Yes - -No - - -
    -person_id - - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -visit_concept_id - -This field contains a concept id representing the kind of visit, like -inpatient or outpatient. All concepts in this field should be standard -and belong to the Visit domain. - -Populate this field based on the kind of visit that took place for the -person. For example this could be “Inpatient Visit”, “Outpatient Visit”, -“Ambulatory Visit”, etc. This table will contain standard concepts in -the Visit domain. These concepts are arranged in a hierarchical -structure to facilitate cohort definitions by rolling up to generally -familiar Visits adopted in most healthcare systems worldwide. - -integer - -Yes - -No - -Yes - -CONCEPT - -Visit -
    -visit_start_date - -For inpatient visits, the start date is typically the admission date. -For outpatient visits the start date and end date will be the same. - -When populating visit_start_date, you should think about the patient -experience to make decisions on how to define visits. In the case of an -inpatient visit this should be the date the patient was admitted to the -hospital or institution. In all other cases this should be the date of -the patient-provider interaction. - -date - -No - -No - -No - - -
    -visit_start_datetime - - -If no time is given for the start date of a visit, set it to midnight -(00:00:0000). - -datetime - -Yes - -No - -No - - -
    -visit_end_date - -For inpatient visits the end date is typically the discharge date. - -Visit end dates are mandatory. If end dates are not provided in the -source there are three ways in which to derive them: Outpatient Visit: -visit_end_datetime = visit_start_datetime Emergency Room Visit: -visit_end_datetime = visit_start_datetime Inpatient Visit: Usually there -is information about discharge. If not, you should be able to derive the -end date from the sudden decline of activity or from the absence of -inpatient procedures/drugs. Non-hospital institution Visits: -Particularly for claims data, if end dates are not provided assume the -visit is for the duration of month that it occurs. For Inpatient Visits -ongoing at the date of ETL, put date of processing the data into -visit_end_datetime and visit_type_concept_id with 32220 “Still patient” -to identify the visit as incomplete. All other Visits: -visit_end_datetime = visit_start_datetime. If this is a one-day visit -the end date should match the start date. - -date - -No - -No - -No - - -
    -visit_end_datetime - - -If no time is given for the end date of a visit, set it to midnight -(00:00:0000). - -datetime - -Yes - -No - -No - - -
    -visit_type_concept_id - -Use this field to understand the provenance of the visit record, or -where the record comes from. - -Populate this field based on the provenance of the visit record, as in -whether it came from an EHR record or billing claim. - -Integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -provider_id - -There will only be one provider per visit record and the ETL document -should clearly state how they were chosen (attending, admitting, etc.). -If there are multiple providers associated with a visit in the source, -this can be reflected in the event tables (CONDITION_OCCURRENCE, -PROCEDURE_OCCURRENCE, etc.) or in the VISIT_DETAIL table. - -If there are multiple providers associated with a visit, you will need -to choose which one to put here. The additional providers can be stored -in the visit_detail table. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -care_site_id - -This field provides information about the care site where the visit took -place. - -There should only be one care site associated with a visit. - -bigint - -No - -No - -Yes - -CARE_SITE - -
    -visit_source_value - -This field houses the verbatim value from the source data representing -the kind of visit that took place (inpatient, outpatient, emergency, -etc.) - -If there is information about the kind of visit in the source data that -value should be stored here. If a visit is an amalgamation of visits -from the source then use a hierarchy to choose the visit source value, -such as IP -> ER-> OP. This should line up with the logic chosen -to determine how visits are created. - -varchar(50) - -No - -No - -No - - -
    -visit_source_concept_id - - -If the visit source value is coded in the source data using an OMOP -supported vocabulary put the concept id representing the source value -here. If not available set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -admitted_from_concept_id - -Use this field to determine where the patient was admitted from. This -concept is part of the visit domain and can indicate if a patient was -admitted to the hospital from a long-term care facility, for example. - -If available, map the admitted_from_source_value to a standard concept -in the visit domain. If not available set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -Visit -
    -admitted_from_source_value - - -This information may be called something different in the source data -but the field is meant to contain a value indicating where a person was -admitted from. Typically this applies only to visits that have a length -of stay, like inpatient visits or long-term care visits. - -varchar(50) - -No - -No - -No - - -
    -discharge_to_concept_id - -Use this field to determine where the patient was discharged to after a -visit. This concept is part of the visit domain and can indicate if a -patient was discharged to home or sent to a long-term care facility, for -example. - -If available, map the discharge_to_source_value to a standard concept in -the visit domain. If not available set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -Visit -
    -discharge_to_source_value - - -This information may be called something different in the source data -but the field is meant to contain a value indicating where a person was -discharged to after a visit, as in they went home or were moved to -long-term care. Typically this applies only to visits that have a length -of stay of a day or more. - -varchar(50) - -No - -No - -No - - -
    -preceding_visit_occurrence_id - -Use this field to find the visit that occurred for the person prior to -the given visit. There could be a few days or a few years in between. - -The preceding_visit_id can be used to link a visit immediately preceding -the current visit. Note this is not symmetrical, and there is no such -thing as a “following_visit_id”. - -bigint - -No - -No - -Yes - -VISIT_OCCURRENCE - -

    visit_detail

    @@ -2146,639 +756,6 @@

    visit_detail

    href="https://athena.ohdsi.org/search-terms/terms/9201">9201 and the VISIT_DETAIL_CONCEPT_IDs either to 9201 or its children to indicate where the patient was in the hospital at the time of care.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -visit_detail_id - -Use this to identify unique interactions between a person and the health -care system. This identifier links across the other CDM event tables to -associate events with a visit detail. - -This should be populated by creating a unique identifier for each unique -interaction between a person and the healthcare system where the person -receives a medical good or service over a span of time. - -bigint - -Yes - -Yes - -No - - -
    -person_id - - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -visit_detail_concept_id - -This field contains a concept id representing the kind of visit detail, -like inpatient or outpatient. All concepts in this field should be -standard and belong to the Visit domain. - -Populate this field based on the kind of visit that took place for the -person. For example this could be “Inpatient Visit”, “Outpatient Visit”, -“Ambulatory Visit”, etc. This table will contain standard concepts in -the Visit domain. These concepts are arranged in a hierarchical -structure to facilitate cohort definitions by rolling up to generally -familiar Visits adopted in most healthcare systems worldwide. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Visit -
    -visit_detail_start_date - -This is the date of the start of the encounter. This may or may not be -equal to the date of the Visit the Visit Detail is associated with. - -When populating visit_start_date, you should think about the patient -experience to make decisions on how to define visits. Most likely this -should be the date of the patient-provider interaction. - -date - -Yes - -No - -No - - -
    -visit_detail_start_datetime - - -If no time is given for the start date of a visit, set it to midnight -(00:00:0000). - -datetime - -No - -No - -No - - -
    -visit_detail_end_date - -This the end date of the patient-provider interaction. - -Visit Detail end dates are mandatory. If end dates are not provided in -the source there are three ways in which to derive them:<br> - -Outpatient Visit Detail: visit_detail_end_datetime = -visit_detail_start_datetime - Emergency Room Visit Detail: -visit_detail_end_datetime = visit_detail_start_datetime - Inpatient -Visit Detail: Usually there is information about discharge. If not, you -should be able to derive the end date from the sudden decline of -activity or from the absence of inpatient procedures/drugs. - -Non-hospital institution Visit Details: Particularly for claims data, if -end dates are not provided assume the visit is for the duration of month -that it occurs.<br> For Inpatient Visit Details ongoing at the -date of ETL, put date of processing the data into -visit_detai_end_datetime and visit_detail_type_concept_id with 32220 -“Still patient” to identify the visit as incomplete. All other Visits -Details: visit_detail_end_datetime = visit_detail_start_datetime. - -date - -Yes - -No - -No - - -
    -visit_detail_end_datetime - - -If no time is given for the end date of a visit, set it to midnight -(00:00:0000). - -datetime - -No - -No - -No - - -
    -visit_detail_type_concept_id - -Use this field to understand the provenance of the visit detail record, -or where the record comes from. - -Populate this field based on the provenance of the visit detail record, -as in whether it came from an EHR record or billing claim. Accepted -Concepts. - -Integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -provider_id - -There will only be one provider per visit record and -the ETL document should clearly state how they were chosen (attending, -admitting, etc.). This is a typical reason for leveraging the -VISIT_DETAIL table as even though each VISIT_DETAIL record can only have -one provider, there is no limit to the number of VISIT_DETAIL records -that can be associated to a VISIT_OCCURRENCE record. - -The additional providers associated to a Visit can be stored in this -table where each VISIT_DETAIL record represents a different provider. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -care_site_id - -This field provides information about the Care Site where the Visit -Detail took place. - -There should only be one Care Site associated with a Visit Detail. - -bigint - -No - -No - -Yes - -CARE_SITE - -
    -visit_detail_source_value - -This field houses the verbatim value from the source data representing -the kind of visit detail that took place (inpatient, outpatient, -emergency, etc.) - -If there is information about the kind of visit detail in the source -data that value should be stored here. If a visit is an amalgamation of -visits from the source then use a hierarchy to choose the -VISIT_DETAIL_SOURCE_VALUE, such as IP -> ER-> OP. This should line -up with the logic chosen to determine how visits are created. - -varchar(50) - -No - -No - -No - - -
    -visit_detail_source_concept_id - - -If the VISIT_DETAIL_SOURCE_VALUE is coded in the source data using an -OMOP supported vocabulary put the concept id representing the source -value here. If not available, map to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -admitted_from_concept_id - - -This information may be called something different in the source data -but the field is meant to contain a value indicating where a person was -admitted from. Typically this applies only to visits that have a length -of stay, like inpatient visits or long-term care visits. - -varchar(50) - -No - -No - -No - - -
    -admitted_from_source_value - -Use this field to determine where the patient was admitted from. This -concept is part of the visit domain and can indicate if a patient was -admitted to the hospital from a long-term care facility, for example. - -If available, map the admitted_from_source_value to a standard concept -in the visit domain. If not available, map to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Visit -
    -discharge_to_source_value - - -This information may be called something different in the source data -but the field is meant to contain a value indicating where a person was -discharged to after a visit, as in they went home or were moved to -long-term care. Typically this applies only to visits that have a length -of stay of a day or more. - -varchar(50) - -No - -No - -No - - -
    -discharge_to_concept_id - -Use this field to determine where the patient was discharged to after a -visit detail record. This concept is part of the visit domain and can -indicate if a patient was discharged to home or sent to a long-term care -facility, for example. - -If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in -the Visit domain. If not available, set to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Visit -
    -preceding_visit_detail_id - -Use this field to find the visit detail that occurred for the person -prior to the given visit detail record. There could be a few days or a -few years in between. - -The PRECEDING_VISIT_DETAIL_ID can be used to link a visit immediately -preceding the current Visit Detail. Note this is not symmetrical, and -there is no such thing as a “following_visit_id”. - -bigint - -No - -No - -Yes - -VISIT_DETAIL - -
    -visit_detail_parent_id - -Use this field to find the visit detail that subsumes the given visit -detail record. This is used in the case that a visit detail record needs -to be nested beyond the VISIT_OCCURRENCE/VISIT_DETAIL relationship. - -If there are multiple nested levels to how Visits are represented in the -source, the VISIT_DETAIL_PARENT_ID can be used to record this -relationship. - -bigint - -No - -No - -Yes - -VISIT_DETAIL - -
    -visit_occurrence_id - -Use this field to link the VISIT_DETAIL record to its VISIT_OCCURRENCE. - -Put the VISIT_OCCURRENCE_ID that subsumes the VISIT_DETAIL record here. - -bigint - -Yes - -No - -Yes - -VISIT_OCCURRENCE - -
    @@ -2821,547 +798,6 @@

    condition_occurrence

    ETL Conventions

    Source codes and source text fields mapped to Standard Concepts of the Condition Domain have to be recorded here.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -condition_occurrence_id - -The unique key given to a condition record for a person. Refer to the -ETL for how duplicate conditions during the same visit were handled. - -Each instance of a condition present in the source data should be -assigned this unique key. In some cases, a person can have multiple -records of the same condition within the same visit. It is valid to keep -these duplicates and assign them individual, unique, -CONDITION_OCCURRENCE_IDs, though it is up to the ETL how they should be -handled. - -bigint - -Yes - -Yes - -No - - -
    -person_id - -The PERSON_ID of the PERSON for whom the condition is recorded. - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -condition_concept_id - -The CONDITION_CONCEPT_ID field is recommended for primary use in -analyses, and must be used for network studies. This is the standard -concept mapped from the source value which represents a condition - -The CONCEPT_ID that the CONDITION_SOURCE_VALUE maps to. Only records -whose source values map to concepts with a domain of “Condition” should -go in this table. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Condition -
    -condition_start_date - -Use this date to determine the start date of the condition - -Most often data sources do not have the idea of a start date for a -condition. Rather, if a source only has one date associated with a -condition record it is acceptable to use that date for both the -CONDITION_START_DATE and the CONDITION_END_DATE. - -date - -Yes - -No - -No - - -
    -condition_start_datetime - - -If a source does not specify datetime the convention is to set the time -to midnight (00:00:0000) - -datetime - -No - -No - -No - - -
    -condition_end_date - -Use this date to determine the end date of the condition - -Most often data sources do not have the idea of a start date for a -condition. Rather, if a source only has one date associated with a -condition record it is acceptable to use that date for both the -CONDITION_START_DATE and the CONDITION_END_DATE. - -date - -No - -No - -No - - -
    -condition_end_datetime - - -If a source does not specify datetime the convention is to set the time -to midnight (00:00:0000) - -datetime - -No - -No - -No - - -
    -condition_type_concept_id - -This field can be used to determine the provenance of the Condition -record, as in whether the condition was from an EHR system, insurance -claim, registry, or other sources. - -Choose the condition_type_concept_id that best represents the provenance -of the record. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -condition_status_concept_id - -This concept represents the point during the visit the diagnosis was -given (admitting diagnosis, final diagnosis), whether the diagnosis was -determined due to laboratory findings, if the diagnosis was -exclusionary, or if it was a preliminary diagnosis, among others. - -Choose the Concept in the Condition Status domain that best represents -the point during the visit when the diagnosis was given. These can -include admitting diagnosis, principal diagnosis, and secondary -diagnosis. If not available, set to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -stop_reason - -The Stop Reason indicates why a Condition is no longer valid with -respect to the purpose within the source data. Note that a Stop Reason -does not necessarily imply that the condition is no longer occurring. - -This information is often not populated in source data and it is a valid -etl choice to leave it blank if the information does not exist. - -varchar(20) - -No - -No - -No - - -
    -provider_id - -The provider associated with condition record, e.g. the provider who -made the diagnosis or the provider who recorded the symptom. - -The ETL may need to make a choice as to which PROVIDER_ID to put here. -Based on what is available this may or may not be different than the -provider associated with the overall VISIT_OCCURRENCE record, for -example the admitting vs attending physician on an EHR record. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -visit_occurrence_id - -The visit during which the condition occurred. - -Depending on the structure of the source data, this may have to be -determined based on dates. If a CONDITION_START_DATE occurs within the -start and end date of a Visit it is a valid ETL choice to choose the -VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not -explicitly stated in the data. While not required, an attempt should be -made to locate the VISIT_OCCURRENCE_ID of the CONDITION_OCCURRENCE -record. - -bigint - -No - -No - -Yes - -VISIT_OCCURRENCE - -
    -visit_detail_id - -The VISIT_DETAIL record during which the condition occurred. For -example, if the person was in the ICU at the time of the diagnosis the -VISIT_OCCURRENCE record would reflect the overall hospital stay and the -VISIT_DETAIL record would reflect the ICU stay during the hospital -visit. - -Same rules apply as for the VISIT_OCCURRENCE_ID. - -bigint - -No - -No - -Yes - -VISIT_DETAIL - -
    -condition_source_value - -This field houses the verbatim value from the source data representing -the condition that occurred. For example, this could be an ICD10 or Read -code. - -This code is mapped to a Standard Condition Concept in the Standardized -Vocabularies and the original code is stored here for reference. - -varchar(50) - -No - -No - -No - - -
    -condition_source_concept_id - -This is the concept representing the condition source value and may not -necessarily be standard. This field is discouraged from use in analysis -because it is not required to contain Standard Concepts that are used -across the OHDSI community, and should only be used when Standard -Concepts do not adequately represent the source detail for the Condition -necessary for a given analytic use case. Consider using -CONDITION_CONCEPT_ID instead to enable standardized analytics that can -be consistent across the network. - -If the CONDITION_SOURCE_VALUE is coded in the source data using an OMOP -supported vocabulary put the concept id representing the source value -here. If not available, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -condition_status_source_value - -This field houses the verbatim value from the source data representing -the condition status. - -This information may be called something different in the source data -but the field is meant to contain a value indicating when and how a -diagnosis was given to a patient. This source value is mapped to a -standard concept which is stored in the CONDITION_STATUS_CONCEPT_ID -field. - -varchar(50) - -No - -No - -No - - -

    drug_exposure

    @@ -3394,791 +830,6 @@

    drug_exposure

    same drug or procedures the ETL should not de-dupe them unless there is probable reason to believe the item is a true data duplicate. Take note on how to handle refills for prescriptions written.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -drug_exposure_id - -The unique key given to records of drug dispensings or administrations -for a person. Refer to the ETL for how duplicate drugs during the same -visit were handled. - -Each instance of a drug dispensing or administration present in the -source data should be assigned this unique key. In some cases, a person -can have multiple records of the same drug within the same visit. It is -valid to keep these duplicates and assign them individual, unique, -DRUG_EXPOSURE_IDs, though it is up to the ETL how they should be -handled. - -bigint - -Yes - -Yes - -No - - -
    -person_id - -The PERSON_ID of the PERSON for whom the drug dispensing or -administration is recorded. This may be a system generated code. - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -drug_concept_id - -The DRUG_CONCEPT_ID field is recommended for primary use in analyses, -and must be used for network studies. This is the standard concept -mapped from the source concept id which represents a drug product or -molecule otherwise introduced to the body. The drug concepts can have a -varying degree of information about drug strength and dose. This -information is relevant in the context of quantity and administration -information in the subsequent fields plus strength information from the -DRUG_STRENGTH table, provided as part of the standard vocabulary -download. - -The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should -be derived either from mapping from the source concept id or by picking -the drug concept representing the most amount of detail you have. -Records whose source values map to standard concepts with a domain of -Drug should go in this table. When the Drug Source Value of the code -cannot be translated into Standard Drug Concept IDs, a Drug exposure -entry is stored with only the corresponding SOURCE_CONCEPT_ID and -DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the -most detailed content of information is preferred during the mapping -process. These are indicated in the CONCEPT_CLASS_ID field of the -Concept and are recorded in the following order of precedence: ‘Branded -Pack’, ‘Clinical Pack’, ‘Branded Drug’, ‘Clinical Drug’, ‘Branded Drug -Component’, ‘Clinical Drug Component’, ‘Branded Drug Form’, ‘Clinical -Drug Form’, and only if no other information is available ‘Ingredient’. -Note: If only the drug class is known, the DRUG_CONCEPT_ID field should -contain 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Drug -
    -drug_exposure_start_date - -Use this date to determine the start date of the drug record. - -Valid entries include a start date of a prescription, the date a -prescription was filled, or the date on which a Drug administration was -recorded. It is a valid ETL choice to use the date the drug was ordered -as the DRUG_EXPOSURE_START_DATE. - -date - -Yes - -No - -No - - -
    -drug_exposure_start_datetime - - -This is not required, though it is in v6. If a source does not specify -datetime the convention is to set the time to midnight (00:00:0000) - -datetime - -No - -No - -No - - -
    -drug_exposure_end_date - -The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for -the patient. - -If this information is not explicitly available in the data, infer the -end date using the following methods:/n/n 1. Start first with duration -or days supply using the calculation drug start date + days supply -1 -day. 2. Use quantity divided by daily dose that you may obtain from the -sig or a source field (or assumed daily dose of 1) for solid, -indivisibile, drug products. If quantity represents ingredient amount, -quantity divided by daily dose * concentration (from drug_strength) drug -concept id tells you the dose form. 3. If it is an administration -record, set drug end date equal to drug start date. If the record is a -written prescription then set end date to start date + 29. If the record -is a mail-order prescription set end date to start date + 89. The end -date must be equal to or greater than the start date. Ibuprofen 20mg/mL -oral solution concept tells us this is oral solution. Calculate duration -as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL) -200*5/20 = 50 days. Examples -by dose form - -date - -Yes - -No - -No - - -
    -drug_exposure_end_datetime - - -This is not required, though it is in v6. If a source does not specify -datetime the convention is to set the time to midnight (00:00:0000) - -datetime - -No - -No - -No - - -
    -verbatim_end_date - -This is the end date of the drug exposure as it appears in the source -data, if it is given - -Put the end date or discontinuation date as it appears from the source -data or leave blank if unavailable. - -date - -No - -No - -No - - -
    -drug_type_concept_id - -You can use the TYPE_CONCEPT_ID to delineate between prescriptions -written vs. prescriptions dispensed vs. medication history -vs. patient-reported exposure, etc. - -Choose the drug_type_concept_id that best represents the provenance of -the record, for example whether it came from a record of a prescription -written or physician administered drug. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -stop_reason - -The reason a person stopped a medication as it is represented in the -source. Reasons include regimen completed, changed, removed, etc. This -field will be retired in v6.0. - -This information is often not populated in source data and it is a valid -etl choice to leave it blank if the information does not exist. - -varchar(20) - -No - -No - -No - - -
    -refills - -This is only filled in when the record is coming from a prescription -written this field is meant to represent intended refills at time of the -prescription. - - -integer - -No - -No - -No - - -
    -quantity - - -To find the dose form of a drug the RELATIONSHIP table can be used where -the relationship_id is ‘Has dose form’. If liquid, quantity stands for -the total amount dispensed or ordered of ingredient in the units given -by the drug_strength table. If the unit from the source data does not -align with the unit in the DRUG_STRENGTH table the quantity should be -converted to the correct unit given in DRUG_STRENGTH. For clinical drugs -with fixed dose forms (tablets etc.) the quantity is the number of -units/tablets/capsules prescribed or dispensed (can be partial, but then -only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms -(injections) the quantity is the amount of ingredient the patient got. -For example, if the injection is 2mg/mL but the patient got 80mL then -quantity is reported as 160. Quantified clinical drugs with divisible -dose forms (prefilled syringes), the quantity is the amount of -ingredient similar to clinical drugs. Please see how to -calculate drug dose for more information. - -float - -No - -No - -No - - -
    -days_supply - -The number of days of supply of the medication as recorded in the -original prescription or dispensing record. Days supply can differ from -actual drug duration (i.e. prescribed days supply vs actual exposure). - -The field should be left empty if the source data does not contain a -verbatim days_supply, and should not be calculated from other -fields.Negative values are not allowed. Several actions are possible: 1) -record is not trustworthy and we remove the record entirely. 2) we trust -the record and leave days_supply empty or 3) record needs to be combined -with other record (e.g. reversal of prescription). High values (>365 -days) should be investigated. If considered an error in the source data -(e.g. typo), the value needs to be excluded to prevent creation of -unrealistic long eras. - -integer - -No - -No - -No - - -
    -sig - -This is the verbatim instruction for the drug as written by the -provider. - -Put the written out instructions for the drug as it is verbatim in the -source, if available. - -varchar(MAX) - -No - -No - -No - - -
    -route_concept_id - - -The standard CONCEPT_ID that the ROUTE_SOURCE_VALUE maps to in the route -domain. - -integer - -No - -No - -Yes - -CONCEPT - -Route -
    -lot_number - - - -varchar(50) - -No - -No - -No - - -
    -provider_id - -The Provider associated with drug record, e.g. the provider who wrote -the prescription or the provider who administered the drug. - -The ETL may need to make a choice as to which PROVIDER_ID to put here. -Based on what is available this may or may not be different than the -provider associated with the overall VISIT_OCCURRENCE record, for -example the ordering vs administering physician on an EHR record. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -visit_occurrence_id - -The Visit during which the drug was prescribed, administered or -dispensed. - -To populate this field drug exposures must be explicitly initiated in -the visit. - -bigint - -No - -No - -Yes - -VISIT_OCCURRENCE - -
    -visit_detail_id - -The VISIT_DETAIL record during which the drug exposure occurred. For -example, if the person was in the ICU at the time of the drug -administration the VISIT_OCCURRENCE record would reflect the overall -hospital stay and the VISIT_DETAIL record would reflect the ICU stay -during the hospital visit. - -Same rules apply as for the VISIT_OCCURRENCE_ID. - -bigint - -No - -No - -Yes - -VISIT_DETAIL - -
    -drug_source_value - -This field houses the verbatim value from the source data representing -the drug exposure that occurred. For example, this could be an NDC or -Gemscript code. - -This code is mapped to a Standard Drug Concept in the Standardized -Vocabularies and the original code is stored here for reference. - -varchar(50) - -No - -No - -No - - -
    -drug_source_concept_id - -This is the concept representing the drug source value and may not -necessarily be standard. This field is discouraged from use in analysis -because it is not required to contain Standard Concepts that are used -across the OHDSI community, and should only be used when Standard -Concepts do not adequately represent the source detail for the Drug -necessary for a given analytic use case. Consider using DRUG_CONCEPT_ID -instead to enable standardized analytics that can be consistent across -the network. - -If the DRUG_SOURCE_VALUE is coded in the source data using an OMOP -supported vocabulary put the concept id representing the source value -here. If unavailable, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -route_source_value - -This field houses the verbatim value from the source data representing -the drug route. - -This information may be called something different in the source data -but the field is meant to contain a value indicating when and how a drug -was given to a patient. This source value is mapped to a standard -concept which is stored in the ROUTE_CONCEPT_ID field. - -varchar(50) - -No - -No - -No - - -
    -dose_unit_source_value - -This field houses the verbatim value from the source data representing -the dose unit of the drug given. - -This information may be called something different in the source data -but the field is meant to contain a value indicating the unit of dosage -of drug given to the patient. This is an older column and will be -deprecated in an upcoming version. - -varchar(50) - -No - -No - -No - - -
    @@ -4208,486 +859,6 @@

    procedure_occurrence

    Occurrence or Visit Detail - Same Provider - Same Modifier for Procedures. Source codes and source text fields mapped to Standard Concepts of the Procedure Domain have to be recorded here.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -procedure_occurrence_id - -The unique key given to a procedure record for a person. Refer to the -ETL for how duplicate procedures during the same visit were handled. - -Each instance of a procedure occurrence in the source data should be -assigned this unique key. In some cases, a person can have multiple -records of the same procedure within the same visit. It is valid to keep -these duplicates and assign them individual, unique, -PROCEDURE_OCCURRENCE_IDs, though it is up to the ETL how they should be -handled. - -bigint - -Yes - -Yes - -No - - -
    -person_id - -The PERSON_ID of the PERSON for whom the procedure is recorded. This may -be a system generated code. - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -procedure_concept_id - -The PROCEDURE_CONCEPT_ID field is recommended for primary use in -analyses, and must be used for network studies. This is the standard -concept mapped from the source value which represents a procedure - -The CONCEPT_ID that the PROCEDURE_SOURCE_VALUE maps to. Only records -whose source values map to standard concepts with a domain of -“Procedure” should go in this table. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Procedure -
    -procedure_date - -Use this date to determine the date the procedure occurred. - -If a procedure lasts more than a day, then it should be recorded as a -separate record for each day the procedure occurred, this logic is in -lieu of the procedure_end_date, which will be added in a future version -of the CDM. - -date - -No - -No - -No - - -
    -procedure_datetime - - -This is not required, though it is in v6. If a source does not specify -datetime the convention is to set the time to midnight (00:00:0000) - -datetime - -Yes - -No - -No - - -
    -procedure_type_concept_id - -This field can be used to determine the provenance of the Procedure -record, as in whether the procedure was from an EHR system, insurance -claim, registry, or other sources. - -Choose the PROCEDURE_TYPE_CONCEPT_ID that best represents the provenance -of the record, for example whether it came from an EHR record or billing -claim. If a procedure is recorded as an EHR encounter, the -PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter record’. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -modifier_concept_id - -The modifiers are intended to give additional information about the -procedure but as of now the vocabulary is under review. - -It is up to the ETL to choose how to map modifiers if they exist in -source data. These concepts are typically distinguished by ‘Modifier’ -concept classes (e.g., ‘CPT4 Modifier’ as part of the ‘CPT4’ -vocabulary). If there is more than one modifier on a record, one should -be chosen that pertains to the procedure rather than provider. If not -available, set to 0. Accepted -Concepts. - -integer - -No - -No - -Yes - -CONCEPT - -
    -quantity - -If the quantity value is omitted, a single procedure is assumed. - -If a Procedure has a quantity of ‘0’ in the source, this should default -to ‘1’ in the ETL. If there is a record in the source it can be assumed -the exposure occurred at least once - -integer - -No - -No - -No - - -
    -provider_id - -The provider associated with the procedure record, e.g. the provider who -performed the Procedure. - -The ETL may need to make a choice as to which PROVIDER_ID to put here. -Based on what is available this may or may not be different than the -provider associated with the overall VISIT_OCCURRENCE record, for -example the admitting vs attending physician on an EHR record. - -bigint - -No - -No - -No - -PROVIDER - -
    -visit_occurrence_id - -The visit during which the procedure occurred. - -Depending on the structure of the source data, this may have to be -determined based on dates. If a PROCEDURE_DATE occurs within the start -and end date of a Visit it is a valid ETL choice to choose the -VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not -explicitly stated in the data. While not required, an attempt should be -made to locate the VISIT_OCCURRENCE_ID of the PROCEDURE_OCCURRENCE -record. - -bigint - -No - -No - -No - -VISIT_OCCURRENCE - -
    -visit_detail_id - -The VISIT_DETAIL record during which the Procedure occurred. For -example, if the Person was in the ICU at the time of the Procedure the -VISIT_OCCURRENCE record would reflect the overall hospital stay and the -VISIT_DETAIL record would reflect the ICU stay during the hospital -visit. - -Same rules apply as for the VISIT_OCCURRENCE_ID. - -bigint - -No - -No - -No - -VISIT_DETAIL - -
    -procedure_source_value - -This field houses the verbatim value from the source data representing -the procedure that occurred. For example, this could be an CPT4 or OPCS4 -code. - -Use this value to look up the source concept id and then map the source -concept id to a standard concept id. - -varchar(50) - -No - -No - -No - - -
    -procedure_source_concept_id - -This is the concept representing the procedure source value and may not -necessarily be standard. This field is discouraged from use in analysis -because it is not required to contain Standard Concepts that are used -across the OHDSI community, and should only be used when Standard -Concepts do not adequately represent the source detail for the Procedure -necessary for a given analytic use case. Consider using -PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can -be consistent across the network. - -If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP -supported vocabulary put the concept id representing the source value -here. If not available, set to 0. - -integer - -Yes - -No - -No - -CONCEPT - -
    -modifier_source_value - - -The original modifier code from the source is stored here for reference. - -varchar(50) - -No - -No - -No - - -

    device_exposure

    @@ -4707,485 +878,6 @@

    device_exposure

    ETL Conventions

    Source codes and source text fields mapped to Standard Concepts of the Device Domain have to be recorded here.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -device_exposure_id - -The unique key given to records a person’s exposure to a foreign -physical object or instrument. - -Each instance of an exposure to a foreign object or device present in -the source data should be assigned this unique key. - -bigint - -Yes - -Yes - -No - - -
    -person_id - - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -device_concept_id - -The DEVICE_CONCEPT_ID field is recommended for primary use in analyses, -and must be used for network studies. This is the standard concept -mapped from the source concept id which represents a foreign object or -instrument the person was exposed to. - -The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to. - -integer - -Yes - -No - -Yes - -CONCEPT - -Device -
    -device_exposure_start_date - -Use this date to determine the start date of the device record. - -Valid entries include a start date of a procedure to implant a device, -the date of a prescription for a device, or the date of device -administration. - -date - -Yes - -No - -No - - -
    -device_exposure_start_datetime - - -This is not required, though it is in v6. If a source does not specify -datetime the convention is to set the time to midnight (00:00:0000) - -datetime - -No - -No - -No - - -
    -device_exposure_end_date - -The DEVICE_EXPOSURE_END_DATE denotes the day the device exposure ended -for the patient, if given. - -Put the end date or discontinuation date as it appears from the source -data or leave blank if unavailable. - -date - -No - -No - -No - - -
    -device_exposure_end_datetime - - -If a source does not specify datetime the convention is to set the time -to midnight (00:00:0000) - -datetime - -No - -No - -No - - -
    -device_type_concept_id - -You can use the TYPE_CONCEPT_ID to denote the provenance of the record, -as in whether the record is from administrative claims or EHR. Accepted -Concepts. - -Choose the drug_type_concept_id that best represents the provenance of -the record, for example whether it came from a record of a prescription -written or physician administered drug. - -integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -unique_device_id - -This is the Unique Device Identification number for devices regulated by -the FDA, if given. - -For medical devices that are regulated by the FDA, a Unique Device -Identification (UDI) is provided if available in the data source and is -recorded in the UNIQUE_DEVICE_ID field. - -varchar(50) - -No - -No - -No - - -
    -quantity - - - -integer - -No - -No - -No - - -
    -provider_id - -The Provider associated with device record, e.g. the provider who wrote -the prescription or the provider who implanted the device. - -The ETL may need to make a choice as to which PROVIDER_ID to put here. -Based on what is available this may or may not be different than the -provider associated with the overall VISIT_OCCURRENCE record. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -visit_occurrence_id - -The Visit during which the device was prescribed or given. - -To populate this field device exposures must be explicitly initiated in -the visit. - -bigint - -No - -No - -Yes - -VISIT_OCCURRENCE - -
    -visit_detail_id - -The Visit Detail during which the device was prescribed or given. - -To populate this field device exposures must be explicitly initiated in -the visit detail record. - -bigint - -No - -No - -Yes - -VISIT_DETAIL - -
    -device_source_value - -This field houses the verbatim value from the source data representing -the device exposure that occurred. For example, this could be an NDC or -Gemscript code. - -This code is mapped to a Standard Device Concept in the Standardized -Vocabularies and the original code is stored here for reference. - -varchar(50) - -No - -No - -No - - -
    -device_source_concept_id - -This is the concept representing the device source value and may not -necessarily be standard. This field is discouraged from use in analysis -because it is not required to contain Standard Concepts that are used -across the OHDSI community, and should only be used when Standard -Concepts do not adequately represent the source detail for the Device -necessary for a given analytic use case. Consider using -DEVICE_CONCEPT_ID instead to enable standardized analytics that can be -consistent across the network. - -If the DEVICE_SOURCE_VALUE is coded in the source data using an OMOP -supported vocabulary put the concept id representing the source value -here. If unavailable, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -

    measurement

    @@ -5231,689 +923,6 @@

    measurement

    ‘Enzyme measurement’ as well as a ‘Maps to value’ record to 4135493 ‘Abnormal’.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -measurement_id - -The unique key given to a Measurement record for a Person. Refer to the -ETL for how duplicate Measurements during the same Visit were handled. - -Each instance of a measurement present in the source data should be -assigned this unique key. In some cases, a person can have multiple -records of the same measurement within the same visit. It is valid to -keep these duplicates and assign them individual, unique, -MEASUREMENT_IDs, though it is up to the ETL how they should be handled. - -bigint - -Yes - -Yes - -No - - -
    -person_id - -The PERSON_ID of the PERSON for whom the measurement is recorded. This -may be a system generated code. - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -measurement_concept_id - -The MEASUREMENT_CONCEPT_ID field is recommended for primary use in -analyses, and must be used for network studies. - -The CONCEPT_ID that the MEASUREMENT_SOURCE_CONCEPT_ID maps to. Only -records whose SOURCE_CONCEPT_IDs map to Standard Concepts with a domain -of “Measurement” should go in this table. - -integer - -Yes - -No - -Yes - -CONCEPT - -Measurement -
    -measurement_date - -Use this date to determine the date of the measurement. - -If there are multiple dates in the source data associated with a record -such as order_date, draw_date, and result_date, choose the one that is -closest to the date the sample was drawn from the patient. - -date - -Yes - -No - -No - - -
    -measurement_datetime - - -This is not required, though it is in v6. If a source does not specify -datetime the convention is to set the time to midnight (00:00:0000) - -datetime - -No - -No - -No - - -
    -measurement_time - - -This is present for backwards compatibility and will be deprecated in an -upcoming version. - -varchar(10) - -No - -No - -No - - -
    -measurement_type_concept_id - -This field can be used to determine the provenance of the Measurement -record, as in whether the measurement was from an EHR system, insurance -claim, registry, or other sources. - -Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the -provenance of the record, for example whether it came from an EHR record -or billing claim. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -operator_concept_id - -The meaning of Concept 4172703 -for ‘=’ is identical to omission of a OPERATOR_CONCEPT_ID value. Since -the use of this field is rare, it’s important when devising analyses to -not to forget testing for the content of this field for values different -from =. - -Operators are <, <=, =, >=, > and these concepts belong to -the ‘Meas Value Operator’ domain. Accepted -Concepts. - -integer - -No - -No - -Yes - -CONCEPT - -
    -value_as_number - -This is the numerical value of the Result of the Measurement, if -available. Note that measurements such as blood pressures will be split -into their component parts i.e. one record for systolic, one record for -diastolic. - -If there is a negative value coming from the source, set the -VALUE_AS_NUMBER to NULL, with the exception of the following -Measurements (listed as LOINC codes):<br>- 1925-7 -Base excess in Arterial blood by calculation - 1927-3 -Base excess in Venous blood by calculation - 8632-2 -QRS-Axis - 11555-0 -Base excess in Blood by calculation - 1926-5 -Base excess in Capillary blood by calculation - 28638-5 -Base excess in Arterial cord blood by calculation 28639-3 -Base excess in Venous cord blood by calculation - -float - -No - -No - -No - - -
    -value_as_concept_id - -If the raw data gives a categorial result for measurements those values -are captured and mapped to standard concepts in the ‘Meas Value’ domain. - -If the raw data provides categorial results as well as continuous -results for measurements, it is a valid ETL choice to preserve both -values. The continuous value should go in the VALUE_AS_NUMBER field and -the categorical value should be mapped to a standard concept in the -‘Meas Value’ domain and put in the VALUE_AS_CONCEPT_ID field. This is -also the destination for the ‘Maps to value’ relationship. - -integer - -No - -No - -Yes - -CONCEPT - -
    -unit_concept_id - -There is currently no recommended unit for individual measurements, -i.e. it is not mandatory to represent Hemoglobin a1C measurements as a -percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in -the Unit domain that best represents the unit as given in the source -data. - -There is no standardization requirement for units associated with -MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to -choose the most plausible unit. - -integer - -No - -No - -Yes - -CONCEPT - -Unit -
    -range_low - -Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are -provided by the source and should remain NULL if not given. - -If reference ranges for upper and lower limit of normal as provided -(typically by a laboratory) these are stored in the RANGE_HIGH and -RANGE_LOW fields. This should be set to NULL if not provided. - -float - -No - -No - -No - - -
    -range_high - -Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are -provided by the source and should remain NULL if not given. - -If reference ranges for upper and lower limit of normal as provided -(typically by a laboratory) these are stored in the RANGE_HIGH and -RANGE_LOW fields. This should be set to NULL if not provided. - -float - -No - -No - -No - - -
    -provider_id - -The provider associated with measurement record, e.g. the provider who -ordered the test or the provider who recorded the result. - -The ETL may need to make a choice as to which PROVIDER_ID to put here. -Based on what is available this may or may not be different than the -provider associated with the overall VISIT_OCCURRENCE record. For -example the admitting vs attending physician on an EHR record. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -visit_occurrence_id - -The visit during which the Measurement occurred. - -Depending on the structure of the source data, this may have to be -determined based on dates. If a MEASUREMENT_DATE occurs within the start -and end date of a Visit it is a valid ETL choice to choose the -VISIT_OCCURRENCE_ID from the visit that subsumes it, even if not -explicitly stated in the data. While not required, an attempt should be -made to locate the VISIT_OCCURRENCE_ID of the measurement record. If a -measurement is related to a visit explicitly in the source data, it is -possible that the result date of the Measurement falls outside of the -bounds of the Visit dates. - -bigint - -No - -No - -Yes - -VISIT_OCCURRENCE - -
    -visit_detail_id - -The VISIT_DETAIL record during which the Measurement occurred. For -example, if the Person was in the ICU at the time the VISIT_OCCURRENCE -record would reflect the overall hospital stay and the VISIT_DETAIL -record would reflect the ICU stay during the hospital visit. - -Same rules apply as for the VISIT_OCCURRENCE_ID. - -bigint - -No - -No - -Yes - -VISIT_DETAIL - -
    -measurement_source_value - -This field houses the verbatim value from the source data representing -the Measurement that occurred. For example, this could be an ICD10 or -Read code. - -This code is mapped to a Standard Measurement Concept in the -Standardized Vocabularies and the original code is stored here for -reference. - -varchar(50) - -No - -No - -No - - -
    -measurement_source_concept_id - -This is the concept representing the MEASUREMENT_SOURCE_VALUE and may -not necessarily be standard. This field is discouraged from use in -analysis because it is not required to contain Standard Concepts that -are used across the OHDSI community, and should only be used when -Standard Concepts do not adequately represent the source detail for the -Measurement necessary for a given analytic use case. Consider using -MEASUREMENT_CONCEPT_ID instead to enable standardized analytics that can -be consistent across the network. - -If the MEASUREMENT_SOURCE_VALUE is coded in the source data using an -OMOP supported vocabulary put the concept id representing the source -value here. If not available, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -unit_source_value - -This field houses the verbatim value from the source data representing -the unit of the Measurement that occurred. - -This code is mapped to a Standard Condition Concept in the Standardized -Vocabularies and the original code is stored here for reference. - -varchar(50) - -No - -No - -No - - -
    -value_source_value - -This field houses the verbatim result value of the Measurement from the -source data . - -If both a continuous and categorical result are given in the source data -such that both VALUE_AS_NUMBER and VALUE_AS_CONCEPT_ID are both -included, store the verbatim value that was mapped to -VALUE_AS_CONCEPT_ID here. - -varchar(50) - -No - -No - -No - - -

    observation

    @@ -5961,703 +970,6 @@

    observation

    It is recommended for Observations that are suggestive statements of positive assertion should have a value of ‘Yes’ (concept_id=4188539), recorded, even though the null value is the equivalent.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -observation_id - -The unique key given to an Observation record for a Person. Refer to the -ETL for how duplicate Observations during the same Visit were handled. - -Each instance of an observation present in the source data should be -assigned this unique key. - -bigint - -Yes - -Yes - -No - - -
    -person_id - -The PERSON_ID of the Person for whom the Observation is recorded. This -may be a system generated code. - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -observation_concept_id - -The OBSERVATION_CONCEPT_ID field is recommended for primary use in -analyses, and must be used for network studies. - -The CONCEPT_ID that the OBSERVATION_SOURCE_CONCEPT_ID maps to. There is -no specified domain that the Concepts in this table must adhere to. The -only rule is that records with Concepts in the Condition, Procedure, -Drug, Measurement, or Device domains MUST go to the corresponding table. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -observation_date - -The date of the Observation. Depending on what the Observation -represents this could be the date of a lab test, the date of a survey, -or the date a patient’s family history was taken. - -For some observations the ETL may need to make a choice as to which date -to choose. - -date - -No - -No - -No - - -
    -observation_datetime - - -If no time is given set to midnight (00:00:00). - -datetime - -Yes - -No - -No - - -
    -observation_type_concept_id - -This field can be used to determine the provenance of the Observation -record, as in whether the measurement was from an EHR system, insurance -claim, registry, or other sources. - -Choose the OBSERVATION_TYPE_CONCEPT_ID that best represents the -provenance of the record, for example whether it came from an EHR record -or billing claim. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -value_as_number - -This is the numerical value of the Result of the Observation, if -applicable and available. It is not expected that all Observations will -have numeric results, rather, this field is here to house values should -they exist. - - -float - -No - -No - -No - - -
    -value_as_string - -This is the categorical value of the Result of the Observation, if -applicable and available. - - -varchar(60) - -No - -No - -No - - -
    -value_as_concept_id - -It is possible that some records destined for the Observation table have -two clinical ideas represented in one source code. This is common with -ICD10 codes that describe a family history of some Condition, for -example. In OMOP the Vocabulary breaks these two clinical ideas into two -codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the -VALUE_AS_CONCEPT_ID. It is important when using the Observation table to -keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID -field for relevant information. - -Note that the value of VALUE_AS_CONCEPT_ID may be provided through -mapping from a source Concept which contains the content of the -Observation. In those situations, the CONCEPT_RELATIONSHIP table in -addition to the ‘Maps to’ record contains a second record with the -relationship_id set to ‘Maps to value’. For example, ICD10 Z82.4 -‘Family history of ischaemic heart disease and other diseases of the -circulatory system’ has a ‘Maps to’ relationship to 4167217 -‘Family history of clinical finding’ as well as a ‘Maps to value’ record -to 134057 -‘Disorder of cardiovascular system’. - -Integer - -No - -No - -Yes - -CONCEPT - -
    -qualifier_concept_id - -This field contains all attributes specifying the clinical fact further, -such as as degrees, severities, drug-drug interaction alerts etc. - -Use your best judgement as to what Concepts to use here and if they are -necessary to accurately represent the clinical record. There is no -restriction on the domain of these Concepts, they just need to be -Standard. - -integer - -No - -No - -Yes - -CONCEPT - -
    -unit_concept_id - -There is currently no recommended unit for individual observation -concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in -the Unit domain that best represents the unit as given in the source -data. - -There is no standardization requirement for units associated with -OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to -choose the most plausible unit. - -integer - -No - -No - -Yes - -CONCEPT - -Unit -
    -provider_id - -The provider associated with the observation record, e.g. the provider -who ordered the test or the provider who recorded the result. - -The ETL may need to make a choice as to which PROVIDER_ID to put here. -Based on what is available this may or may not be different than the -provider associated with the overall VISIT_OCCURRENCE record. For -example the admitting vs attending physician on an EHR record. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -visit_occurrence_id - -The visit during which the Observation occurred. - -Depending on the structure of the source data, this may have to be -determined based on dates. If an OBSERVATION_DATE occurs within the -start and end date of a Visit it is a valid ETL choice to choose the -VISIT_OCCURRENCE_ID from the visit that subsumes it, even if not -explicitly stated in the data. While not required, an attempt should be -made to locate the VISIT_OCCURRENCE_ID of the observation record. If an -observation is related to a visit explicitly in the source data, it is -possible that the result date of the Observation falls outside of the -bounds of the Visit dates. - -bigint - -No - -No - -Yes - -VISIT_OCCURRENCE - -
    -visit_detail_id - -The VISIT_DETAIL record during which the Observation occurred. For -example, if the Person was in the ICU at the time the VISIT_OCCURRENCE -record would reflect the overall hospital stay and the VISIT_DETAIL -record would reflect the ICU stay during the hospital visit. - -Same rules apply as for the VISIT_OCCURRENCE_ID. - -bigint - -No - -No - -Yes - -VISIT_DETAIL - -
    -observation_source_value - -This field houses the verbatim value from the source data representing -the Observation that occurred. For example, this could be an ICD10 or -Read code. - -This code is mapped to a Standard Concept in the Standardized -Vocabularies and the original code is stored here for reference. - -varchar(50) - -No - -No - -No - - -
    -observation_source_concept_id - -This is the concept representing the OBSERVATION_SOURCE_VALUE and may -not necessarily be standard. This field is discouraged from use in -analysis because it is not required to contain Standard Concepts that -are used across the OHDSI community, and should only be used when -Standard Concepts do not adequately represent the source detail for the -Observation necessary for a given analytic use case. Consider using -OBSERVATION_CONCEPT_ID instead to enable standardized analytics that can -be consistent across the network. - -If the OBSERVATION_SOURCE_VALUE is coded in the source data using an -OMOP supported vocabulary put the concept id representing the source -value here. If not available, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -unit_source_value - -This field houses the verbatim value from the source data representing -the unit of the Observation that occurred. - -This code is mapped to a Standard Condition Concept in the Standardized -Vocabularies and the original code is stored here for reference. - -varchar(50) - -No - -No - -No - - -
    -qualifier_source_value - -This field houses the verbatim value from the source data representing -the qualifier of the Observation that occurred. - -This code is mapped to a Standard Condition Concept in the Standardized -Vocabularies and the original code is stored here for reference. - -varchar(50) - -No - -No - -No - - -
    -observation_event_id - -If the Observation record is related to another record in the database, -this field is the primary key of the linked record. - -Put the primary key of the linked record, if applicable, here. See the -ETL -Conventions for the OBSERVATION table for more details. - -bigint - -No - -No - -No - - -
    -obs_event_field_concept_id - -If the Observation record is related to another record in the database, -this field is the CONCEPT_ID that identifies which table the primary key -of the linked record came from. - -Put the CONCEPT_ID that identifies which table and field the -OBSERVATION_EVENT_ID came from. - -integer - -No - -No - -Yes - -CONCEPT - -
    -value_as_datetime - -It is possible that some Observation records might store a result as a -date value. - - -datetime - -No - -No - -No - - -

    note

    @@ -6696,483 +1008,6 @@

    note

    dimensions will necessarily yield an existing LOINC code. Each of these dimensions are contained in the OMOP Vocabulary under the domain of ‘Meas Value’ with each dimension represented as a Concept Class.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -note_id - -A unique identifier for each note. - - -integer - -Yes - -Yes - -No - - -
    -person_id - - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -note_event_id - - - -bigint - -No - -No - -No - - -
    -note_event_field_concept_id - - - -integer - -No - -No - -Yes - -CONCEPT - -
    -note_date - -The date the note was recorded. - - -date - -Yes - -No - -No - - -
    -note_datetime - - -If time is not given set the time to midnight. - -datetime - -No - -No - -No - - -
    -note_type_concept_id - -The provenance of the note. Most likely this will be EHR. - -Put the source system of the note, as in EHR record. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -note_class_concept_id - -A Standard Concept Id representing the HL7 LOINC Document Type -Vocabulary classification of the note. - -Map the note classification to a Standard Concept. For more information -see the ETL Conventions in the description of the NOTE table. AcceptedConcepts. -This Concept can alternatively be represented by concepts with the -relationship ‘Kind of (LOINC)’ to 706391 -(Note). - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -note_title - -The title of the note. - - -varchar(250) - -No - -No - -No - - -
    -note_text - -The content of the note. - - -varchar(MAX) - -Yes - -No - -No - - -
    -encoding_concept_id - -This is the Concept representing the character encoding type. - -Put the Concept Id that represents the encoding character type here. -Currently the only option is UTF-8 (32678). It -the note is encoded in any other type, like ASCII then put 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -language_concept_id - -The language of the note. - -Use Concepts that are descendants of the concept 4182347 -(World Languages). - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -provider_id - -The Provider who wrote the note. - -The ETL may need to make a determination on which provider to put here. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -visit_occurrence_id - -The Visit during which the note was written. - - -bigint - -No - -No - -Yes - -VISIT_OCCURRENCE - -
    -visit_detail_id - -The Visit Detail during which the note was written. - - -bigint - -No - -No - -Yes - -VISIT_DETAIL - -
    -note_source_value - - -The source value mapped to the NOTE_CLASS_CONCEPT_ID. - -varchar(50) - -No - -No - -No - - -

    note_nlp

    @@ -7183,425 +1018,6 @@

    note_nlp

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -note_nlp_id - -A unique identifier for the NLP record. - - -bigint - -Yes - -Yes - -No - - -
    -note_id - -This is the NOTE_ID for the NOTE record the NLP record is associated to. - - -integer - -Yes - -No - -No - - -
    -section_concept_id - - -The SECTION_CONCEPT_ID should be used to represent the note section -contained in the NOTE_NLP record. These concepts can be found as parts -of document panels and are based on the type of note written, i.e. a -discharge summary. These panels can be found as concepts with the -relationship ‘Subsumes’ to CONCEPT_ID 45875957. - -integer - -No - -No - -Yes - -CONCEPT - -
    -snippet - -A small window of text surrounding the term - - -varchar(250) - -No - -No - -No - - -
    -"offset" - -Character offset of the extracted term in the input note - - -varchar(50) - -No - -No - -No - - -
    -lexical_variant - -Raw text extracted from the NLP tool. - - -varchar(250) - -Yes - -No - -No - - -
    -note_nlp_concept_id - - - -integer - -No - -No - -Yes - -CONCEPT - -
    -note_nlp_source_concept_id - - - -integer - -No - -No - -Yes - -CONCEPT - -
    -nlp_system - - -Name and version of the NLP system that extracted the term. Useful for -data provenance. - -varchar(250) - -No - -No - -No - - -
    -nlp_date - -The date of the note processing. - - -date - -Yes - -No - -No - - -
    -nlp_datetime - -The date and time of the note processing. - - -datetime - -No - -No - -No - - -
    -term_exists - - -Term_exists is defined as a flag that indicates if the patient actually -has or had the condition. Any of the following modifiers would make -Term_exists false: Negation = true Subject = [anything other than the -patient] Conditional = true/li> Rule_out = true Uncertain = very low -certainty or any lower certainties A complete lack of modifiers would -make Term_exists true. - -varchar(1) - -No - -No - -No - - -
    -term_temporal - - -Term_temporal is to indicate if a condition is present or just in the -past. The following would be past:<br><br> - History = true -- Concept_date = anything before the time of the report - -varchar(50) - -No - -No - -No - - -
    -term_modifiers - - -For the modifiers that are there, they would have to have these -values:<br><br> - Negation = false - Subject = patient - -Conditional = false - Rule_out = false - Uncertain = true or high or -moderate or even low (could argue about low). Term_modifiers will -concatenate all modifiers for different types of entities (conditions, -drugs, labs etc) into one string. Lab values will be saved as one of the -modifiers. - -varchar(2000) - -No - -No - -No - - -

    specimen

    @@ -7614,449 +1030,6 @@

    specimen

    Anatomic site is coded at the most specific level of granularity possible, such that higher level classifications can be derived using the Standardized Vocabularies.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -specimen_id - -Unique identifier for each specimen. - - -bigint - -Yes - -Yes - -No - - -
    -person_id - -The person from whom the specimen is collected. - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -specimen_concept_id - - -The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the -specimen domain. Accepted -Concepts - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -specimen_type_concept_id - - -Put the source of the specimen record, as in an EHR system. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Type Concept -
    -specimen_date - -The date the specimen was collected. - - -date - -Yes - -No - -No - - -
    -specimen_datetime - - - -datetime - -No - -No - -No - - -
    -quantity - -The amount of specimen collected from the person. - - -float - -No - -No - -No - - -
    -unit_concept_id - -The unit for the quantity of the specimen. - -Map the UNIT_SOURCE_VALUE to a Standard Concept in the Unit domain. Accepted -Concepts - -integer - -No - -No - -Yes - -CONCEPT - -
    -anatomic_site_concept_id - -This is the site on the body where the specimen is from. - -Map the ANATOMIC_SITE_SOURCE_VALUE to a Standard Concept in the Spec -Anatomic Site domain. This should be coded at the lowest level of -granularity Accepted -Concepts - -integer - -No - -No - -Yes - -CONCEPT - -
    -disease_status_concept_id - - - -integer - -No - -No - -Yes - -CONCEPT - -
    -specimen_source_id - -This is the identifier for the specimen from the source system. - - -varchar(50) - -No - -No - -No - - -
    -specimen_source_value - - - -varchar(50) - -No - -No - -No - - -
    -unit_source_value - - -This unit for the quantity of the specimen, as represented in the -source. - -varchar(50) - -No - -No - -No - - -
    -anatomic_site_source_value - - -This is the site on the body where the specimen was taken from, as -represented in the source. - -varchar(50) - -No - -No - -No - - -
    -disease_status_source_value - - - -varchar(50) - -No - -No - -No - - -

    fact_relationship

    @@ -8081,169 +1054,6 @@

    fact_relationship

    records are in the FACT_RELATIONSHIP table (all strings in fact concept_id records in the Concept table: - Person, 1, Person, 2, parent of - Person, 2, Person, 1, child of

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -domain_concept_id_1 - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -fact_id_1 - - - -bigint - -Yes - -No - -No - - -
    -domain_concept_id_2 - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -fact_id_2 - - - -bigint - -Yes - -No - -No - - -
    -relationship_concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -

    survey_conduct

    @@ -8261,701 +1071,6 @@

    survey_conduct

    to a specific Visit in order to link it both to the Visit during which it was completed and any subsequent Visit where treatment was assigned based on the patient’s responses.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -survey_conduct_id - -Unique identifier for each completed survey. - -For each instance of a survey completion create a unique identifier. - -bigint - -Yes - -Yes - -No - - -
    -person_id - - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -survey_concept_id - -This is the Concept that represents the survey that was completed. - -Put the CONCEPT_ID that identifies the survey that the Person completed. -There is no specified domain for this table but the concept class -‘staging/scales’ contains many common surveys. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -survey_start_date - -Date on which the survey was started. - - -date - -No - -No - -No - - -
    -survey_start_datetime - - -If no time given, set to midnight. - -datetime - -No - -No - -No - - -
    -survey_end_date - -Date on which the survey was completed. - - -date - -No - -No - -No - - -
    -survey_end_datetime - - -If no time given, set to midnight. - -datetime - -Yes - -No - -No - - -
    -provider_id - -This is the Provider associated with the survey completion. - -The ETL may need to make a choice as to which Provider to put here. This -could either be the provider that ordered the survey or the provider who -observed the completion of the survey. - -bigint - -No - -No - -Yes - -PROVIDER - -
    -assisted_concept_id - -This is a Concept that represents whether the survey was completed with -assistance or independently. - -There is no specific domain or class for this field, just choose the one -that best represents the value given in the source. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -respondent_type_concept_id - -This is a Concept that represents who actually recorded the answers to -the survey. For example, this could be the patient or a research -associate. - -There is no specific domain or class for this field, just choose the one -that best represents the value given in the source. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -timing_concept_id - -This is a Concept that represents the timing of the survey. For example -this could be the 3-month follow-up appointment. - -There is no specific domain or class for this field, just choose the one -that best represents the value given in the source. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -collection_method_concept_id - -This Concept represents how the responses were collected. - -Use the concepts that have the relationship ‘Has Answer’ with the -CONCEPT_ID 42529316. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -assisted_source_value - -Source value representing whether patient required assistance to -complete the survey. Example: ‘Completed without assistance’, ‘Completed -with assistance’. - - -varchar(50) - -No - -No - -No - - -
    -respondent_type_source_value - -Source code representing role of person who completed the survey. - - -varchar(100) - -No - -No - -No - - -
    -timing_source_value - -Text string representing the timing of the survey. Example: Baseline, -6-month follow-up. - - -varchar(100) - -No - -No - -No - - -
    -collection_method_source_value - -The collection method as it appears in the source data. - - -varchar(100) - -No - -No - -No - - -
    -survey_source_value - -The survey name as it appears in the source data. - - -varchar(100) - -No - -No - -No - - -
    -survey_source_concept_id - - -If unavailable, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -survey_source_identifier - -Unique identifier for each completed survey in source system. - - -varchar(100) - -No - -No - -No - - -
    -validated_survey_concept_id - - -If unavailable, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -validated_survey_source_value - -Source value representing the validation status of the survey. - - -varchar(100) - -No - -No - -No - - -
    -survey_version_number - -Version number of the questionnaire or survey used. - - -varchar(20) - -No - -No - -No - - -
    -visit_occurrence_id - -The Visit during which the Survey occurred. - - -bigint - -No - -No - -Yes - -VISIT_OCCURRENCE - -
    -response_visit_occurrence_id - -The Visit during which any treatment related to the Survey was carried -out. - - -bigint - -No - -No - -Yes - -VISIT_OCCURRENCE - -

    location

    @@ -8974,306 +1089,6 @@

    location

    with information from the Care Site. For standardized geospatial visualization and analysis, addresses need to be, at the minimum be geocoded into latitude and longitude.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -location_id - -The unique key given to a unique Location. - -Each instance of a Location in the source data should be assigned this -unique key. - -bigint - -Yes - -Yes - -No - - -
    -address_1 - -This is the first line of the address. - - -varchar(50) - -No - -No - -No - - -
    -address_2 - -This is the second line of the address - - -varchar(50) - -No - -No - -No - - -
    -city - - - -varchar(50) - -No - -No - -No - - -
    -state - - - -varchar(2) - -No - -No - -No - - -
    -zip - - -Zip codes are handled as strings of up to 9 characters length. For US -addresses, these represent either a 3-digit abbreviated Zip code as -provided by many sources for patient protection reasons, the full -5-digit Zip or the 9-digit (ZIP + 4) codes. Unless for specific reasons -analytical methods should expect and utilize only the first 3 digits. -For international addresses, different rules apply. - -varchar(9) - -No - -No - -No - - -
    -county - - - -varchar(20) - -No - -No - -No - - -
    -location_source_value - - -Put the verbatim value for the location here, as it shows up in the -source. - -varchar(50) - -No - -No - -No - - -
    -latitude - -The geocoded latitude. - - -float - -No - -No - -No - - -
    -longitude - -The geocoded longitude. - - -float - -No - -No - -No - - -

    location_history

    @@ -9285,207 +1100,6 @@

    location_history

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -location_id - -This is the LOCATION_ID for the LOCATION_HISTORY record. - - -bigint - -Yes - -No - -Yes - -LOCATION - -
    -relationship_type_concept_id - -This is the relationship between the location and the entity (PERSON, -PROVIDER, or CARE_SITE) - -Concepts in this field must be in the Location class. Accepted -Concepts. If the DOMAIN_ID is CARE_SITE this should be 0 and when -the domain is PROVIDER the value is Office. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -domain_id - - -The domain of the entity that is related to the location. Either PERSON, -PROVIDER, or CARE_SITE. - -varchar(50) - -Yes - -No - -No - - -
    -entity_id - - -The unique identifier for the entity. References either person_id, -provider_id, or care_site_id, depending on domain_id. - -bigint - -Yes - -No - -No - - -
    -start_date - -The date the relationship started - - -date - -Yes - -No - -No - - -
    -end_date - -The date the relationship ended - - -date - -No - -No - -No - - -

    care_site

    @@ -9509,213 +1123,6 @@

    care_site

    hospitals, which in turn can belong to hospital systems, which in turn can belong to HMOs.The relationships between Care Sites are defined in the FACT_RELATIONSHIP table.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -care_site_id - - -Assign an id to each unique combination of location_id and -place_of_service_source_value. - -bigint - -Yes - -Yes - -No - - -
    -care_site_name - -The name of the care_site as it appears in the source data - - -varchar(255) - -No - -No - -No - - -
    -place_of_service_concept_id - -This is a high-level way of characterizing a Care Site. Typically, -however, Care Sites can provide care in multiple settings (inpatient, -outpatient, etc.) and this granularity should be reflected in the visit. - -Choose the concept in the visit domain that best represents the setting -in which healthcare is provided in the Care Site. If most visits in a -Care Site are Inpatient, then the place_of_service_concept_id should -represent Inpatient. If information is present about a unique Care Site -(e.g. Pharmacy) then a Care Site record should be created. If this -information is not available then set to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -location_id - -The location_id from the LOCATION table representing the physical -location of the care_site. - - -bigint - -No - -No - -Yes - -LOCATION - -
    -care_site_source_value - -The identifier of the care_site as it appears in the source data. This -could be an identifier separate from the name of the care_site. - - -varchar(50) - -No - -No - -No - - -
    -place_of_service_source_value - - -Put the place of service of the care_site as it appears in the source -data. - -varchar(50) - -No - -No - -No - - -

    provider

    @@ -9732,429 +1139,6 @@

    provider

    or ‘pooled’ Provider records are listed in the PROVIDER table.

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -provider_id - -It is assumed that every provider with a different unique identifier is -in fact a different person and should be treated independently. - -This identifier can be the original id from the source data provided it -is an integer, otherwise it can be an autogenerated number. - -bigint - -Yes - -Yes - -No - - -
    -provider_name - - -This field is not necessary as it is not necessary to have the actual -identity of the Provider. Rather, the idea is to uniquely and -anonymously identify providers of care across the database. - -varchar(255) - -No - -No - -No - - -
    -npi - -This is the National Provider Number issued to health care providers in -the US by the Centers for Medicare and Medicaid Services (CMS). - - -varchar(20) - -No - -No - -No - - -
    -dea - -This is the identifier issued by the DEA, a US federal agency, that -allows a provider to write prescriptions for controlled substances. - - -varchar(20) - -No - -No - -No - - -
    -specialty_concept_id - -This field either represents the most common specialty that occurs in -the data or the most specific concept that represents all specialties -listed, should the provider have more than one. This includes physician -specialties such as internal medicine, emergency medicine, etc. and -allied health professionals such as nurses, midwives, and pharmacists. - -If a Provider has more than one Specialty, there are two options: 1. -Choose a concept_id which is a common ancestor to the multiple -specialties, or, 2. Choose the specialty that occurs most often for the -provider. Concepts in this field should be Standard with a domain of -Provider. If not available, set to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -care_site_id - -This is the CARE_SITE_ID for the location that the provider primarily -practices in. - -If a Provider has more than one Care Site, the main or most often -exerted CARE_SITE_ID should be recorded. - -bigint - -No - -No - -Yes - -CARE_SITE - -
    -year_of_birth - - - -integer - -No - -No - -No - - -
    -gender_concept_id - -This field represents the recorded gender of the provider in the source -data. - -If given, put a concept from the gender domain representing the recorded -gender of the provider. If not available, set to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -Gender -
    -provider_source_value - -Use this field to link back to providers in the source data. This is -typically used for error checking of ETL logic. - -Some use cases require the ability to link back to providers in the -source data. This field allows for the storing of the provider -identifier as it appears in the source. - -varchar(50) - -No - -No - -No - - -
    -specialty_source_value - -This is the kind of provider or specialty as it appears in the source -data. This includes physician specialties such as internal medicine, -emergency medicine, etc. and allied health professionals such as nurses, -midwives, and pharmacists. - -Put the kind of provider as it appears in the source data. This field is -up to the discretion of the ETL-er as to whether this should be the -coded value from the source or the text description of the lookup value. - -varchar(50) - -No - -No - -No - - -
    -specialty_source_concept_id - -This is often zero as many sites use proprietary codes to store -physician speciality. - -If the source data codes provider specialty in an OMOP supported -vocabulary store the concept_id here. If not available, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -gender_source_value - -This is provider’s gender as it appears in the source data. - -Put the provider’s gender as it appears in the source data. This field -is up to the discretion of the ETL-er as to whether this should be the -coded value from the source or the text description of the lookup value. - -varchar(50) - -No - -No - -No - - -
    -gender_source_concept_id - -This is often zero as many sites use proprietary codes to store provider -gender. - -If the source data codes provider gender in an OMOP supported vocabulary -store the concept_id here. If not available, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -

    payer_plan_period

    @@ -10180,661 +1164,6 @@

    payer_plan_period

    the Plans are different.

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -payer_plan_period_id - -A unique identifier for each unique combination of a Person, Payer, -Plan, and Period of time. - - -bigint - -Yes - -Yes - - - -
    -person_id - -The Person covered by the Plan. - -A single Person can have multiple, overlapping, PAYER_PLAN_PERIOD -records - -bigint - -Yes - -No - -Yes - -PERSON - -
    -contract_person_id - -The Person who is the primary subscriber/contract owner for Plan. - -This may or may not be the same as the PERSON_ID. For example, if a -mother has her son on her plan and the PAYER_PLAN_PERIOD record is the -for son, the sons’s PERSON_ID would go in PAYER_PLAN_PERIOD.PERSON_ID -and the mother’s PERSON_ID would go in -PAYER_PLAN_PERIOD.CONTRACT_PERSON_ID. - -bigint - -No - -No - -Yes - -PERSON - -
    -payer_plan_period_start_date - -Start date of Plan coverage. - - -date - -Yes - -No - -No - - -
    -payer_plan_period_end_date - -End date of Plan coverage. - - -date - -Yes - -No - -No - - -
    -payer_concept_id - -This field represents the organization who reimburses the provider which -administers care to the Person. - -Map the Payer directly to a standard CONCEPT_ID. If one does not exists -please contact the vocabulary team. There is no global controlled -vocabulary available for this information. The point is to stratify on -this information and identify if Persons have the same payer, though the -name of the Payer is not necessary. If not available, set to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -payer_source_value - -This is the Payer as it appears in the source data. - - -varchar(50) - -No - -No - -No - - -
    -payer_source_concept_id - - -If the source data codes the Payer in an OMOP supported vocabulary store -the concept_id here. If not available, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -plan_concept_id - -This field represents the specific health benefit Plan the Person is -enrolled in. - -Map the Plan directly to a standard CONCEPT_ID. If one does not exists -please contact the vocabulary team. There is no global controlled -vocabulary available for this information. The point is to stratify on -this information and identify if Persons have the same health benefit -Plan though the name of the Plan is not necessary. If not available, set -to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -plan_source_value - -This is the health benefit Plan of the Person as it appears in the -source data. - - -varchar(50) - -No - -No - -No - - -
    -plan_source_concept_id - - -If the source data codes the Plan in an OMOP supported vocabulary store -the concept_id here. If not available, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -contract_concept_id - -This field represents the relationship between the PERSON_ID and -CONTRACT_PERSON_ID. It should be read as PERSON_ID is the -CONTRACT_CONCEPT_ID of the CONTRACT_PERSON_ID. So if -CONTRACT_CONCEPT_ID represents the relationship ‘Stepdaughter’ then the -Person for whom PAYER_PLAN_PERIOD record was recorded is the -stepdaughter of the CONTRACT_PERSON_ID. - -If available, use this field to represent the relationship between the -PERSON_ID and the CONTRACT_PERSON_ID. If the Person for whom the -PAYER_PLAN_PERIOD record was recorded is the stepdaughter of the -CONTRACT_PERSON_ID then CONTRACT_CONCEPT_ID would be 4330864. -If not available, set to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -contract_source_value - -This is the relationship of the PERSON_ID to CONTRACT_PERSON_ID as it -appears in the source data. - - -varchar(50) - -Yes - -No - -No - - -
    -contract_source_concept_id - - -If the source data codes the relationship between the PERSON_ID and -CONTRACT_PERSON_ID in an OMOP supported vocabulary store the concept_id -here. If not available, set to 0. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -sponsor_concept_id - -This field represents the sponsor of the Plan who finances the Plan. -This includes self-insured, small group health plan and large group -health plan. - -Map the sponsor directly to a standard CONCEPT_ID. If one does not -exists please contact the vocabulary team. There is no global controlled -vocabulary available for this information. The point is to stratify on -this information and identify if Persons have the same sponsor though -the name of the sponsor is not necessary. If not available, set to 0. Accepted -Concepts. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -sponsor_source_value - -The Plan sponsor as it appears in the source data. - - -varchar(50) - -No - -No - -No - - -
    -sponsor_source_concept_id - - -If the source data codes the sponsor in an OMOP supported vocabulary -store the concept_id here. - -integer - -No - -No - -Yes - -CONCEPT - -
    -family_source_value - -The common identifier for all people (often a family) that covered by -the same policy. - -Often these are the common digits of the enrollment id of the policy -members. - -varchar(50) - -No - -No - -No - - -
    -stop_reason_concept_id - -This field represents the reason the Person left the Plan, if known. - -Map the stop reason directly to a standard CONCEPT_ID. If one does not -exists please contact the vocabulary team. There is no global controlled -vocabulary available for this information. Accepted -Concepts. - -integer - -No - -No - -Yes - -CONCEPT - -
    -stop_reason_source_value - -The Plan stop reason as it appears in the source data. - - -varchar(50) - -No - -No - -No - - -
    -stop_reason_source_concept_id - - -If the source data codes the stop reason in an OMOP supported vocabulary -store the concept_id here. - -integer - -No - -No - -Yes - -CONCEPT - -

    cost

    @@ -10869,537 +1198,6 @@

    cost

    field. Drug costs are composed of ingredient cost (the amount charged by the wholesale distributor or manufacturer), the dispensing fee (the amount charged by the pharmacy and the sales tax).

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -cost_id - -A unique identifier for each COST record. - - -bigint - -Yes - -Yes - -No - - -
    -person_id - - - -bigint - -Yes - -No - -No - - -
    -cost_event_id - -If the Cost record is related to another record in the database, this -field is the primary key of the linked record. - -Put the primary key of the linked record, if applicable, here. - -bigint - -Yes - -No - -No - - -
    -cost_event_field_concept_id - -If the Cost record is related to another record in the database, this -field is the CONCEPT_ID that identifies which table the primary key of -the linked record came from. - -Put the CONCEPT_ID that identifies which table and field the -COST_EVENT_ID came from. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -cost_concept_id - -A foreign key that refers to a Standard Cost Concept identifier in the -Standardized Vocabularies belonging to the ‘Cost’ vocabulary. - - -integer - -No - -No - -Yes - -CONCEPT - -
    -cost_type_concept_id - -A foreign key identifier to a concept in the CONCEPT table for the -provenance or the source of the COST data and belonging to the ‘Type -Concept’ vocabulary - - -integer - -No - -No - -Yes - -CONCEPT - -Type Concept -
    -cost_source_concept_id - -A foreign key to a Cost Concept that refers to the code used in the -source. - - -integer - -No - -No - -Yes - -CONCEPT - -
    -cost_source_value - -The source value for the cost as it appears in the source data - - -varchar(50) - -No - -No - -No - - -
    -currency_concept_id - -A foreign key identifier to the concept representing the 3-letter code -used to delineate international currencies, such as USD for US Dollar. -These belong to the ‘Currency’ vocabulary - - -integer - -No - -No - -No - -CONCEPT - -
    -cost - -The actual financial cost amount - - -float - -No - -No - -No - - -
    -incurred_date - -The first date of service of the clinical event corresponding to the -cost as in table capturing the information (e.g. date of visit, date of -procedure, date of condition, date of drug etc). - - -date - -No - -No - -No - - -
    -billed_date - -The date a bill was generated for a service or encounter - - -date - -No - -No - -No - - -
    -paid_date - -The date payment was received for a service or encounter - - -date - -No - -No - -No - - -
    -revenue_code_concept_id - -A foreign key referring to a Standard Concept ID in the Standardized -Vocabularies for Revenue codes belonging to the ‘Revenue Code’ -vocabulary. - - -integer - -No - -No - -Yes - -CONCEPT - -
    -drg_concept_id - -A foreign key referring to a Standard Concept ID in the Standardized -Vocabularies for DRG codes belonging to the ‘DRG’ vocabulary. - - -integer - -No - -No - -Yes - -CONCEPT - -
    -revenue_code_source_value - -The source value for the Revenue code as it appears in the source data, -stored here for reference. - - -varchar(50) - -No - -No - -No - - -
    -drg_source_value - -The source value for the 3-digit DRG source code as it appears in the -source data, stored here for reference. - - -varchar(50) - -No - -No - -No - - -
    -payer_plan_period_id - -A foreign key to the PAYER_PLAN_PERIOD table, where the details of the -Payer, Plan and Family are stored. Record the payer_plan_id that relates -to the payer who contributed to the paid_by_payer field. - - -bigint - -No - -No - -No - - -

    drug_era

    @@ -11415,247 +1213,6 @@

    drug_era

    ETL Conventions

    The SQL script for generating DRUG_ERA records can be found here.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -drug_era_id - - - -bigint - -Yes - -Yes - -No - - -
    -person_id - - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -drug_concept_id - -The Concept Id representing the specific drug ingredient. - - -integer - -Yes - -No - -Yes - -CONCEPT - -Drug -
    -drug_era_start_datetime - - -The Drug Era Start Date is the start date of the first Drug Exposure for -a given ingredient, with at least 31 days since the previous exposure. - -datetime - -Yes - -No - -No - - -
    -drug_era_end_datetime - - -The Drug Era End Date is the end date of the last Drug Exposure. The End -Date of each Drug Exposure is either taken from the field -drug_exposure_end_date or, as it is typically not available, inferred -using the following rules: For pharmacy prescription data, the date when -the drug was dispensed plus the number of days of supply are used to -extrapolate the End Date for the Drug Exposure. Depending on the -country-specific healthcare system, this supply information is either -explicitly provided in the day_supply field or inferred from package -size or similar information. For Procedure Drugs, usually the drug is -administered on a single date (i.e., the administration date). A -standard Persistence Window of 30 days (gap, slack) is permitted between -two subsequent such extrapolated DRUG_EXPOSURE records to be considered -to be merged into a single Drug Era. - -datetime - -Yes - -No - -No - - -
    -drug_exposure_count - -The count of grouped DRUG_EXPOSURE records that were included in the -DRUG_ERA row. - - -integer - -No - -No - -No - - -
    -gap_days - - -The Gap Days determine how many total drug-free days are observed -between all Drug Exposure events that contribute to a DRUG_ERA record. -It is assumed that the drugs are “not stockpiled” by the patient, -i.e. that if a new drug prescription or refill is observed (a new -DRUG_EXPOSURE record is written), the remaining supply from the previous -events is abandoned. The difference between Persistence Window and Gap -Days is that the former is the maximum drug-free time allowed between -two subsequent DRUG_EXPOSURE records, while the latter is the sum of -actual drug-free days for the given Drug Era under the above assumption -of non-stockpiling. - -integer - -No - -No - -No - - -

    dose_era

    @@ -11671,229 +1228,6 @@

    dose_era

    patient changes between different formulations, or different manufacturers with the same formulation, the Dose Era is still spanning the entire time of exposure to the Ingredient.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -dose_era_id - - - -bigint - -Yes - -Yes - -No - - -
    -person_id - - - -bigint - -Yes - -No - -Yes - -PERSON - -
    -drug_concept_id - -The Concept Id representing the specific drug ingredient. - - -integer - -Yes - -No - -Yes - -CONCEPT - -Drug -
    -unit_concept_id - -The Concept Id representing the unit of the specific drug ingredient. - - -integer - -Yes - -No - -Yes - -CONCEPT - -Unit -
    -dose_value - -The numeric value of the dosage of the drug_ingredient. - - -float - -Yes - -No - -No - - -
    -dose_era_start_datetime - -The date the Person started on the specific dosage, with at least 31 -days since any prior exposure. - - -datetime - -Yes - -No - -No - - -
    -dose_era_end_datetime - - -The date the Person was no longer exposed to the dosage of the specific -drug ingredient. An era is ended if there are 31 days or more between -dosage records. - -datetime - -Yes - -No - -No - - -

    condition_era

    @@ -11933,204 +1267,6 @@

    condition_era

    of 30 days, meaning, if no occurrence of the same condition_concept_id happens within 30 days of any one occurrence, it will be considered the condition_era_end_date.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -condition_era_id - - - -bigint - -Yes - -Yes - -No - - -
    -person_id - - - -bigint - -Yes - -No - -No - -PERSON - -
    -condition_concept_id - -The Concept Id representing the Condition. - - -integer - -Yes - -No - -Yes - -CONCEPT - -Condition -
    -condition_era_start_datetime - -The start date for the Condition Era constructed from the individual -instances of Condition Occurrences. It is the start date of the very -first chronologically recorded instance of the condition with at least -31 days since any prior record of the same Condition. - - -datetime - -Yes - -No - -No - - -
    -condition_era_end_datetime - -The end date for the Condition Era constructed from the individual -instances of Condition Occurrences. It is the end date of the final -continuously recorded instance of the Condition. - - -datetime - -Yes - -No - -No - - -
    -condition_occurrence_count - -The number of individual Condition Occurrences used to construct the -condition era. - - -integer - -No - -No - -No - - -

    metadata

    @@ -12141,219 +1277,6 @@

    metadata

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -metadata_concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -metadata_type_concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -name - - - -varchar(250) - -Yes - -No - -No - - -
    -value_as_string - - - -varchar(250) - -No - -No - -No - - -
    -value_as_concept_id - - - -integer - -No - -No - -Yes - -CONCEPT - -
    -metadata_date - - - -date - -No - -No - -No - - -
    -metadata_datetime - - - -datetime - -No - -No - -No - - -

    cdm_source

    @@ -12365,298 +1288,6 @@

    cdm_source

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -cdm_source_name - -The name of the CDM instance. - - -varchar(255) - -Yes - -No - -No - - -
    -cdm_source_abbreviation - -The abbreviation of the CDM instance. - - -varchar(25) - -No - -No - -No - - -
    -cdm_holder - -The holder of the CDM instance. - - -varchar(255) - -No - -No - -No - - -
    -source_description - -The description of the CDM instance. - - -varchar(MAX) - -No - -No - -No - - -
    -source_documentation_reference - - - -varchar(255) - -No - -No - -No - - -
    -cdm_etl_reference - - -Put the link to the CDM version used. - -varchar(255) - -No - -No - -No - - -
    -source_release_date - -The release date of the source data. - - -date - -No - -No - -No - - -
    -cdm_release_date - -The release data of the CDM instance. - - -date - -No - -No - -No - - -
    -cdm_version - - - -varchar(10) - -No - -No - -No - - -
    -vocabulary_version - - - -varchar(20) - -No - -No - -No - - -

    concept

    @@ -12685,319 +1316,6 @@

    concept

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -concept_id - -A unique identifier for each Concept across all domains. - - -integer - -Yes - -Yes - -No - - -
    -concept_name - -An unambiguous, meaningful and descriptive name for the Concept. - - -varchar(255) - -Yes - -No - -No - - -
    -domain_id - -A foreign key to the DOMAIN -table the Concept belongs to. - - -varchar(20) - -Yes - -No - -Yes - -DOMAIN - -
    -vocabulary_id - -A foreign key to the VOCABULARY -table indicating from which source the Concept has been adapted. - - -varchar(20) - -Yes - -No - -Yes - -VOCABULARY - -
    -concept_class_id - -The attribute or concept class of the Concept. Examples are ‘Clinical -Drug’, ‘Ingredient’, ‘Clinical Finding’ etc. - - -varchar(20) - -Yes - -No - -Yes - -CONCEPT_CLASS - -
    -standard_concept - -This flag determines where a Concept is a Standard Concept, i.e. is used -in the data, a Classification Concept, or a non-standard Source Concept. -The allowable values are ‘S’ (Standard Concept) and ‘C’ (Classification -Concept), otherwise the content is NULL. - - -varchar(1) - -No - -No - -No - - -
    -concept_code - -The concept code represents the identifier of the Concept in the source -vocabulary, such as SNOMED-CT concept IDs, RxNorm RXCUIs etc. Note that -concept codes are not unique across vocabularies. - - -varchar(50) - -Yes - -No - -No - - -
    -valid_start_date - -The date when the Concept was first recorded. The default value is -1-Jan-1970, meaning, the Concept has no (known) date of inception. - - -date - -Yes - -No - -No - - -
    -valid_end_date - -The date when the Concept became invalid because it was deleted or -superseded (updated) by a new concept. The default value is 31-Dec-2099, -meaning, the Concept is valid until it becomes deprecated. - - -date - -Yes - -No - -No - - -
    -invalid_reason - -Reason the Concept was invalidated. Possible values are D (deleted), U -(replaced with an update) or NULL when valid_end_date has the default -value. - - -varchar(1) - -No - -No - -No - - -

    vocabulary

    @@ -13011,176 +1329,6 @@

    vocabulary

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -vocabulary_id - -A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. - - -varchar(20) - -Yes - -Yes - -No - - -
    -vocabulary_name - -The name describing the vocabulary, for example International -Classification of Diseases, Ninth Revision, Clinical Modification, -Volume 1 and 2 (NCHS) etc. - - -varchar(255) - -Yes - -No - -No - - -
    -vocabulary_reference - -External reference to documentation or available download of the about -the vocabulary. - - -varchar(255) - -Yes - -No - -No - - -
    -vocabulary_version - -Version of the Vocabulary as indicated in the source. - - -varchar(255) - -No - -No - -No - - -
    -vocabulary_concept_id - -A Concept that represents the Vocabulary the VOCABULARY record belongs -to. - - -integer - -Yes - -No - -Yes - -CONCEPT - -

    domain

    @@ -13197,121 +1345,6 @@

    domain

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -domain_id - -A unique key for each domain. - - -varchar(20) - -Yes - -Yes - -No - - -
    -domain_name - -The name describing the Domain, e.g. Condition, Procedure, Measurement -etc. - - -varchar(255) - -Yes - -No - -No - - -
    -domain_concept_id - -A Concept representing the Domain Concept the DOMAIN record belongs to. - - -integer - -Yes - -No - -Yes - -CONCEPT - -

    concept_class

    @@ -13324,121 +1357,6 @@

    concept_class

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -concept_class_id - -A unique key for each class. - - -varchar(20) - -Yes - -Yes - -No - - -
    -concept_class_name - -The name describing the Concept Class, e.g. Clinical Finding, -Ingredient, etc. - - -varchar(255) - -Yes - -No - -No - - -
    -concept_class_concept_id - -A Concept that represents the Concept Class. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    @@ -13452,202 +1370,6 @@

    concept_relationship

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -concept_id_1 - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -concept_id_2 - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -relationship_id - -The relationship between CONCEPT_ID_1 and CONCEPT_ID_2. Please see the -Vocabulary -Conventions. for more information. - - -varchar(20) - -Yes - -No - -Yes - -RELATIONSHIP - -
    -valid_start_date - -The date when the relationship is first recorded. - - -date - -Yes - -No - -No - - -
    -valid_end_date - -The date when the relationship is invalidated. - - -date - -Yes - -No - -No - - -
    -invalid_reason - -Reason the relationship was invalidated. Possible values are ‘D’ -(deleted), ‘U’ (updated) or NULL. - - -varchar(1) - -No - -No - -No - - -

    relationship

    @@ -13659,192 +1381,6 @@

    relationship

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -relationship_id - - - -varchar(20) - -Yes - -Yes - -No - - -
    -relationship_name - - - -varchar(255) - -Yes - -No - -No - - -
    -is_hierarchical - - - -varchar(1) - -Yes - -No - -No - - -
    -defines_ancestry - - - -varchar(1) - -Yes - -No - -No - - -
    -reverse_relationship_id - - - -varchar(20) - -Yes - -No - -No - - -
    -relationship_concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -

    concept_synonym

    @@ -13855,118 +1391,6 @@

    concept_synonym

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -concept_synonym_name - - - -varchar(1000) - -Yes - -No - -No - - -
    -language_concept_id - - - -integer - -Yes - -No - -Yes - -CONCEPT - -

    concept_ancestor

    @@ -13988,153 +1412,6 @@

    concept_ancestor

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -ancestor_concept_id - -The Concept Id for the higher-level concept that forms the ancestor in -the relationship. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -descendant_concept_id - -The Concept Id for the lower-level concept that forms the descendant in -the relationship. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -min_levels_of_separation - -The minimum separation in number of levels of hierarchy between ancestor -and descendant concepts. This is an attribute that is used to simplify -hierarchic analysis. - - -integer - -Yes - -No - -No - - -
    -max_levels_of_separation - -The maximum separation in number of levels of hierarchy between ancestor -and descendant concepts. This is an attribute that is used to simplify -hierarchic analysis. - - -integer - -Yes - -No - -No - - -
    @@ -14152,288 +1429,6 @@

    source_to_concept_map

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -source_code - -The source code being translated into a Standard Concept. - - -varchar(50) - -Yes - -No - -No - - -
    -source_concept_id - -A foreign key to the Source Concept that is being translated into a -Standard Concept. - -This is either 0 or should be a number above 2 billion, which are the -Concepts reserved for site-specific codes and mappings. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -source_vocabulary_id - -A foreign key to the VOCABULARY table defining the vocabulary of the -source code that is being translated to a Standard Concept. - - -varchar(20) - -Yes - -No - -No - - -
    -source_code_description - -An optional description for the source code. This is included as a -convenience to compare the description of the source code to the name of -the concept. - - -varchar(255) - -No - -No - -No - - -
    -target_concept_id - -The target Concept to which the source code is being mapped. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -target_vocabulary_id - -The Vocabulary of the target Concept. - - -varchar(20) - -Yes - -No - -Yes - -VOCABULARY - -
    -valid_start_date - -The date when the mapping instance was first recorded. - - -date - -Yes - -No - -No - - -
    -valid_end_date - -The date when the mapping instance became invalid because it was deleted -or superseded (updated) by a new relationship. Default value is -31-Dec-2099. - - -date - -Yes - -No - -No - - -
    -invalid_reason - -Reason the mapping instance was invalidated. Possible values are D -(deleted), U (replaced with an update) or NULL when valid_end_date has -the default value. - - -varchar(1) - -No - -No - -No - - -

    drug_strength

    @@ -14446,371 +1441,6 @@

    drug_strength

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -drug_concept_id - -The Concept representing the Branded Drug or Clinical Drug Product. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -ingredient_concept_id - -The Concept representing the active ingredient contained within the drug -product. - -Combination Drugs will have more than one record in this table, one for -each active Ingredient. - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -amount_value - -The numeric value or the amount of active ingredient contained within -the drug product. - - -float - -No - -No - -No - - -
    -amount_unit_concept_id - -The Concept representing the Unit of measure for the amount of active -ingredient contained within the drug product. - - -integer - -No - -No - -Yes - -CONCEPT - -
    -numerator_value - -The concentration of the active ingredient contained within the drug -product. - - -float - -No - -No - -No - - -
    -numerator_unit_concept_id - -The Concept representing the Unit of measure for the concentration of -active ingredient. - - -integer - -No - -No - -Yes - -CONCEPT - -
    -denominator_value - -The amount of total liquid (or other divisible product, such as -ointment, gel, spray, etc.). - - -float - -No - -No - -No - - -
    -denominator_unit_concept_id - -The Concept representing the denominator unit for the concentration of -active ingredient. - - -integer - -No - -No - -Yes - -CONCEPT - -
    -box_size - -The number of units of Clinical Branded Drug or Quantified Clinical or -Branded Drug contained in a box as dispensed to the patient. - - -integer - -No - -No - -No - - -
    -valid_start_date - -The date when the Concept was first recorded. The default value is -1-Jan-1970. - - -date - -Yes - -No - -No - - -
    -valid_end_date - -The date when then Concept became invalid. - - -date - -Yes - -No - -No - - -
    -invalid_reason - -Reason the concept was invalidated. Possible values are D (deleted), U -(replaced with an update) or NULL when valid_end_date has the default -value. - - -varchar(1) - -No - -No - -No - - -

    cohort

    @@ -14839,141 +1469,6 @@

    cohort

    the cohort table for any moment of time, i.e. it is not possible for a person to contain multiple records indicating cohort membership that are overlapping in time

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -cohort_definition_id - - - -integer - -Yes - -No - -No - - -
    -subject_id - - - -integer - -Yes - -No - -No - - -
    -cohort_start_date - - - -date - -Yes - -No - -No - - -
    -cohort_end_date - - - -date - -Yes - -No - -No - - -

    cohort_definition

    @@ -14991,229 +1486,6 @@

    cohort_definition

    NA

    ETL Conventions

    NA

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -CDM Field - -User Guide - -ETL Conventions - -Datatype - -Required - -Primary Key - -Foreign Key - -FK Table - -FK Domain -
    -cohort_definition_id - -This is the identifier given to the cohort, usually by the ATLAS -application - - -integer - -Yes - -No - -Yes - -COHORT - -
    -cohort_definition_name - -A short description of the cohort - - -varchar(255) - -Yes - -No - -No - - -
    -cohort_definition_description - -A complete description of the cohort. - - -varchar(MAX) - -No - -No - -No - - -
    -definition_type_concept_id - -Type defining what kind of Cohort Definition the record represents and -how the syntax may be executed. - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -cohort_definition_syntax - -Syntax or code to operationalize the Cohort Definition. - - -varchar(MAX) - -No - -No - -No - - -
    -subject_concept_id - -This field contains a Concept that represents the domain of the subjects -that are members of the cohort (e.g., Person, Provider, Visit). - - -integer - -Yes - -No - -Yes - -CONCEPT - -
    -cohort_initiation_date - -A date to indicate when the Cohort was initiated in the COHORT table. - - -date - -No - -No - -No - - -
    diff --git a/docs/cdmDecisionTree.html b/docs/cdmDecisionTree.html index 9a0dd67b..b2946dcb 100644 --- a/docs/cdmDecisionTree.html +++ b/docs/cdmDecisionTree.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/cdmPrivacy.html b/docs/cdmPrivacy.html index 1a7b0b91..05df5b3f 100644 --- a/docs/cdmPrivacy.html +++ b/docs/cdmPrivacy.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/cdmRPackage.html b/docs/cdmRPackage.html index cdb3beaa..3bc51cec 100644 --- a/docs/cdmRPackage.html +++ b/docs/cdmRPackage.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/cdmRefreshProcess.html b/docs/cdmRefreshProcess.html index 1d596ba8..f2eae162 100644 --- a/docs/cdmRefreshProcess.html +++ b/docs/cdmRefreshProcess.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/cdmRequestProcess.html b/docs/cdmRequestProcess.html index 380bc8d3..f1f71d38 100644 --- a/docs/cdmRequestProcess.html +++ b/docs/cdmRequestProcess.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/contactVocab.html b/docs/contactVocab.html index 1c38844b..7c5c2a85 100644 --- a/docs/contactVocab.html +++ b/docs/contactVocab.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/contribute.html b/docs/contribute.html index 7a4f70c6..18e45d98 100644 --- a/docs/contribute.html +++ b/docs/contribute.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/customConcepts.html b/docs/customConcepts.html new file mode 100644 index 00000000..23d775cd --- /dev/null +++ b/docs/customConcepts.html @@ -0,0 +1,748 @@ + + + + + + + + + + + + + +Custom Concepts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + +

    By Maxim Moinat and the Themis Working Group

    +

    The Themis Working Group convened on October 6th and December 7th +2023 to discuss the creation this convention for creating custom +concepts.

    +
    +

    Introduction

    +

    While the OMOP vocabularies are very comprehensive, it is not always +possible to use concepts existing in the OMOP vocabularies. For example, +when using a vocabulary that is only used in your institution or having +custom defined variables. In these cases, custom concepts can be used. +Custom concepts are concepts that are not part of the OMOP vocabularies, +and are only used in your institution. There are two main reasons to +define custom concepts in your local OMOP CDM vocabulary. The first is +that they are available in your local Atlas instance, which has several +use cases: - When viewing a standard concept, you can see which custom +concepts are mapped to it. This allows you to better understand what the +standard concept represents in your institution. - You can search for a +custom concept and find which standard concepts it is mapped to, to +include in your standard concept set. - For studies only using your +local data, you can define cohorts using custom concepts (through ‘Add +attribute’->‘Add … Source Concept’). The second reason is using the +custom concepts in your ETL. By creating both the custom concept, and +the ‘Maps to’ relationship (example below), we can use this in the same +way as mapping other source vocabularies.

    +

    Custom concepts are only defined locally. These cannot be +used for network research. Therefore it remains very important to map to +standard concepts.

    +
    +
    +

    Conventions

    +

    It is important to follow a set of conventions when creating custom +concepts, to avoid negatively impacting network studies. The conventions +are as follows:

    +
      +
    • Custom concepts have a concept_id larger than +2,000,000,000. This is to avoid clashes with existing +concepts.†
      • +
    • Custom concepts are always non-standard +(concept.standard_concept = NULL).
      • +
    • Custom concepts can only be used in the +_source_concept_id fields +(e.g. procedure_source_concept_id)
      • +
    • If the field _source_concept_id does not exist, add a +custom column to your table (e.g. a +drug_exposure.route_source_concept_id)1. If +there is a wide need in the community, a proposal can be submitted to +the CDM Working Group to add these fields in a future OMOP CDM +version.
      • +
    • Always add custom concepts to a new vocabulary specifically for your +source (see example below). If you have a need to add concepts to an +existing vocabulary, please contact the OHDSI Vocabulary Working +Group.
      • +
    • Do NOT add custom concepts to the hierarchy of existing vocabularies +(either in the concept_ancestor table or +subsumes/is a relations in the +concept_relationship table). This is to avoid descendant +concepts to differ between sites.
      • +
    +

    In addition, it is recommended to follow these suggestions:

    +
      +
    • For the domain_id, choose an appropriate existing value +from the domain table (‘Condition’, ‘Drug’, ‘Procedure’, etc.). Note +that this determines the target table the concept can be used in.
      • +
    • For the concept_class_id, it is not required to create +new classes for your source vocabulary. To leave the class empty +explicitly, use class ‘Undefined’. It is also allowed to reuse existing +concept classes (e.g. SNOMED’s ‘Clinical Finding’ for conditions or +RxNorm drug classes ‘Ingredient’, ‘Clinical Drug’, ‘Branded Drug’ +etc.).
      • +
    • In the new vocabulary record, the vocabulary_concept_id +can be set to 0, as this is often not used in the OMOP CDM.
      • +
    • Create mappings between custom concepts and standard concepts. This +can be done by adding rows to the concept_relationship +table, with the Maps to relation. The reverse relation, +Mapped from, should also be added. This allows for easy +navigation between custom and standard concepts2. The ‘mapped +to’ concept should be a standard concept.
      • +
    • Officially, concept_hierarchy is only for standard +concepts. However, if you local use case requires this (e.g. for +selection of descendants of custom concepts), the custom concepts can be +added into their own, isolated, hierarchy. ## Example In this example, +we will add one custom concept for the ‘DHD Diagnose Thesaurus’. This is +a Dutch vocabulary, which is not part of the OMOP vocabularies. We will +add the concept ‘diabetes mellitus type 1’. This concept has a mapping +to the standard concept ‘Diabetes mellitus type 1 (disorder)’, +concept_id 3341872.
      • +
    +

    After creating these records, we can use the custom concept in our +ETL to populate the condition_source_concept_id field.

    +
    +

    Custom vocabulary

    + ++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    FieldValue
    vocabulary_idDHD Diagnose Thesaurus
    vocabulary_nameDutch Hospital Data Diagnosethesaurus
    vocabulary_referencehttps://www.dhd.nl/producten-diensten/diagnosethesaurus/Paginas/diagnosethesaurus.asp
    vocabulary_version2023-04-20
    vocabulary_concept_id0
    +
    +
    +

    Custom concept

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    FieldValue
    concept_id2 000 000 001
    concept_namediabetes mellitus type 1
    domain_idCondition
    vocabulary_idDHD Diagnose Thesaurus
    concept_class_idUndefined
    standard_conceptNULL
    concept_code0000002630
    valid_start_date2017-08-01
    valid_end_date2099-12-31
    invalid_reasonNULL
    +
    +
    +

    Mapping relationship

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    FieldValue
    concept_id_12 000 000 001
    concept_id_23341872
    relationship_idMaps to
    valid_start_date2017-08-01
    valid_end_date2099-12-31
    invalid_reasonNULL
    FieldValue
    ——-——-
    concept_id_13341872
    concept_id_22 000 000 001
    relationship_idMapped from
    valid_start_date2017-08-01
    valid_end_date2099-12-31
    invalid_reasonNULL
    +

    See the Source +To Standard query to map a code in the source data to a standard +concept.

    +
    +
    +
    +

    Getting your vocabulary into the OMOP vocabularies

    +

    If you think your custom concepts are useful for others, you can +submit them to the OMOP vocabularies. This could be as a supported +source vocabulary (like ICD) or a new vocabulary with standard concepts +(like LOINC). This is a separate process from the conventions described +above. Please see the this +support page.

    +
    + + + + + +
    + + + + + + + + + + + + + + + diff --git a/docs/dataModelConventions.html b/docs/dataModelConventions.html index 2e4edf26..8cc7cd16 100644 --- a/docs/dataModelConventions.html +++ b/docs/dataModelConventions.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/download.html b/docs/download.html index 014312cc..8ebe269d 100644 --- a/docs/download.html +++ b/docs/download.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/drug_dose.html b/docs/drug_dose.html index 31a4a57b..f0cfda09 100644 --- a/docs/drug_dose.html +++ b/docs/drug_dose.html @@ -292,6 +292,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/ehrObsPeriods.html b/docs/ehrObsPeriods.html index a28abe3a..74789183 100644 --- a/docs/ehrObsPeriods.html +++ b/docs/ehrObsPeriods.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/faq.html b/docs/faq.html index 0075e46a..27b96dec 100644 --- a/docs/faq.html +++ b/docs/faq.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/index.html b/docs/index.html index 9851ad87..2828247f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -293,6 +293,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • @@ -472,22 +475,22 @@

    Calendar

    href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">this form and check “Common Data Model”

    -
    - - - + - - +

    -
    +
    - +
    diff --git a/docs/indices-primary-foreign.html b/docs/indices-primary-foreign.html index 1502c671..4cee1280 100644 --- a/docs/indices-primary-foreign.html +++ b/docs/indices-primary-foreign.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/leaveAsIs.html b/docs/leaveAsIs.html index 0b621fe5..738b24f5 100644 --- a/docs/leaveAsIs.html +++ b/docs/leaveAsIs.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/localChange.html b/docs/localChange.html index 61813210..f08abe93 100644 --- a/docs/localChange.html +++ b/docs/localChange.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/networkUseCase.html b/docs/networkUseCase.html index 717f8c02..cfb624d8 100644 --- a/docs/networkUseCase.html +++ b/docs/networkUseCase.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/oncology.html b/docs/oncology.html index 0d99face..fe71c6a9 100644 --- a/docs/oncology.html +++ b/docs/oncology.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/queries.html b/docs/queries.html index dd0a368b..0a28f9dd 100644 --- a/docs/queries.html +++ b/docs/queries.html @@ -292,6 +292,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/reviewProposals.html b/docs/reviewProposals.html index 45d00c9e..b6f01cc2 100644 --- a/docs/reviewProposals.html +++ b/docs/reviewProposals.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/sqlScripts.html b/docs/sqlScripts.html index 80d3096c..b8364479 100644 --- a/docs/sqlScripts.html +++ b/docs/sqlScripts.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • @@ -508,7 +511,7 @@

    Source to Standard

    script will show ALL mappings, not just those to Standard, Valid Concepts. Be sure to add a filter that will only grab the correct Standard, Valid codes.

    -
    SELECT c.concept_code AS SOURCE_CODE, c.concept_id AS SOURCE_CONCEPT_ID, c.concept_name AS SOURCE_CODE_DESCRIPTION, c.vocabulary_id AS SOURCE_VOCABULARY_ID, c.domain_id AS SOURCE_DOMAIN_ID, c.CONCEPT_CLASS_ID AS SOURCE_CONCEPT_CLASS_ID, c.VALID_START_DATE AS SOURCE_VALID_START_DATE, c.VALID_END_DATE AS SOURCE_VALID_END_DATE, c.INVALID_REASON AS SOURCE_INVALID_REASON, c1.concept_id AS TARGET_CONCEPT_ID, c1.concept_name AS TARGET_CONCEPT_NAME, c1.VOCABULARY_ID AS TARGET_VOCABUALRY_ID, c1.domain_id AS TARGET_DOMAIN_ID, c1.concept_class_id AS TARGET_CONCEPT_CLASS_ID, c1.INVALID_REASON AS TARGET_INVALID_REASON, c1.standard_concept AS TARGET_STANDARD_CONCEPT
+
    SELECT c.concept_code AS SOURCE_CODE, c.concept_id AS SOURCE_CONCEPT_ID, c.concept_name AS SOURCE_CODE_DESCRIPTION, c.vocabulary_id AS SOURCE_VOCABULARY_ID, c.domain_id AS SOURCE_DOMAIN_ID, c.CONCEPT_CLASS_ID AS SOURCE_CONCEPT_CLASS_ID, c.VALID_START_DATE AS SOURCE_VALID_START_DATE, c.VALID_END_DATE AS SOURCE_VALID_END_DATE, c.INVALID_REASON AS SOURCE_INVALID_REASON, c1.concept_id AS TARGET_CONCEPT_ID, c1.concept_name AS TARGET_CONCEPT_NAME, c1.VOCABULARY_ID AS TARGET_VOCABULARY_ID, c1.domain_id AS TARGET_DOMAIN_ID, c1.concept_class_id AS TARGET_CONCEPT_CLASS_ID, c1.INVALID_REASON AS TARGET_INVALID_REASON, c1.standard_concept AS TARGET_STANDARD_CONCEPT
        FROM CONCEPT C
              JOIN CONCEPT_RELATIONSHIP CR
                         ON C.CONCEPT_ID = CR.CONCEPT_ID_1
diff --git a/docs/useCaseN.html b/docs/useCaseN.html
index b9e2b9a1..6b56af84 100644
--- a/docs/useCaseN.html
+++ b/docs/useCaseN.html
@@ -290,6 +290,9 @@
     
  • 
       Patient Privacy and OMOP
     
    • 
+    
  • 
+      Custom Concepts
+    
    •
  • diff --git a/docs/useCaseY.html b/docs/useCaseY.html index 499784ef..7518230d 100644 --- a/docs/useCaseY.html +++ b/docs/useCaseY.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/vocabN.html b/docs/vocabN.html index 72f99a8d..d48661f8 100644 --- a/docs/vocabN.html +++ b/docs/vocabN.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/vocabRequest.html b/docs/vocabRequest.html index faf60312..bc3a5695 100644 --- a/docs/vocabRequest.html +++ b/docs/vocabRequest.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/vocabY.html b/docs/vocabY.html index 70ccedad..457a2473 100644 --- a/docs/vocabY.html +++ b/docs/vocabY.html @@ -290,6 +290,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/docs/vocabulary.html b/docs/vocabulary.html index f27289b7..e6feea65 100644 --- a/docs/vocabulary.html +++ b/docs/vocabulary.html @@ -366,6 +366,9 @@
  • Patient Privacy and OMOP
    • +
  • + Custom Concepts +
  • diff --git a/rmd/_site.yml b/rmd/_site.yml index 7932406e..7650b266 100644 --- a/rmd/_site.yml +++ b/rmd/_site.yml @@ -33,6 +33,8 @@ navbar: href: ehrObsPeriods.html - text: "Patient Privacy and OMOP" href: cdmPrivacy.html + - text: "Custom Concepts" + href: customConcepts.html - text: "CDM Versions" icon: fa-history menu: diff --git a/rmd/customConcepts.Rmd b/rmd/customConcepts.Rmd new file mode 100644 index 00000000..0e1eddbf --- /dev/null +++ b/rmd/customConcepts.Rmd @@ -0,0 +1,99 @@ +--- +title: "**Custom Concepts**" +output: html_document +--- + +*By Maxim Moinat and the Themis Working Group* + +The Themis Working Group convened on October 6th and December 7th 2023 to discuss the creation this convention for creating custom concepts. + +## Introduction + +While the OMOP vocabularies are very comprehensive, it is not always possible to use concepts existing in the OMOP vocabularies. For example, when using a vocabulary that is only used in your institution or having custom defined variables. In these cases, custom concepts can be used. Custom concepts are concepts that are not part of the OMOP vocabularies, and are only used in your institution. +There are two main reasons to define custom concepts in your local OMOP CDM vocabulary. The first is that they are available in your local Atlas instance, which has several use cases: + - When viewing a standard concept, you can see which custom concepts are mapped to it. This allows you to better understand what the standard concept represents in your institution. + - You can search for a custom concept and find which standard concepts it is mapped to, to include in your standard concept set. + - For studies only using your local data, you can define cohorts using custom concepts (through 'Add attribute'->'Add ... Source Concept'). +The second reason is using the custom concepts in your ETL. By creating both the custom concept, and the 'Maps to' relationship (example below), we can use this in the same way as mapping other source vocabularies. + +**Custom concepts are only defined locally. These cannot be used for network research. Therefore it remains very important to map to standard concepts.** + +## Conventions + +It is important to follow a set of conventions when creating custom concepts, to avoid negatively impacting network studies. The conventions are as follows: + +- Custom concepts have a `concept_id` larger than 2,000,000,000. This is to avoid clashes with existing concepts.† +- Custom concepts are always non-standard (`concept.standard_concept = NULL`). +- Custom concepts can only be used in the `_source_concept_id` fields (e.g. `procedure_source_concept_id`) +- If the field `_source_concept_id` does not exist, add a custom column to your table (e.g. a `drug_exposure.route_source_concept_id`)1. If there is a wide need in the community, a proposal can be submitted to the CDM Working Group to add these fields in a future OMOP CDM version. +- Always add custom concepts to a new vocabulary specifically for your source (see example below). If you have a need to add concepts to an existing vocabulary, please contact the OHDSI Vocabulary Working Group. +- Do NOT add custom concepts to the hierarchy of existing vocabularies (either in the `concept_ancestor` table or `subsumes`/`is a` relations in the `concept_relationship` table). This is to avoid descendant concepts to differ between sites. + +In addition, it is recommended to follow these suggestions: + +- For the `domain_id`, choose an appropriate existing value from the domain table ('Condition', 'Drug', 'Procedure', etc.). Note that this determines the target table the concept can be used in. +- For the `concept_class_id`, it is not required to create new classes for your source vocabulary. To leave the class empty explicitly, use class 'Undefined'. It is also allowed to reuse existing concept classes (e.g. SNOMED's 'Clinical Finding' for conditions or RxNorm drug classes 'Ingredient', 'Clinical Drug', 'Branded Drug' etc.). +- In the new vocabulary record, the `vocabulary_concept_id` can be set to 0, as this is often not used in the OMOP CDM. +- Create mappings between custom concepts and standard concepts. This can be done by adding rows to the `concept_relationship` table, with the `Maps to` relation. The reverse relation, `Mapped from`, should also be added. This allows for easy navigation between custom and standard concepts2. The 'mapped to' concept should be a standard concept. +- Officially, `concept_hierarchy` is only for standard concepts. However, if you local use case requires this (e.g. for selection of descendants of custom concepts), the custom concepts can be added into their own, isolated, hierarchy. +## Example +In this example, we will add one custom concept for the 'DHD Diagnose Thesaurus'. This is a Dutch vocabulary, which is not part of the OMOP vocabularies. We will add the concept 'diabetes mellitus type 1'. This concept has a mapping to the standard concept 'Diabetes mellitus type 1 (disorder)', concept_id 3341872. + +After creating these records, we can use the custom concept in our ETL to populate the `condition_source_concept_id` field. + +### Custom vocabulary + +| Field | Value | +|-------|-------| +| vocabulary_id | DHD Diagnose Thesaurus | +| vocabulary_name | Dutch Hospital Data Diagnosethesaurus | +| vocabulary_reference | https://www.dhd.nl/producten-diensten/diagnosethesaurus/Paginas/diagnosethesaurus.asp | +| vocabulary_version | 2023-04-20 | +| vocabulary_concept_id | 0 | + +### Custom concept + +| Field | Value | +|-------|-------| +| concept_id | 2 000 000 001 | +| concept_name | diabetes mellitus type 1 | +| domain_id | Condition | +| vocabulary_id | DHD Diagnose Thesaurus | +| concept_class_id | Undefined | +| standard_concept | `NULL` | +| concept_code | 0000002630 | +| valid_start_date | 2017-08-01 | +| valid_end_date | 2099-12-31 | +| invalid_reason | `NULL` | + +### Mapping relationship + +| Field | Value | +|-------|-------| +| concept_id_1 | 2 000 000 001 | +| concept_id_2 | 3341872 | +| relationship_id | Maps to | +| valid_start_date | 2017-08-01 | +| valid_end_date | 2099-12-31 | +| invalid_reason | `NULL` | +| Field | Value | +|-------|-------| +| concept_id_1 | 3341872 | +| concept_id_2 | 2 000 000 001 | +| relationship_id | Mapped from | +| valid_start_date | 2017-08-01 | +| valid_end_date | 2099-12-31 | +| invalid_reason | `NULL` | + +See the [Source To Standard query](https://ohdsi.github.io/CommonDataModel/sqlScripts.html#Source_to_Standard) to map a code in the source data to a standard concept. + +## Getting your vocabulary into the OMOP vocabularies + +If you think your custom concepts are useful for others, you can submit them to the OMOP vocabularies. This could be as a supported source vocabulary (like ICD) or a new vocabulary with standard concepts (like LOINC). This is a separate process from the conventions described above. Please see the [this support page](https://ohdsi.github.io/CommonDataModel/vocabRequest.html). + +## References +1[Melanie Philofsky; Implementing & adopting a customized OMOP Common Data Model; OHDSI Symposium 2021](https://www.ohdsi.org/2021-global-symposium-showcase-18/) + +2[Melanie Philofsky; Mapping Custom Source Codes to Standard Concepts: A Comparison of Two Approaches; OHDSI Symposium 2020](https://www.ohdsi.org/wp-content/uploads/2020/10/Melanie-Philofsky-Philofsky-Mapping-Source-Codes-Poster.pdf) +
    +†this is why custom concepts are sometimes referred to as "2B+" or "2billionaires".