diff --git a/CommonDataModel.Rproj b/CommonDataModel.Rproj index ce013e1..c763d05 100644 --- a/CommonDataModel.Rproj +++ b/CommonDataModel.Rproj @@ -1,21 +1,21 @@ -Version: 1.0 - -RestoreWorkspace: Default -SaveWorkspace: Default -AlwaysSaveHistory: Default - -EnableCodeIndexing: Yes -UseSpacesForTab: Yes -NumSpacesForTab: 2 -Encoding: UTF-8 - -RnwWeave: Sweave -LaTeX: XeLaTeX - -AutoAppendNewline: Yes -StripTrailingWhitespace: Yes - -BuildType: Package -PackageUseDevtools: Yes -PackageInstallArgs: --no-multiarch --with-keep.source -PackageRoxygenize: rd,collate,namespace +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: XeLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace diff --git a/docs/indices-primary-foreign.html b/docs/indices-primary-foreign.html new file mode 100644 index 0000000..8e98c81 --- /dev/null +++ b/docs/indices-primary-foreign.html @@ -0,0 +1,603 @@ + + + + + + + + + + + + + +Indices, Primary Keys and Foreign Key Constraints + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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To Do

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  • Need something for hashing
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  • What about constraints that aren’t foreign keys
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Overview

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Database indices improve the performance of queries against a database by organizing the data in a way that increase query execution.

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This article was written to provide guidance on the setting of indices, primary and foreign keys for data that has been transformed into the Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM). The community that supports the design and development of the OHDSI/CommonDataModel Github repository is a diverse collaborative of healthcare and technical profesisonals whom have limited data base adminstrative (DBA) experience. As a result, the comments below should be interpreted as suggestions and recommendations to help increase performance. Your teams needs may call for a modified configuration.

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General Recommendations

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Should your database of choice support indexing, the OMOP CDM Working Group recommends

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  • Indexing on all columns containing an "_id" (e.g. condition_occurrence_id, drug_exposure_id, measurement_id, procedure_occurrence_id, etc.)
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  • Indexing on primary and foreign keys
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For all databases, regardless of custom indice support, primary and foreign keys should be set. This is a step towards ensuring data integrity.

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Database support

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The OHDSI/CommonDataModel package leverages OHDSI/SQLRender and as a result is only capable of supporting sources that are supported by OHDSI/SQLRender. The following databases are currently supported.

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Microsoft SQL Server

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Oracle

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PostgreSQL

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Amazon Redshift

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On AWS Redshift it is important to ensure that your data is properly distributed and sorted across nodes. Compression on certain columns may also help. The designed DDL does set DISTKEYS in an effort to optimize performance. This configuration can be seen within the Redshift-specific DDL.

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Impala

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IBM Netezza

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Google BigQuery

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Google BigQuery does not require manual optimization and/or sizing. Google BigQuery does massive parallel full table scans and intensive caching, all under the hood. Reference

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Microsoft Parallel Data Warehouse (PDW)

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SQLite

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Databricks

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This database type is not yet supported but is actively being worked on by a number of collaborators. For more informtion, please contact Ajit Londhe of Amgen.

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+ + + + + + + + + + + + + + + + diff --git a/docs/site_libs/navigation-1.1/codefolding.js b/docs/site_libs/navigation-1.1/codefolding.js index 1e16fde..8a0d36f 100644 --- a/docs/site_libs/navigation-1.1/codefolding.js +++ b/docs/site_libs/navigation-1.1/codefolding.js @@ -23,7 +23,6 @@ window.initializeCodeFolding = function(show) { // create a collapsable div to wrap the code in var div = $('
'); var showThis = (show || $(this).hasClass('fold-show')) && !$(this).hasClass('fold-hide'); - if (showThis) div.addClass('in'); var id = 'rcode-643E0F36' + currentIndex++; div.attr('id', id); $(this).before(div); @@ -31,7 +30,7 @@ window.initializeCodeFolding = function(show) { // add a show code button right above var showCodeText = $('' + (showThis ? 'Hide' : 'Code') + ''); - var showCodeButton = $(''); + var showCodeButton = $(''); showCodeButton.append(showCodeText); showCodeButton .attr('data-toggle', 'collapse') @@ -47,13 +46,27 @@ window.initializeCodeFolding = function(show) { div.before(buttonRow); + // show the div if necessary + if (showThis) div.collapse('show'); + // update state of button on show/hide - div.on('hidden.bs.collapse', function () { + // * Change text + // * add a class for intermediate states styling + div.on('hide.bs.collapse', function () { showCodeText.text('Code'); + showCodeButton.addClass('btn-collapsing'); + }); + div.on('hidden.bs.collapse', function () { + showCodeButton.removeClass('btn-collapsing'); }); div.on('show.bs.collapse', function () { showCodeText.text('Hide'); + showCodeButton.addClass('btn-expanding'); }); + div.on('shown.bs.collapse', function () { + showCodeButton.removeClass('btn-expanding'); + }); + }); } diff --git a/docs/site_libs/tocify-1.9.1/jquery.tocify.js b/docs/site_libs/tocify-1.9.1/jquery.tocify.js index ba24a7d..ca47b5f 100644 --- a/docs/site_libs/tocify-1.9.1/jquery.tocify.js +++ b/docs/site_libs/tocify-1.9.1/jquery.tocify.js @@ -176,7 +176,7 @@ self._setEventHandlers(); // Binding to the Window load event to make sure the correct scrollTop is calculated - $(window).load(function() { + $(window).on("load", function() { // Sets the active TOC item self._setActiveElement(true); diff --git a/inst/csv/OMOP_CDMv5.4_Field_Level.csv b/inst/csv/OMOP_CDMv5.4_Field_Level.csv index c01a9eb..fc59bf8 100644 --- a/inst/csv/OMOP_CDMv5.4_Field_Level.csv +++ b/inst/csv/OMOP_CDMv5.4_Field_Level.csv @@ -1,224 +1,224 @@ -cdmTableName,cdmFieldName,isRequired,cdmDatatype,userGuidance,etlConventions,isPrimaryKey,isForeignKey,fkTableName,fkFieldName,fkDomain,fkClass,unique DQ identifiers -PERSON,person_id,Yes,integer,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.",Yes,No,,,,, -PERSON,gender_concept_id,Yes,integer,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](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table. [Accepted gender concepts](http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,Gender,, -PERSON,year_of_birth,Yes,integer,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.",No,No,,,,, -PERSON,month_of_birth,No,integer,,"For data sources that provide the precise date of birth, the month should be extracted and stored in this field.",No,No,,,,, -PERSON,day_of_birth,No,integer,,"For data sources that provide the precise date of birth, the day should be extracted and stored in this field.",No,No,,,,, -PERSON,birth_datetime,No,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).",No,No,,,,, -PERSON,race_concept_id,Yes,integer,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](http://athena.ohdsi.org/search-terms/terms?domain=Race&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Race,, -PERSON,ethnicity_concept_id,Yes,integer,"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](http://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&standardConcept=Standard&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,Ethnicity,, -PERSON,location_id,No,integer,The location refers to the physical address of the person. This field should capture the last known location of the person. ,"Put the location_id from the [LOCATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#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. ",No,Yes,LOCATION,LOCATION_ID,,, -PERSON,provider_id,No,integer,The Provider refers to the last known primary care provider (General Practitioner).,"Put the provider_id from the [PROVIDER](https://ohdsi.github.io/CommonDataModel/cdm531.html#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.",No,Yes,PROVIDER,PROVIDER_ID,,, -PERSON,care_site_id,No,integer,The Care Site refers to where the Provider typically provides the primary care.,,No,Yes,CARE_SITE,CARE_SITE_ID,,, -PERSON,person_source_value,No,varchar(50),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.,No,No,,,,, -PERSON,gender_source_value,No,varchar(50),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.,No,No,,,,, -PERSON,gender_source_concept_id,No,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,,, -PERSON,race_source_value,No,varchar(50),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.,No,No,,,,, -PERSON,race_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, -PERSON,ethnicity_source_value,No,varchar(50),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.",No,No,,,,, -PERSON,ethnicity_source_concept_id,No,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,,, -OBSERVATION_PERIOD,observation_period_id,Yes,integer,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.,Yes,No,,,,, -OBSERVATION_PERIOD,person_id,Yes,integer,The Person ID of the PERSON record for which the Observation Period is recorded.,,No,Yes,PERSON,PERSON_ID,,, -OBSERVATION_PERIOD,observation_period_start_date,Yes,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](https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period).",No,No,,,,, -OBSERVATION_PERIOD,observation_period_end_date,Yes,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.",No,No,,,,, -OBSERVATION_PERIOD,period_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -VISIT_OCCURRENCE,visit_occurrence_id,Yes,integer,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.,Yes,No,,,,, -VISIT_OCCURRENCE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, -VISIT_OCCURRENCE,visit_concept_id,Yes,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, -VISIT_OCCURRENCE,visit_start_date,Yes,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.",No,No,,,,, -VISIT_OCCURRENCE,visit_start_datetime,No,datetime,,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,,,,, +cdmTableName,cdmFieldName,isRequired,cdmDatatype,userGuidance,etlConventions,isPrimaryKey,isForeignKey,fkTableName,fkFieldName,fkDomain,fkClass,unique DQ identifiers +PERSON,person_id,Yes,integer,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.",Yes,No,,,,, +PERSON,gender_concept_id,Yes,integer,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](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table. [Accepted gender concepts](http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,Gender,, +PERSON,year_of_birth,Yes,integer,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.",No,No,,,,, +PERSON,month_of_birth,No,integer,,"For data sources that provide the precise date of birth, the month should be extracted and stored in this field.",No,No,,,,, +PERSON,day_of_birth,No,integer,,"For data sources that provide the precise date of birth, the day should be extracted and stored in this field.",No,No,,,,, +PERSON,birth_datetime,No,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).",No,No,,,,, +PERSON,race_concept_id,Yes,integer,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](http://athena.ohdsi.org/search-terms/terms?domain=Race&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Race,, +PERSON,ethnicity_concept_id,Yes,integer,"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](http://athena.ohdsi.org/search-terms/terms?domain=Ethnicity&standardConcept=Standard&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,Ethnicity,, +PERSON,location_id,No,integer,The location refers to the physical address of the person. This field should capture the last known location of the person. ,"Put the location_id from the [LOCATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#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. ",No,Yes,LOCATION,LOCATION_ID,,, +PERSON,provider_id,No,integer,The Provider refers to the last known primary care provider (General Practitioner).,"Put the provider_id from the [PROVIDER](https://ohdsi.github.io/CommonDataModel/cdm531.html#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.",No,Yes,PROVIDER,PROVIDER_ID,,, +PERSON,care_site_id,No,integer,The Care Site refers to where the Provider typically provides the primary care.,,No,Yes,CARE_SITE,CARE_SITE_ID,,, +PERSON,person_source_value,No,varchar(50),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.,No,No,,,,, +PERSON,gender_source_value,No,varchar(50),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.,No,No,,,,, +PERSON,gender_source_concept_id,No,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,,, +PERSON,race_source_value,No,varchar(50),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.,No,No,,,,, +PERSON,race_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, +PERSON,ethnicity_source_value,No,varchar(50),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.",No,No,,,,, +PERSON,ethnicity_source_concept_id,No,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,,, +OBSERVATION_PERIOD,observation_period_id,Yes,integer,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.,Yes,No,,,,, +OBSERVATION_PERIOD,person_id,Yes,integer,The Person ID of the PERSON record for which the Observation Period is recorded.,,No,Yes,PERSON,PERSON_ID,,, +OBSERVATION_PERIOD,observation_period_start_date,Yes,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](https://ohdsi.github.io/CommonDataModel/cdm531.html#payer_plan_period).",No,No,,,,, +OBSERVATION_PERIOD,observation_period_end_date,Yes,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.",No,No,,,,, +OBSERVATION_PERIOD,period_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +VISIT_OCCURRENCE,visit_occurrence_id,Yes,integer,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.,Yes,No,,,,, +VISIT_OCCURRENCE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, +VISIT_OCCURRENCE,visit_concept_id,Yes,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, +VISIT_OCCURRENCE,visit_start_date,Yes,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.",No,No,,,,, +VISIT_OCCURRENCE,visit_start_datetime,No,datetime,,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,,,,, VISIT_OCCURRENCE,visit_end_date,Yes,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.",No,No,,,,, -VISIT_OCCURRENCE,visit_end_datetime,No,datetime,,"If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,, -VISIT_OCCURRENCE,visit_type_concept_id,Yes,Integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -VISIT_OCCURRENCE,provider_id,No,integer,"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](https://ohdsi.github.io/CommonDataModel/cdm531.html#visit_detail) table.",No,Yes,PROVIDER,PROVIDER_ID,,, -VISIT_OCCURRENCE,care_site_id,No,integer,This field provides information about the Care Site where the Visit took place.,There should only be one Care Site associated with a Visit.,No,Yes,CARE_SITE,CARE_SITE_ID,,, -VISIT_OCCURRENCE,visit_source_value,No,varchar(50),"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.",No,No,,,,, -VISIT_OCCURRENCE,visit_source_concept_id,No,integer,,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.,No,Yes,CONCEPT,CONCEPT_ID,,, -VISIT_OCCURRENCE,admitted_from_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, -VISIT_OCCURRENCE,admitted_from_source_value,No,varchar(50),,"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.",No,No,,,,, -VISIT_OCCURRENCE,discharged_to_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, -VISIT_OCCURRENCE,discharged_to_source_value,No,varchar(50),,"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.",No,No,,,,, -VISIT_OCCURRENCE,preceding_visit_occurrence_id,No,integer,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.,"This field 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"".",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, -VISIT_DETAIL,visit_detail_id,Yes,integer,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.,Yes,No,,,,, -VISIT_DETAIL,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, -VISIT_DETAIL,visit_detail_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, -VISIT_DETAIL,visit_detail_start_date,Yes,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_DETAIL_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.",No,No,,,,, -VISIT_DETAIL,visit_detail_start_datetime,No,datetime,,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,,,,, +- All other Visits: visit_end_datetime = visit_start_datetime. If this is a one-day visit the end date should match the start date.",No,No,,,,, +VISIT_OCCURRENCE,visit_end_datetime,No,datetime,,"If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,, +VISIT_OCCURRENCE,visit_type_concept_id,Yes,Integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +VISIT_OCCURRENCE,provider_id,No,integer,"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](https://ohdsi.github.io/CommonDataModel/cdm531.html#visit_detail) table.",No,Yes,PROVIDER,PROVIDER_ID,,, +VISIT_OCCURRENCE,care_site_id,No,integer,This field provides information about the Care Site where the Visit took place.,There should only be one Care Site associated with a Visit.,No,Yes,CARE_SITE,CARE_SITE_ID,,, +VISIT_OCCURRENCE,visit_source_value,No,varchar(50),"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.",No,No,,,,, +VISIT_OCCURRENCE,visit_source_concept_id,No,integer,,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.,No,Yes,CONCEPT,CONCEPT_ID,,, +VISIT_OCCURRENCE,admitted_from_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, +VISIT_OCCURRENCE,admitted_from_source_value,No,varchar(50),,"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.",No,No,,,,, +VISIT_OCCURRENCE,discharged_to_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, +VISIT_OCCURRENCE,discharged_to_source_value,No,varchar(50),,"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.",No,No,,,,, +VISIT_OCCURRENCE,preceding_visit_occurrence_id,No,integer,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.,"This field 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"".",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, +VISIT_DETAIL,visit_detail_id,Yes,integer,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.,Yes,No,,,,, +VISIT_DETAIL,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, +VISIT_DETAIL,visit_detail_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, +VISIT_DETAIL,visit_detail_start_date,Yes,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_DETAIL_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.",No,No,,,,, +VISIT_DETAIL,visit_detail_start_datetime,No,datetime,,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,,,,, VISIT_DETAIL,visit_detail_end_date,Yes,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:
- 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.
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. ",No,No,,,,, -VISIT_DETAIL,visit_detail_end_datetime,No,datetime,,"If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,, -VISIT_DETAIL,visit_detail_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -VISIT_DETAIL,provider_id,No,integer,"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.,No,Yes,PROVIDER,PROVIDER_ID,,, -VISIT_DETAIL,care_site_id,No,integer,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.,No,Yes,CARE_SITE,CARE_SITE_ID,,, -VISIT_DETAIL,visit_detail_source_value,No,varchar(50),"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.",No,No,,,,, -VISIT_DETAIL,visit_detail_source_concept_id,No,Integer,,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.,No,Yes,CONCEPT,CONCEPT_ID,,, -VISIT_DETAIL,admitted_from_concept_id,No,Integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, -VISIT_DETAIL,admitted_from_source_value,No,Varchar(50),,"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.",No,No,,,,, -VISIT_DETAIL,discharged_to_source_value,No,Varchar(50),,"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.",No,No,,,,, -VISIT_DETAIL,discharged_to_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, -VISIT_DETAIL,preceding_visit_detail_id,No,integer,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"".",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, -VISIT_DETAIL,parent_visit_detail_id,No,integer,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. ",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, -VISIT_DETAIL,visit_occurrence_id,Yes,integer,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.,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, -CONDITION_OCCURRENCE,condition_occurrence_id,Yes,integer,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.",Yes,No,,,,, -CONDITION_OCCURRENCE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the condition is recorded.,,No,Yes,PERSON,PERSON_ID,,, -CONDITION_OCCURRENCE,condition_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Condition&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Condition,, -CONDITION_OCCURRENCE,condition_start_date,Yes,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.",No,No,,,,, -CONDITION_OCCURRENCE,condition_start_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,, -CONDITION_OCCURRENCE,condition_end_date,No,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.",No,No,,,,, -CONDITION_OCCURRENCE,condition_end_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,, -CONDITION_OCCURRENCE,condition_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -CONDITION_OCCURRENCE,condition_status_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Condition Status,, -CONDITION_OCCURRENCE,stop_reason,No,varchar(20),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.,No,No,,,,, -CONDITION_OCCURRENCE,provider_id,No,integer,"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.",No,Yes,PROVIDER,PROVIDER_ID,,, -CONDITION_OCCURRENCE,visit_occurrence_id,No,integer,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.",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, -CONDITION_OCCURRENCE,visit_detail_id,No,integer,"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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, -CONDITION_OCCURRENCE,condition_source_value,No,varchar(50),"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.,No,No,,,,, -CONDITION_OCCURRENCE,condition_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, -CONDITION_OCCURRENCE,condition_status_source_value,No,varchar(50),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.,No,No,,,,, -DRUG_EXPOSURE,drug_exposure_id,Yes,integer,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.",Yes,No,,,,, -DRUG_EXPOSURE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the drug dispensing or administration is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,, -DRUG_EXPOSURE,drug_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,, -DRUG_EXPOSURE,drug_exposure_start_date,Yes,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.",No,No,,,,, -DRUG_EXPOSURE,drug_exposure_start_datetime,No,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)",No,No,,,,, -DRUG_EXPOSURE,drug_exposure_end_date,Yes,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:

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](https://ohdsi.github.io/CommonDataModel/drug_dose.html)",No,No,,,,, -DRUG_EXPOSURE,drug_exposure_end_datetime,No,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)",No,No,,,,, -DRUG_EXPOSURE,verbatim_end_date,No,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.,No,No,,,,, -DRUG_EXPOSURE,drug_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -DRUG_EXPOSURE,stop_reason,No,varchar(20),"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.,No,No,,,,, -DRUG_EXPOSURE,refills,No,integer,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.,,No,No,,,,, +All other Visits Details: visit_detail_end_datetime = visit_detail_start_datetime. ",No,No,,,,, +VISIT_DETAIL,visit_detail_end_datetime,No,datetime,,"If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,, +VISIT_DETAIL,visit_detail_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +VISIT_DETAIL,provider_id,No,integer,"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.,No,Yes,PROVIDER,PROVIDER_ID,,, +VISIT_DETAIL,care_site_id,No,integer,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.,No,Yes,CARE_SITE,CARE_SITE_ID,,, +VISIT_DETAIL,visit_detail_source_value,No,varchar(50),"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.",No,No,,,,, +VISIT_DETAIL,visit_detail_source_concept_id,No,Integer,,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.,No,Yes,CONCEPT,CONCEPT_ID,,, +VISIT_DETAIL,admitted_from_concept_id,No,Integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, +VISIT_DETAIL,admitted_from_source_value,No,Varchar(50),,"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.",No,No,,,,, +VISIT_DETAIL,discharged_to_source_value,No,Varchar(50),,"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.",No,No,,,,, +VISIT_DETAIL,discharged_to_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,, +VISIT_DETAIL,preceding_visit_detail_id,No,integer,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"".",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, +VISIT_DETAIL,parent_visit_detail_id,No,integer,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. ",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, +VISIT_DETAIL,visit_occurrence_id,Yes,integer,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.,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, +CONDITION_OCCURRENCE,condition_occurrence_id,Yes,integer,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.",Yes,No,,,,, +CONDITION_OCCURRENCE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the condition is recorded.,,No,Yes,PERSON,PERSON_ID,,, +CONDITION_OCCURRENCE,condition_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Condition&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Condition,, +CONDITION_OCCURRENCE,condition_start_date,Yes,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.",No,No,,,,, +CONDITION_OCCURRENCE,condition_start_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,, +CONDITION_OCCURRENCE,condition_end_date,No,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.",No,No,,,,, +CONDITION_OCCURRENCE,condition_end_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,, +CONDITION_OCCURRENCE,condition_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +CONDITION_OCCURRENCE,condition_status_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Condition Status,, +CONDITION_OCCURRENCE,stop_reason,No,varchar(20),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.,No,No,,,,, +CONDITION_OCCURRENCE,provider_id,No,integer,"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.",No,Yes,PROVIDER,PROVIDER_ID,,, +CONDITION_OCCURRENCE,visit_occurrence_id,No,integer,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.",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, +CONDITION_OCCURRENCE,visit_detail_id,No,integer,"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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, +CONDITION_OCCURRENCE,condition_source_value,No,varchar(50),"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.,No,No,,,,, +CONDITION_OCCURRENCE,condition_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, +CONDITION_OCCURRENCE,condition_status_source_value,No,varchar(50),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.,No,No,,,,, +DRUG_EXPOSURE,drug_exposure_id,Yes,integer,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.",Yes,No,,,,, +DRUG_EXPOSURE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the drug dispensing or administration is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,, +DRUG_EXPOSURE,drug_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,, +DRUG_EXPOSURE,drug_exposure_start_date,Yes,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.",No,No,,,,, +DRUG_EXPOSURE,drug_exposure_start_datetime,No,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)",No,No,,,,, +DRUG_EXPOSURE,drug_exposure_end_date,Yes,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:

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](https://ohdsi.github.io/CommonDataModel/drug_dose.html)",No,No,,,,, +DRUG_EXPOSURE,drug_exposure_end_datetime,No,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)",No,No,,,,, +DRUG_EXPOSURE,verbatim_end_date,No,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.,No,No,,,,, +DRUG_EXPOSURE,drug_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +DRUG_EXPOSURE,stop_reason,No,varchar(20),"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.,No,No,,,,, +DRUG_EXPOSURE,refills,No,integer,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.,,No,No,,,,, DRUG_EXPOSURE,quantity,No,float,,"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](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. -",No,No,,,,, -DRUG_EXPOSURE,days_supply,No,integer,,Days supply of the drug. This should be the verbatim days_supply as given on the prescription. If the drug is physician administered use duration end date if given or set to 1 as default if duration is not available.,No,No,,,,, -DRUG_EXPOSURE,sig,No,varchar(MAX),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.",No,No,,,,, -DRUG_EXPOSURE,route_concept_id,No,integer,,The standard CONCEPT_ID that the ROUTE_SOURCE_VALUE maps to in the route domain.,No,Yes,CONCEPT,CONCEPT_ID,Route,, -DRUG_EXPOSURE,lot_number,No,varchar(50),,,No,No,,,,, -DRUG_EXPOSURE,provider_id,No,integer,"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.",No,Yes,PROVIDER,PROVIDER_ID,,, -DRUG_EXPOSURE,visit_occurrence_id,No,integer,"The Visit during which the drug was prescribed, administered or dispensed.",To populate this field drug exposures must be explicitly initiated in the visit.,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, -DRUG_EXPOSURE,visit_detail_id,No,integer,"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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, -DRUG_EXPOSURE,drug_source_value,No,varchar(50),"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.,No,No,,,,, -DRUG_EXPOSURE,drug_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, -DRUG_EXPOSURE,route_source_value,No,varchar(50),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.,No,No,,,,, -DRUG_EXPOSURE,dose_unit_source_value,No,varchar(50),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.,No,No,,,,, -PROCEDURE_OCCURRENCE,procedure_occurrence_id,Yes,integer,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.",Yes,No,,,,, -PROCEDURE_OCCURRENCE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the procedure is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,, -PROCEDURE_OCCURRENCE,procedure_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Procedure&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Procedure,, -PROCEDURE_OCCURRENCE,procedure_date,Yes,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.",No,No,,,,, -PROCEDURE_OCCURRENCE,procedure_datetime,No,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)",No,No,,,,, -PROCEDURE_OCCURRENCE,procedure_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -PROCEDURE_OCCURRENCE,modifier_concept_id,No,integer,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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?conceptClass=CPT4+Modifier&conceptClass=HCPCS+Modifier&vocabulary=CPT4&vocabulary=HCPCS&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, -PROCEDURE_OCCURRENCE,quantity,No,integer,"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",No,No,,,,, -PROCEDURE_OCCURRENCE,provider_id,No,integer,"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.",No,No,PROVIDER,PROVIDER_ID,,, -PROCEDURE_OCCURRENCE,visit_occurrence_id,No,integer,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.",No,No,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, -PROCEDURE_OCCURRENCE,visit_detail_id,No,integer,"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.,No,No,VISIT_DETAIL,VISIT_DETAIL_ID,,, -PROCEDURE_OCCURRENCE,procedure_source_value,No,varchar(50),"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.,No,No,,,,, -PROCEDURE_OCCURRENCE,procedure_source_concept_id,No,integer,"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.,No,No,CONCEPT,CONCEPT_ID,,, -PROCEDURE_OCCURRENCE,modifier_source_value,No,varchar(50),,The original modifier code from the source is stored here for reference.,No,No,,,,, -PROCEDURE_OCCURRENCE,procedure_status_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the procedure status (primary or secondary).,"This information may be called something different in the source data but the field is meant to contain a value indicating whether the procedure was the primary reason for performing a surgical operation, infusion, etc. This source value is mapped to a standard concept which is stored in the PROCEDURE_STATUS_CONCEPT_ID field.",,,,,,, -PROCEDURE_OCCURRENCE,procedure_status_concept_id,Yes,integer,"This concept represents if the procedure was the primary reason for the surgical operation, infusion, etc . ",Choose the Concept in the Procedure Status domain that best represents the status ( [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status&standardConcept=Standard&page=1&pageSize=15&query=).,,,,,,, -DEVICE_EXPOSURE,device_exposure_id,Yes,integer,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. ,Yes,No,,,,, -DEVICE_EXPOSURE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, -DEVICE_EXPOSURE,device_concept_id,Yes,integer,"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. ,No,Yes,CONCEPT,CONCEPT_ID,Device,, -DEVICE_EXPOSURE,device_exposure_start_date,Yes,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. ",No,No,,,,, -DEVICE_EXPOSURE,device_exposure_start_datetime,No,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)",No,No,,,,, -DEVICE_EXPOSURE,device_exposure_end_date,No,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.,No,No,,,,, -DEVICE_EXPOSURE,device_exposure_end_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,, -DEVICE_EXPOSURE,device_type_concept_id,Yes,integer,"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. ","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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -DEVICE_EXPOSURE,unique_device_id,No,varchar(255),"This is the Unique Device Identification (UDI-DI) 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.",No,No,,,,, -DEVICE_EXPOSURE,production_id,No,varchar(255),This is the Production Identifier (UDI-PI) portion of the Unique Device Identification.,,,,,,,, -DEVICE_EXPOSURE,quantity,No,integer,,,No,No,,,,, -DEVICE_EXPOSURE,provider_id,No,integer,"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.,No,Yes,PROVIDER,PROVIDER_ID,,, -DEVICE_EXPOSURE,visit_occurrence_id,No,integer,The Visit during which the device was prescribed or given.,To populate this field device exposures must be explicitly initiated in the visit.,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, -DEVICE_EXPOSURE,visit_detail_id,No,integer,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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, -DEVICE_EXPOSURE,device_source_value,No,varchar(50),"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.,No,No,,,,, -DEVICE_EXPOSURE,device_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, -DEVICE_EXPOSURE,unit_concept_id,No,integer,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 DEVICE_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If there is no unit associated with a Device record, set to NULL.",,,,,,, -DEVICE_EXPOSURE,unit_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the unit of the Device. For example, blood transfusions are considered devices and can be given in mL quantities. ","This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. Using the blood transfusion example, blood transfusion is represented by the DEVICE_CONCEPT_ID and the unit (mL) would be housed in the UNIT_SOURCE_VALUE and mapped to a standard concept in the unit domain. ",,,,,,, -DEVICE_EXPOSURE,unit_source_concept_id,No,integer,"This is the concept representing the UNIT_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 Unit necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. ,,,,,,, -MEASUREMENT,measurement_id,Yes,integer,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.",Yes,No,,,,, -MEASUREMENT,person_id,Yes,integer,The PERSON_ID of the Person for whom the Measurement is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,, -MEASUREMENT,measurement_concept_id,Yes,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,Measurement,, -MEASUREMENT,measurement_date,Yes,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.",No,No,,,,, -MEASUREMENT,measurement_datetime,No,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)",No,No,,,,, -MEASUREMENT,measurement_time,No,varchar(10),,This is present for backwards compatibility and will be deprecated in an upcoming version.,No,No,,,,, -MEASUREMENT,measurement_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -MEASUREMENT,operator_concept_id,No,integer,"The meaning of Concept [4172703](https://athena.ohdsi.org/search-terms/terms/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](https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, -MEASUREMENT,value_as_number,No,float,"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):
- [1925-7](https://athena.ohdsi.org/search-terms/terms/3003396) Base excess in Arterial blood by calculation - [1927-3](https://athena.ohdsi.org/search-terms/terms/3002032) Base excess in Venous blood by calculation - [8632-2](https://athena.ohdsi.org/search-terms/terms/3006277) QRS-Axis - [11555-0](https://athena.ohdsi.org/search-terms/terms/3012501) Base excess in Blood by calculation - [1926-5](https://athena.ohdsi.org/search-terms/terms/3003129) Base excess in Capillary blood by calculation - [28638-5](https://athena.ohdsi.org/search-terms/terms/3004959) Base excess in Arterial cord blood by calculation [28639-3](https://athena.ohdsi.org/search-terms/terms/3007435) Base excess in Venous cord blood by calculation",No,No,,,,, -MEASUREMENT,value_as_concept_id,No,integer,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.",No,Yes,CONCEPT,CONCEPT_ID,,, -MEASUREMENT,unit_concept_id,No,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,Unit,, -MEASUREMENT,range_low,No,float,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.,No,No,,,,, -MEASUREMENT,range_high,No,float,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.,No,No,,,,, -MEASUREMENT,provider_id,No,integer,"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.,No,Yes,PROVIDER,PROVIDER_ID,,, -MEASUREMENT,visit_occurrence_id,No,integer,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.",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, -MEASUREMENT,visit_detail_id,No,integer,"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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, -MEASUREMENT,measurement_source_value,No,varchar(50),"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.,No,No,,,,, -MEASUREMENT,measurement_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, -MEASUREMENT,unit_source_value,No,varchar(50),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.,No,No,,,,, -MEASUREMENT,unit_source_concept_id,No,integer,"""This is the concept representing the UNIT_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 UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.""",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,, -MEASUREMENT,value_source_value,No,varchar(50),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.",No,No,,,,, -OBSERVATION,observation_id,Yes,integer,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. ,Yes,No,,,,, -OBSERVATION,person_id,Yes,integer,The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,, -OBSERVATION,observation_concept_id,Yes,integer,"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. ",No,Yes,CONCEPT,CONCEPT_ID,,, -OBSERVATION,observation_date,Yes,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.,No,No,,,,, -OBSERVATION,observation_datetime,No,datetime,,If no time is given set to midnight (00:00:00).,No,No,,,,, -OBSERVATION,observation_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -OBSERVATION,value_as_number,No,float,"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. ",,No,No,,,,, -OBSERVATION,value_as_string,No,varchar(60),"This is the categorical value of the Result of the Observation, if applicable and available. ",,No,No,,,,, -OBSERVATION,value_as_concept_id,No,Integer,"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](https://athena.ohdsi.org/search-terms/terms/45581076) 'Family history of ischaemic heart disease and other diseases of the circulatory system' has a 'Maps to' relationship to [4167217](https://athena.ohdsi.org/search-terms/terms/4167217) 'Family history of clinical finding' as well as a 'Maps to value' record to [134057](https://athena.ohdsi.org/search-terms/terms/134057) 'Disorder of cardiovascular system'.",No,Yes,CONCEPT,CONCEPT_ID,,, -OBSERVATION,qualifier_concept_id,No,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,,, -OBSERVATION,unit_concept_id,No,integer,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.",No,Yes,CONCEPT,CONCEPT_ID,Unit,, -OBSERVATION,provider_id,No,integer,"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.,No,Yes,PROVIDER,PROVIDER_ID,,, -OBSERVATION,visit_occurrence_id,No,integer,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.",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, -OBSERVATION,visit_detail_id,No,integer,"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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, -OBSERVATION,observation_source_value,No,varchar(50),"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.,No,No,,,,, -OBSERVATION,observation_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, -OBSERVATION,unit_source_value,No,varchar(50),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.,No,No,,,,, -OBSERVATION,qualifier_source_value,No,varchar(50),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.,No,No,,,,, -OBSERVATION,value_source_value,No,varchar(50),This field houses the verbatim result value of the Observation from the source data. Do not get confused with the Observation_source_value which captures source value of the observation mapped to observation_concept_id. This field is the observation result value from the source.,"If the observation_source_value was a question, for example, or an observation that requires a result then this field is the answer/ result from the source data. Store the verbatim value that represents the result of the observation_source_value.",No,No,,,,, -DEATH,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, -DEATH,death_date,Yes,date,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day.",No,No,,,,, -DEATH,death_datetime,No,datetime,,If not available set time to midnight (00:00:00),No,No,,,,, -DEATH,death_type_concept_id,No,integer,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -DEATH,cause_concept_id,No,integer,"This is the Standard Concept representing the Person's cause of death, if available.","There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death.",No,Yes,CONCEPT,CONCEPT_ID,,, -DEATH,cause_source_value,No,varchar(50),,"If available, put the source code representing the cause of death here. ",No,No,,,,, -DEATH,cause_source_concept_id,No,integer,,If the cause of death was coded using a Vocabulary present in the OMOP Vocabularies put the CONCEPT_ID representing the cause of death here.,No,Yes,CONCEPT,CONCEPT_ID,,, -NOTE,note_id,Yes,integer,A unique identifier for each note.,,Yes,No,,,,, -NOTE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, -NOTE,note_date,Yes,date,The date the note was recorded.,,No,No,,,,, -NOTE,note_datetime,No,datetime,,If time is not given set the time to midnight.,No,No,,,,, -NOTE,note_type_concept_id,Yes,integer,The provenance of the note. Most likely this will be EHR. ,"Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +",No,No,,,,, +DRUG_EXPOSURE,days_supply,No,integer,,Days supply of the drug. This should be the verbatim days_supply as given on the prescription. If the drug is physician administered use duration end date if given or set to 1 as default if duration is not available.,No,No,,,,, +DRUG_EXPOSURE,sig,No,varchar(MAX),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.",No,No,,,,, +DRUG_EXPOSURE,route_concept_id,No,integer,,The standard CONCEPT_ID that the ROUTE_SOURCE_VALUE maps to in the route domain.,No,Yes,CONCEPT,CONCEPT_ID,Route,, +DRUG_EXPOSURE,lot_number,No,varchar(50),,,No,No,,,,, +DRUG_EXPOSURE,provider_id,No,integer,"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.",No,Yes,PROVIDER,PROVIDER_ID,,, +DRUG_EXPOSURE,visit_occurrence_id,No,integer,"The Visit during which the drug was prescribed, administered or dispensed.",To populate this field drug exposures must be explicitly initiated in the visit.,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, +DRUG_EXPOSURE,visit_detail_id,No,integer,"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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, +DRUG_EXPOSURE,drug_source_value,No,varchar(50),"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.,No,No,,,,, +DRUG_EXPOSURE,drug_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, +DRUG_EXPOSURE,route_source_value,No,varchar(50),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.,No,No,,,,, +DRUG_EXPOSURE,dose_unit_source_value,No,varchar(50),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.,No,No,,,,, +PROCEDURE_OCCURRENCE,procedure_occurrence_id,Yes,integer,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.",Yes,No,,,,, +PROCEDURE_OCCURRENCE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the procedure is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,, +PROCEDURE_OCCURRENCE,procedure_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Procedure&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Procedure,, +PROCEDURE_OCCURRENCE,procedure_date,Yes,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.",No,No,,,,, +PROCEDURE_OCCURRENCE,procedure_datetime,No,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)",No,No,,,,, +PROCEDURE_OCCURRENCE,procedure_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +PROCEDURE_OCCURRENCE,modifier_concept_id,No,integer,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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?conceptClass=CPT4+Modifier&conceptClass=HCPCS+Modifier&vocabulary=CPT4&vocabulary=HCPCS&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, +PROCEDURE_OCCURRENCE,quantity,No,integer,"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",No,No,,,,, +PROCEDURE_OCCURRENCE,provider_id,No,integer,"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.",No,No,PROVIDER,PROVIDER_ID,,, +PROCEDURE_OCCURRENCE,visit_occurrence_id,No,integer,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.",No,No,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, +PROCEDURE_OCCURRENCE,visit_detail_id,No,integer,"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.,No,No,VISIT_DETAIL,VISIT_DETAIL_ID,,, +PROCEDURE_OCCURRENCE,procedure_source_value,No,varchar(50),"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.,No,No,,,,, +PROCEDURE_OCCURRENCE,procedure_source_concept_id,No,integer,"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.,No,No,CONCEPT,CONCEPT_ID,,, +PROCEDURE_OCCURRENCE,modifier_source_value,No,varchar(50),,The original modifier code from the source is stored here for reference.,No,No,,,,, +PROCEDURE_OCCURRENCE,procedure_status_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the procedure status (primary or secondary).,"This information may be called something different in the source data but the field is meant to contain a value indicating whether the procedure was the primary reason for performing a surgical operation, infusion, etc. This source value is mapped to a standard concept which is stored in the PROCEDURE_STATUS_CONCEPT_ID field.",,,,,,, +PROCEDURE_OCCURRENCE,procedure_status_concept_id,Yes,integer,"This concept represents if the procedure was the primary reason for the surgical operation, infusion, etc . ",Choose the Concept in the Procedure Status domain that best represents the status ( [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status&standardConcept=Standard&page=1&pageSize=15&query=).,,,,,,, +DEVICE_EXPOSURE,device_exposure_id,Yes,integer,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. ,Yes,No,,,,, +DEVICE_EXPOSURE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, +DEVICE_EXPOSURE,device_concept_id,Yes,integer,"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. ,No,Yes,CONCEPT,CONCEPT_ID,Device,, +DEVICE_EXPOSURE,device_exposure_start_date,Yes,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. ",No,No,,,,, +DEVICE_EXPOSURE,device_exposure_start_datetime,No,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)",No,No,,,,, +DEVICE_EXPOSURE,device_exposure_end_date,No,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.,No,No,,,,, +DEVICE_EXPOSURE,device_exposure_end_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,, +DEVICE_EXPOSURE,device_type_concept_id,Yes,integer,"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. ","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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +DEVICE_EXPOSURE,unique_device_id,No,varchar(255),"This is the Unique Device Identification (UDI-DI) 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.",No,No,,,,, +DEVICE_EXPOSURE,production_id,No,varchar(255),This is the Production Identifier (UDI-PI) portion of the Unique Device Identification.,,,,,,,, +DEVICE_EXPOSURE,quantity,No,integer,,,No,No,,,,, +DEVICE_EXPOSURE,provider_id,No,integer,"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.,No,Yes,PROVIDER,PROVIDER_ID,,, +DEVICE_EXPOSURE,visit_occurrence_id,No,integer,The Visit during which the device was prescribed or given.,To populate this field device exposures must be explicitly initiated in the visit.,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, +DEVICE_EXPOSURE,visit_detail_id,No,integer,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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, +DEVICE_EXPOSURE,device_source_value,No,varchar(50),"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.,No,No,,,,, +DEVICE_EXPOSURE,device_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, +DEVICE_EXPOSURE,unit_concept_id,No,integer,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 DEVICE_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If there is no unit associated with a Device record, set to NULL.",,,,,,, +DEVICE_EXPOSURE,unit_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the unit of the Device. For example, blood transfusions are considered devices and can be given in mL quantities. ","This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. Using the blood transfusion example, blood transfusion is represented by the DEVICE_CONCEPT_ID and the unit (mL) would be housed in the UNIT_SOURCE_VALUE and mapped to a standard concept in the unit domain. ",,,,,,, +DEVICE_EXPOSURE,unit_source_concept_id,No,integer,"This is the concept representing the UNIT_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 Unit necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. ,,,,,,, +MEASUREMENT,measurement_id,Yes,integer,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.",Yes,No,,,,, +MEASUREMENT,person_id,Yes,integer,The PERSON_ID of the Person for whom the Measurement is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,, +MEASUREMENT,measurement_concept_id,Yes,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,Measurement,, +MEASUREMENT,measurement_date,Yes,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.",No,No,,,,, +MEASUREMENT,measurement_datetime,No,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)",No,No,,,,, +MEASUREMENT,measurement_time,No,varchar(10),,This is present for backwards compatibility and will be deprecated in an upcoming version.,No,No,,,,, +MEASUREMENT,measurement_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +MEASUREMENT,operator_concept_id,No,integer,"The meaning of Concept [4172703](https://athena.ohdsi.org/search-terms/terms/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](https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, +MEASUREMENT,value_as_number,No,float,"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):
- [1925-7](https://athena.ohdsi.org/search-terms/terms/3003396) Base excess in Arterial blood by calculation - [1927-3](https://athena.ohdsi.org/search-terms/terms/3002032) Base excess in Venous blood by calculation - [8632-2](https://athena.ohdsi.org/search-terms/terms/3006277) QRS-Axis - [11555-0](https://athena.ohdsi.org/search-terms/terms/3012501) Base excess in Blood by calculation - [1926-5](https://athena.ohdsi.org/search-terms/terms/3003129) Base excess in Capillary blood by calculation - [28638-5](https://athena.ohdsi.org/search-terms/terms/3004959) Base excess in Arterial cord blood by calculation [28639-3](https://athena.ohdsi.org/search-terms/terms/3007435) Base excess in Venous cord blood by calculation",No,No,,,,, +MEASUREMENT,value_as_concept_id,No,integer,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.",No,Yes,CONCEPT,CONCEPT_ID,,, +MEASUREMENT,unit_concept_id,No,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,Unit,, +MEASUREMENT,range_low,No,float,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.,No,No,,,,, +MEASUREMENT,range_high,No,float,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.,No,No,,,,, +MEASUREMENT,provider_id,No,integer,"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.,No,Yes,PROVIDER,PROVIDER_ID,,, +MEASUREMENT,visit_occurrence_id,No,integer,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.",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, +MEASUREMENT,visit_detail_id,No,integer,"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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, +MEASUREMENT,measurement_source_value,No,varchar(50),"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.,No,No,,,,, +MEASUREMENT,measurement_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, +MEASUREMENT,unit_source_value,No,varchar(50),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.,No,No,,,,, +MEASUREMENT,unit_source_concept_id,No,integer,"""This is the concept representing the UNIT_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 UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.""",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,, +MEASUREMENT,value_source_value,No,varchar(50),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.",No,No,,,,, +OBSERVATION,observation_id,Yes,integer,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. ,Yes,No,,,,, +OBSERVATION,person_id,Yes,integer,The PERSON_ID of the Person for whom the Observation is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,, +OBSERVATION,observation_concept_id,Yes,integer,"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. ",No,Yes,CONCEPT,CONCEPT_ID,,, +OBSERVATION,observation_date,Yes,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.,No,No,,,,, +OBSERVATION,observation_datetime,No,datetime,,If no time is given set to midnight (00:00:00).,No,No,,,,, +OBSERVATION,observation_type_concept_id,Yes,integer,"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](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +OBSERVATION,value_as_number,No,float,"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. ",,No,No,,,,, +OBSERVATION,value_as_string,No,varchar(60),"This is the categorical value of the Result of the Observation, if applicable and available. ",,No,No,,,,, +OBSERVATION,value_as_concept_id,No,Integer,"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](https://athena.ohdsi.org/search-terms/terms/45581076) 'Family history of ischaemic heart disease and other diseases of the circulatory system' has a 'Maps to' relationship to [4167217](https://athena.ohdsi.org/search-terms/terms/4167217) 'Family history of clinical finding' as well as a 'Maps to value' record to [134057](https://athena.ohdsi.org/search-terms/terms/134057) 'Disorder of cardiovascular system'.",No,Yes,CONCEPT,CONCEPT_ID,,, +OBSERVATION,qualifier_concept_id,No,integer,"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.",No,Yes,CONCEPT,CONCEPT_ID,,, +OBSERVATION,unit_concept_id,No,integer,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.",No,Yes,CONCEPT,CONCEPT_ID,Unit,, +OBSERVATION,provider_id,No,integer,"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.,No,Yes,PROVIDER,PROVIDER_ID,,, +OBSERVATION,visit_occurrence_id,No,integer,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.",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, +OBSERVATION,visit_detail_id,No,integer,"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.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, +OBSERVATION,observation_source_value,No,varchar(50),"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.,No,No,,,,, +OBSERVATION,observation_source_concept_id,No,integer,"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.,No,Yes,CONCEPT,CONCEPT_ID,,, +OBSERVATION,unit_source_value,No,varchar(50),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.,No,No,,,,, +OBSERVATION,qualifier_source_value,No,varchar(50),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.,No,No,,,,, +OBSERVATION,value_source_value,No,varchar(50),This field houses the verbatim result value of the Observation from the source data. Do not get confused with the Observation_source_value which captures source value of the observation mapped to observation_concept_id. This field is the observation result value from the source.," If the observation_source_value was a question, for example, or an observation that requires a result then this field is the answer/ result from the source data. Store the verbatim value that represents the result of the observation_source_value. ",No,No,,,,, +DEATH,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, +DEATH,death_date,Yes,date,The date the person was deceased.,"If the precise date include day or month is not known or not allowed, December is used as the default month, and the last day of the month the default day.",No,No,,,,, +DEATH,death_datetime,No,datetime,,If not available set time to midnight (00:00:00),No,No,,,,, +DEATH,death_type_concept_id,No,integer,"This is the provenance of the death record, i.e., where it came from. It is possible that an administrative claims database would source death information from a government file so do not assume the Death Type is the same as the Visit Type, etc.",Use the type concept that be reflects the source of the death record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +DEATH,cause_concept_id,No,integer,"This is the Standard Concept representing the Person's cause of death, if available.","There is no specified domain for this concept, just choose the Standard Concept Id that best represents the person's cause of death.",No,Yes,CONCEPT,CONCEPT_ID,,, +DEATH,cause_source_value,No,varchar(50),,"If available, put the source code representing the cause of death here. ",No,No,,,,, +DEATH,cause_source_concept_id,No,integer,,If the cause of death was coded using a Vocabulary present in the OMOP Vocabularies put the CONCEPT_ID representing the cause of death here.,No,Yes,CONCEPT,CONCEPT_ID,,, +NOTE,note_id,Yes,integer,A unique identifier for each note.,,Yes,No,,,,, +NOTE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, +NOTE,note_date,Yes,date,The date the note was recorded.,,No,No,,,,, +NOTE,note_datetime,No,datetime,,If time is not given set the time to midnight.,No,No,,,,, +NOTE,note_type_concept_id,Yes,integer,The provenance of the note. Most likely this will be EHR. ,"Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, NOTE,note_class_concept_id,Yes,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&conceptClass=Doc+Kind&conceptClass=Doc+Role&conceptClass=Doc+Setting&conceptClass=Doc+Subject+Matter&conceptClass=Doc+Type+of+Service&domain=Meas+Value&page=1&pageSize=15&query=). This Concept can alternatively be represented by concepts with the relationship 'Kind of (LOINC)' to [706391](https://athena.ohdsi.org/search-terms/terms/706391) (Note).,No,Yes,CONCEPT,CONCEPT_ID,,, -NOTE,note_title,No,varchar(250),The title of the note.,,No,No,,,,, -NOTE,note_text,Yes,varchar(MAX),The content of the note.,,No,No,,,,, -NOTE,encoding_concept_id,Yes,integer,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](https://athena.ohdsi.org/search-terms/terms/32678)). It the note is encoded in any other type, like ASCII then put 0. ",No,Yes,CONCEPT,CONCEPT_ID,,, -NOTE,language_concept_id,Yes,integer,The language of the note. ,Use Concepts that are descendants of the concept [4182347](https://athena.ohdsi.org/search-terms/terms/4182347) (World Languages).,No,Yes,CONCEPT,CONCEPT_ID,,, -NOTE,provider_id,No,integer,The Provider who wrote the note.,The ETL may need to make a determination on which provider to put here.,No,Yes,PROVIDER,PROVIDER_ID,,, -NOTE,visit_occurrence_id,No,integer,The Visit during which the note was written. ,,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, -NOTE,visit_detail_id,No,integer,The Visit Detail during which the note was written.,,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, -NOTE,note_source_value,No,varchar(50),,The source value mapped to the NOTE_CLASS_CONCEPT_ID.,No,No,,,,, -NOTE_NLP,note_nlp_id,Yes,integer,A unique identifier for the NLP record.,,Yes,No,,,,, -NOTE_NLP,note_id,Yes,integer,This is the NOTE_ID for the NOTE record the NLP record is associated to.,,No,No,,,,, -NOTE_NLP,section_concept_id,No,integer,,"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](https://athena.ohdsi.org/search-terms/terms/45875957).",No,Yes,CONCEPT,CONCEPT_ID,,, -NOTE_NLP,snippet,No,varchar(250),A small window of text surrounding the term,,No,No,,,,, -NOTE_NLP,offset,No,varchar(50),Character offset of the extracted term in the input note,,No,No,,,,, -NOTE_NLP,lexical_variant,Yes,varchar(250),Raw text extracted from the NLP tool.,,No,No,,,,, -NOTE_NLP,note_nlp_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -NOTE_NLP,note_nlp_source_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -NOTE_NLP,nlp_system,No,varchar(250),,Name and version of the NLP system that extracted the term. Useful for data provenance.,No,No,,,,, -NOTE_NLP,nlp_date,Yes,date,The date of the note processing.,,No,No,,,,, -NOTE_NLP,nlp_datetime,No,datetime,The date and time of the note processing.,,No,No,,,,, +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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&conceptClass=Doc+Kind&conceptClass=Doc+Role&conceptClass=Doc+Setting&conceptClass=Doc+Subject+Matter&conceptClass=Doc+Type+of+Service&domain=Meas+Value&page=1&pageSize=15&query=). This Concept can alternatively be represented by concepts with the relationship 'Kind of (LOINC)' to [706391](https://athena.ohdsi.org/search-terms/terms/706391) (Note).,No,Yes,CONCEPT,CONCEPT_ID,,, +NOTE,note_title,No,varchar(250),The title of the note.,,No,No,,,,, +NOTE,note_text,Yes,varchar(MAX),The content of the note.,,No,No,,,,, +NOTE,encoding_concept_id,Yes,integer,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](https://athena.ohdsi.org/search-terms/terms/32678)). It the note is encoded in any other type, like ASCII then put 0. ",No,Yes,CONCEPT,CONCEPT_ID,,, +NOTE,language_concept_id,Yes,integer,The language of the note. ,Use Concepts that are descendants of the concept [4182347](https://athena.ohdsi.org/search-terms/terms/4182347) (World Languages).,No,Yes,CONCEPT,CONCEPT_ID,,, +NOTE,provider_id,No,integer,The Provider who wrote the note.,The ETL may need to make a determination on which provider to put here.,No,Yes,PROVIDER,PROVIDER_ID,,, +NOTE,visit_occurrence_id,No,integer,The Visit during which the note was written. ,,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,, +NOTE,visit_detail_id,No,integer,The Visit Detail during which the note was written.,,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,, +NOTE,note_source_value,No,varchar(50),,The source value mapped to the NOTE_CLASS_CONCEPT_ID.,No,No,,,,, +NOTE_NLP,note_nlp_id,Yes,integer,A unique identifier for the NLP record.,,Yes,No,,,,, +NOTE_NLP,note_id,Yes,integer,This is the NOTE_ID for the NOTE record the NLP record is associated to.,,No,No,,,,, +NOTE_NLP,section_concept_id,No,integer,,"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](https://athena.ohdsi.org/search-terms/terms/45875957).",No,Yes,CONCEPT,CONCEPT_ID,,, +NOTE_NLP,snippet,No,varchar(250),A small window of text surrounding the term,,No,No,,,,, +NOTE_NLP,offset,No,varchar(50),Character offset of the extracted term in the input note,,No,No,,,,, +NOTE_NLP,lexical_variant,Yes,varchar(250),Raw text extracted from the NLP tool.,,No,No,,,,, +NOTE_NLP,note_nlp_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +NOTE_NLP,note_nlp_source_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +NOTE_NLP,nlp_system,No,varchar(250),,Name and version of the NLP system that extracted the term. Useful for data provenance.,No,No,,,,, +NOTE_NLP,nlp_date,Yes,date,The date of the note processing.,,No,No,,,,, +NOTE_NLP,nlp_datetime,No,datetime,The date and time of the note processing.,,No,No,,,,, NOTE_NLP,term_exists,No,varchar(1),,"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] @@ -226,302 +226,304 @@ Conditional = true/li> Rule_out = true Uncertain = very low certainty or any lower certainties A complete lack of modifiers would make Term_exists true. -",No,No,,,,, +",No,No,,,,, NOTE_NLP,term_temporal,No,varchar(50),,"Term_temporal is to indicate if a condition is present or just in the past. The following would be past:

- History = true -- Concept_date = anything before the time of the report",No,No,,,,, +- Concept_date = anything before the time of the report",No,No,,,,, NOTE_NLP,term_modifiers,No,varchar(2000),,"For the modifiers that are there, they would have to have these values:

- 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. ",No,No,,,,, -SPECIMEN,specimen_id,Yes,integer,Unique identifier for each specimen.,,Yes,No,,,,, -SPECIMEN,person_id,Yes,integer,The person from whom the specimen is collected.,,No,Yes,PERSON,PERSON_ID,,, -SPECIMEN,specimen_concept_id,Yes,integer,,The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the specimen domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Specimen&standardConcept=Standard&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,,, -SPECIMEN,specimen_type_concept_id,Yes,integer,,"Put the source of the specimen record, as in an EHR system. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, -SPECIMEN,specimen_date,Yes,date,The date the specimen was collected.,,No,No,,,,, -SPECIMEN,specimen_datetime,No,datetime,,,No,No,,,,, -SPECIMEN,quantity,No,float,The amount of specimen collected from the person.,,No,No,,,,, -SPECIMEN,unit_concept_id,No,integer,The unit for the quantity of the specimen.,Map the UNIT_SOURCE_VALUE to a Standard Concept in the Unit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Unit&standardConcept=Standard&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,,, -SPECIMEN,anatomic_site_concept_id,No,integer,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](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Spec+Anatomic+Site&conceptClass=Body+Structure&page=4&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,,, -SPECIMEN,disease_status_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -SPECIMEN,specimen_source_id,No,varchar(50),This is the identifier for the specimen from the source system. ,,No,No,,,,, -SPECIMEN,specimen_source_value,No,varchar(50),,,No,No,,,,, -SPECIMEN,unit_source_value,No,varchar(50),,"This unit for the quantity of the specimen, as represented in the source.",No,No,,,,, -SPECIMEN,anatomic_site_source_value,No,varchar(50),,"This is the site on the body where the specimen was taken from, as represented in the source.",No,No,,,,, -SPECIMEN,disease_status_source_value,No,varchar(50),,,No,No,,,,, -FACT_RELATIONSHIP,domain_concept_id_1,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -FACT_RELATIONSHIP,fact_id_1,Yes,integer,,,No,No,,,,, -FACT_RELATIONSHIP,domain_concept_id_2,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -FACT_RELATIONSHIP,fact_id_2,Yes,integer,,,No,No,,,,, -FACT_RELATIONSHIP,relationship_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -LOCATION,location_id,Yes,integer,The unique key given to a unique Location.,Each instance of a Location in the source data should be assigned this unique key.,Yes,No,,,,, -LOCATION,address_1,No,varchar(50),This is the first line of the address.,,No,No,,,,, -LOCATION,address_2,No,varchar(50),This is the second line of the address,,No,No,,,,, -LOCATION,city,No,varchar(50),,,No,No,,,,, -LOCATION,state,No,varchar(2),,,No,No,,,,, -LOCATION,zip,No,varchar(9),,"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.",No,No,,,,, -LOCATION,county,No,varchar(20),,,No,No,,,,, -LOCATION,location_source_value,No,varchar(50),,"Put the verbatim value for the location here, as it shows up in the source. ",No,No,,,,, -LOCATION,country_concept_id,No,integer,The Concept Id representing the country. Values should conform to the [Geography](https://athena.ohdsi.org/search-terms/terms?domain=Geography&standardConcept=Standard&page=1&pageSize=15&query=&boosts) domain. ,,,,,,,, -LOCATION,country_source_value,No,varchar(80),The name of the country.,,,,,,,, -LOCATION,latitude,No,float,,Must be between -90 and 90.,,,,,,, -LOCATION,longitude,No,float,,Must be between -180 and 180.,,,,,,, -CARE_SITE,care_site_id,Yes,integer,,Assign an id to each unique combination of location_id and place_of_service_source_value,Yes,No,,,,, -CARE_SITE,care_site_name,No,varchar(255),The name of the care_site as it appears in the source data,,No,No,,,,, -CARE_SITE,place_of_service_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=2&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, -CARE_SITE,location_id,No,integer,The location_id from the LOCATION table representing the physical location of the care_site.,,No,Yes,LOCATION,LOCATION_ID,,, -CARE_SITE,care_site_source_value,No,varchar(50),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.,,No,No,,,,, -CARE_SITE,place_of_service_source_value,No,varchar(50),,Put the place of service of the care_site as it appears in the source data.,No,No,,,,, -PROVIDER,provider_id,Yes,integer,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.",Yes,No,,,,, -PROVIDER,provider_name,No,varchar(255),,"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.",No,No,,,,, -PROVIDER,npi,No,varchar(20),This is the National Provider Number issued to health care providers in the US by the Centers for Medicare and Medicaid Services (CMS).,,No,No,,,,, -PROVIDER,dea,No,varchar(20),"This is the identifier issued by the DEA, a US federal agency, that allows a provider to write prescriptions for controlled substances.",,No,No,,,,, -PROVIDER,specialty_concept_id,No,integer,"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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Provider&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, -PROVIDER,care_site_id,No,integer,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.",No,Yes,CARE_SITE,CARE_SITE_ID,,, -PROVIDER,year_of_birth,No,integer,,,No,No,,,,, -PROVIDER,gender_concept_id,No,integer,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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Gender,, -PROVIDER,provider_source_value,No,varchar(50),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.,No,No,,,,, -PROVIDER,specialty_source_value,No,varchar(50),"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.,No,No,,,,, -PROVIDER,specialty_source_concept_id,No,integer,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.,No,Yes,CONCEPT,CONCEPT_ID,,, -PROVIDER,gender_source_value,No,varchar(50),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.,No,No,,,,, -PROVIDER,gender_source_concept_id,No,integer,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.,No,Yes,CONCEPT,CONCEPT_ID,,, -PAYER_PLAN_PERIOD,payer_plan_period_id,Yes,integer,"A unique identifier for each unique combination of a Person, Payer, Plan, and Period of time.",,Yes,Yes,PERSON,PERSON_ID,,, -PAYER_PLAN_PERIOD,person_id,Yes,integer,The Person covered by the Plan.,"A single Person can have multiple, overlapping, PAYER_PLAN_PERIOD records",No,Yes,PERSON,PERSON_ID,,, -PAYER_PLAN_PERIOD,payer_plan_period_start_date,Yes,date,Start date of Plan coverage.,,No,No,,,,, -PAYER_PLAN_PERIOD,payer_plan_period_end_date,Yes,date,End date of Plan coverage.,,No,No,,,,, -PAYER_PLAN_PERIOD,payer_concept_id,No,integer,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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Payer&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, -PAYER_PLAN_PERIOD,payer_source_value,No,varchar(50),This is the Payer as it appears in the source data.,,No,No,,,,, -PAYER_PLAN_PERIOD,payer_source_concept_id,No,integer,,If the source data codes the Payer in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,,, -PAYER_PLAN_PERIOD,plan_concept_id,No,integer,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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Plan&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,,, -PAYER_PLAN_PERIOD,plan_source_value,No,varchar(50),This is the health benefit Plan of the Person as it appears in the source data.,,No,No,,,,, -PAYER_PLAN_PERIOD,plan_source_concept_id,No,integer,,If the source data codes the Plan in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,,, -PAYER_PLAN_PERIOD,sponsor_concept_id,No,integer,"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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Sponsor&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,,, -PAYER_PLAN_PERIOD,sponsor_source_value,No,varchar(50),The Plan sponsor as it appears in the source data.,,No,No,,,,, -PAYER_PLAN_PERIOD,sponsor_source_concept_id,No,integer,,If the source data codes the sponsor in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,,, -PAYER_PLAN_PERIOD,family_source_value,No,varchar(50),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.,No,No,,,,, -PAYER_PLAN_PERIOD,stop_reason_concept_id,No,integer,"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](http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,,, -PAYER_PLAN_PERIOD,stop_reason_source_value,No,varchar(50),The Plan stop reason as it appears in the source data.,,No,No,,,,, -PAYER_PLAN_PERIOD,stop_reason_source_concept_id,No,integer,,If the source data codes the stop reason in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,,, -COST,cost_id,Yes,integer,,,Yes,No,,,,, -COST,cost_event_id,Yes,integer,,,No,No,,,,, -COST,cost_domain_id,Yes,varchar(20),,,No,Yes,DOMAIN,DOMAIN_ID,,, -COST,cost_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -COST,currency_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -COST,total_charge,No,float,,,No,No,,,,, -COST,total_cost,No,float,,,No,No,,,,, -COST,total_paid,No,float,,,No,No,,,,, -COST,paid_by_payer,No,float,,,No,No,,,,, -COST,paid_by_patient,No,float,,,No,No,,,,, -COST,paid_patient_copay,No,float,,,No,No,,,,, -COST,paid_patient_coinsurance,No,float,,,No,No,,,,, -COST,paid_patient_deductible,No,float,,,No,No,,,,, -COST,paid_by_primary,No,float,,,No,No,,,,, -COST,paid_ingredient_cost,No,float,,,No,No,,,,, -COST,paid_dispensing_fee,No,float,,,No,No,,,,, -COST,payer_plan_period_id,No,integer,,,No,No,,,,, -COST,amount_allowed,No,float,,,No,No,,,,, -COST,revenue_code_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -COST,revenue_code_source_value,No,varchar(50),Revenue codes are a method to charge for a class of procedures and conditions in the U.S. hospital system.,,No,No,,,,, -COST,drg_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -COST,drg_source_value,No,varchar(3),Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups. ,,No,No,,,,, -DRUG_ERA,drug_era_id,Yes,integer,,,Yes,No,,,,, -DRUG_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, -DRUG_ERA,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient, -DRUG_ERA,drug_era_start_date,Yes,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. ",No,No,,,,, +- 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. ",No,No,,,,, +SPECIMEN,specimen_id,Yes,integer,Unique identifier for each specimen.,,Yes,No,,,,, +SPECIMEN,person_id,Yes,integer,The person from whom the specimen is collected.,,No,Yes,PERSON,PERSON_ID,,, +SPECIMEN,specimen_concept_id,Yes,integer,,The standard CONCEPT_ID that the SPECIMEN_SOURCE_VALUE maps to in the specimen domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Specimen&standardConcept=Standard&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,,, +SPECIMEN,specimen_type_concept_id,Yes,integer,,"Put the source of the specimen record, as in an EHR system. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,, +SPECIMEN,specimen_date,Yes,date,The date the specimen was collected.,,No,No,,,,, +SPECIMEN,specimen_datetime,No,datetime,,,No,No,,,,, +SPECIMEN,quantity,No,float,The amount of specimen collected from the person.,,No,No,,,,, +SPECIMEN,unit_concept_id,No,integer,The unit for the quantity of the specimen.,Map the UNIT_SOURCE_VALUE to a Standard Concept in the Unit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Unit&standardConcept=Standard&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,,, +SPECIMEN,anatomic_site_concept_id,No,integer,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](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Spec+Anatomic+Site&conceptClass=Body+Structure&page=4&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,,, +SPECIMEN,disease_status_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +SPECIMEN,specimen_source_id,No,varchar(50),This is the identifier for the specimen from the source system. ,,No,No,,,,, +SPECIMEN,specimen_source_value,No,varchar(50),,,No,No,,,,, +SPECIMEN,unit_source_value,No,varchar(50),,"This unit for the quantity of the specimen, as represented in the source.",No,No,,,,, +SPECIMEN,anatomic_site_source_value,No,varchar(50),,"This is the site on the body where the specimen was taken from, as represented in the source.",No,No,,,,, +SPECIMEN,disease_status_source_value,No,varchar(50),,,No,No,,,,, +FACT_RELATIONSHIP,domain_concept_id_1,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +FACT_RELATIONSHIP,fact_id_1,Yes,integer,,,No,No,,,,, +FACT_RELATIONSHIP,domain_concept_id_2,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +FACT_RELATIONSHIP,fact_id_2,Yes,integer,,,No,No,,,,, +FACT_RELATIONSHIP,relationship_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +LOCATION,location_id,Yes,integer,The unique key given to a unique Location.,Each instance of a Location in the source data should be assigned this unique key.,Yes,No,,,,, +LOCATION,address_1,No,varchar(50),This is the first line of the address.,,No,No,,,,, +LOCATION,address_2,No,varchar(50),This is the second line of the address,,No,No,,,,, +LOCATION,city,No,varchar(50),,,No,No,,,,, +LOCATION,state,No,varchar(2),,,No,No,,,,, +LOCATION,zip,No,varchar(9),,"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.",No,No,,,,, +LOCATION,county,No,varchar(20),,,No,No,,,,, +LOCATION,location_source_value,No,varchar(50),,"Put the verbatim value for the location here, as it shows up in the source. ",No,No,,,,, +LOCATION,country_concept_id,No,integer,The Concept Id representing the country. Values should conform to the [Geography](https://athena.ohdsi.org/search-terms/terms?domain=Geography&standardConcept=Standard&page=1&pageSize=15&query=&boosts) domain. ,,,,,,,, +LOCATION,country_source_value,No,varchar(80),The name of the country.,,,,,,,, +LOCATION,latitude,No,float,,Must be between -90 and 90.,,,,,,, +LOCATION,longitude,No,float,,Must be between -180 and 180.,,,,,,, +CARE_SITE,care_site_id,Yes,integer,,Assign an id to each unique combination of location_id and place_of_service_source_value,Yes,No,,,,, +CARE_SITE,care_site_name,No,varchar(255),The name of the care_site as it appears in the source data,,No,No,,,,, +CARE_SITE,place_of_service_concept_id,No,integer,"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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=2&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, +CARE_SITE,location_id,No,integer,The location_id from the LOCATION table representing the physical location of the care_site.,,No,Yes,LOCATION,LOCATION_ID,,, +CARE_SITE,care_site_source_value,No,varchar(50),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.,,No,No,,,,, +CARE_SITE,place_of_service_source_value,No,varchar(50),,Put the place of service of the care_site as it appears in the source data.,No,No,,,,, +PROVIDER,provider_id,Yes,integer,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.",Yes,No,,,,, +PROVIDER,provider_name,No,varchar(255),,"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.",No,No,,,,, +PROVIDER,npi,No,varchar(20),This is the National Provider Number issued to health care providers in the US by the Centers for Medicare and Medicaid Services (CMS).,,No,No,,,,, +PROVIDER,dea,No,varchar(20),"This is the identifier issued by the DEA, a US federal agency, that allows a provider to write prescriptions for controlled substances.",,No,No,,,,, +PROVIDER,specialty_concept_id,No,integer,"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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Provider&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, +PROVIDER,care_site_id,No,integer,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.",No,Yes,CARE_SITE,CARE_SITE_ID,,, +PROVIDER,year_of_birth,No,integer,,,No,No,,,,, +PROVIDER,gender_concept_id,No,integer,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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Gender,, +PROVIDER,provider_source_value,No,varchar(50),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.,No,No,,,,, +PROVIDER,specialty_source_value,No,varchar(50),"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.,No,No,,,,, +PROVIDER,specialty_source_concept_id,No,integer,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.,No,Yes,CONCEPT,CONCEPT_ID,,, +PROVIDER,gender_source_value,No,varchar(50),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.,No,No,,,,, +PROVIDER,gender_source_concept_id,No,integer,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.,No,Yes,CONCEPT,CONCEPT_ID,,, +PAYER_PLAN_PERIOD,payer_plan_period_id,Yes,integer,"A unique identifier for each unique combination of a Person, Payer, Plan, and Period of time.",,Yes,Yes,PERSON,PERSON_ID,,, +PAYER_PLAN_PERIOD,person_id,Yes,integer,The Person covered by the Plan.,"A single Person can have multiple, overlapping, PAYER_PLAN_PERIOD records",No,Yes,PERSON,PERSON_ID,,, +PAYER_PLAN_PERIOD,payer_plan_period_start_date,Yes,date,Start date of Plan coverage.,,No,No,,,,, +PAYER_PLAN_PERIOD,payer_plan_period_end_date,Yes,date,End date of Plan coverage.,,No,No,,,,, +PAYER_PLAN_PERIOD,payer_concept_id,No,integer,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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Payer&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,, +PAYER_PLAN_PERIOD,payer_source_value,No,varchar(50),This is the Payer as it appears in the source data.,,No,No,,,,, +PAYER_PLAN_PERIOD,payer_source_concept_id,No,integer,,If the source data codes the Payer in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,,, +PAYER_PLAN_PERIOD,plan_concept_id,No,integer,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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Plan&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,,, +PAYER_PLAN_PERIOD,plan_source_value,No,varchar(50),This is the health benefit Plan of the Person as it appears in the source data.,,No,No,,,,, +PAYER_PLAN_PERIOD,plan_source_concept_id,No,integer,,If the source data codes the Plan in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,,, +PAYER_PLAN_PERIOD,sponsor_concept_id,No,integer,"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. [Accepted Concepts](http://athena.ohdsi.org/search-terms/terms?domain=Sponsor&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,,, +PAYER_PLAN_PERIOD,sponsor_source_value,No,varchar(50),The Plan sponsor as it appears in the source data.,,No,No,,,,, +PAYER_PLAN_PERIOD,sponsor_source_concept_id,No,integer,,If the source data codes the sponsor in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,,, +PAYER_PLAN_PERIOD,family_source_value,No,varchar(50),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.,No,No,,,,, +PAYER_PLAN_PERIOD,stop_reason_concept_id,No,integer,"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](http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,,, +PAYER_PLAN_PERIOD,stop_reason_source_value,No,varchar(50),The Plan stop reason as it appears in the source data.,,No,No,,,,, +PAYER_PLAN_PERIOD,stop_reason_source_concept_id,No,integer,,If the source data codes the stop reason in an OMOP supported vocabulary store the concept_id here.,No,Yes,CONCEPT,CONCEPT_ID,,, +COST,cost_id,Yes,integer,,,Yes,No,,,,, +COST,cost_event_id,Yes,integer,,,No,No,,,,, +COST,cost_domain_id,Yes,varchar(20),,,No,Yes,DOMAIN,DOMAIN_ID,,, +COST,cost_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +COST,currency_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +COST,total_charge,No,float,,,No,No,,,,, +COST,total_cost,No,float,,,No,No,,,,, +COST,total_paid,No,float,,,No,No,,,,, +COST,paid_by_payer,No,float,,,No,No,,,,, +COST,paid_by_patient,No,float,,,No,No,,,,, +COST,paid_patient_copay,No,float,,,No,No,,,,, +COST,paid_patient_coinsurance,No,float,,,No,No,,,,, +COST,paid_patient_deductible,No,float,,,No,No,,,,, +COST,paid_by_primary,No,float,,,No,No,,,,, +COST,paid_ingredient_cost,No,float,,,No,No,,,,, +COST,paid_dispensing_fee,No,float,,,No,No,,,,, +COST,payer_plan_period_id,No,integer,,,No,No,,,,, +COST,amount_allowed,No,float,,,No,No,,,,, +COST,revenue_code_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +COST,revenue_code_source_value,No,varchar(50),Revenue codes are a method to charge for a class of procedures and conditions in the U.S. hospital system.,,No,No,,,,, +COST,drg_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +COST,drg_source_value,No,varchar(3),Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups. ,,No,No,,,,, +DRUG_ERA,drug_era_id,Yes,integer,,,Yes,No,,,,, +DRUG_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, +DRUG_ERA,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient, +DRUG_ERA,drug_era_start_date,Yes,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. ",No,No,,,,, DRUG_ERA,drug_era_end_date,Yes,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.",No,No,,,,, -DRUG_ERA,drug_exposure_count,No,integer,,,No,No,,,,, -DRUG_ERA,gap_days,No,integer,,"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.",No,No,,,,, -DOSE_ERA,dose_era_id,Yes,integer,,,Yes,No,,,,, -DOSE_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, -DOSE_ERA,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient, -DOSE_ERA,unit_concept_id,Yes,integer,The Concept Id representing the unit of the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Unit,, -DOSE_ERA,dose_value,Yes,float,The numeric value of the dosage of the drug_ingredient.,,No,No,,,,, -DOSE_ERA,dose_era_start_date,Yes,datetime,"The date the Person started on the specific dosage, with at least 31 days since any prior exposure.",,No,No,,,,, -DOSE_ERA,dose_era_end_date,Yes,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.,No,No,,,,, -CONDITION_ERA,condition_era_id,Yes,integer,,,Yes,No,,,,, -CONDITION_ERA,person_id,Yes,integer,,,No,No,PERSON,PERSON_ID,,, -CONDITION_ERA,condition_concept_id,Yes,integer,The Concept Id representing the Condition.,,No,Yes,CONCEPT,CONCEPT_ID,Condition,, +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.",No,No,,,,, +DRUG_ERA,drug_exposure_count,No,integer,,,No,No,,,,, +DRUG_ERA,gap_days,No,integer,,"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.",No,No,,,,, +DOSE_ERA,dose_era_id,Yes,integer,,,Yes,No,,,,, +DOSE_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,, +DOSE_ERA,drug_concept_id,Yes,integer,The Concept Id representing the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Drug,Ingredient, +DOSE_ERA,unit_concept_id,Yes,integer,The Concept Id representing the unit of the specific drug ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,Unit,, +DOSE_ERA,dose_value,Yes,float,The numeric value of the dosage of the drug_ingredient.,,No,No,,,,, +DOSE_ERA,dose_era_start_date,Yes,datetime,"The date the Person started on the specific dosage, with at least 31 days since any prior exposure.",,No,No,,,,, +DOSE_ERA,dose_era_end_date,Yes,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.,No,No,,,,, +CONDITION_ERA,condition_era_id,Yes,integer,,,Yes,No,,,,, +CONDITION_ERA,person_id,Yes,integer,,,No,No,PERSON,PERSON_ID,,, +CONDITION_ERA,condition_concept_id,Yes,integer,The Concept Id representing the Condition.,,No,Yes,CONCEPT,CONCEPT_ID,Condition,, CONDITION_ERA,condition_era_start_date,Yes,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. ",,No,No,,,,, +the condition with at least 31 days since any prior record of the same Condition. ",,No,No,,,,, CONDITION_ERA,condition_era_end_date,Yes,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.",,No,No,,,,, +Condition.",,No,No,,,,, CONDITION_ERA,condition_occurrence_count,No,integer,"The number of individual Condition Occurrences used to construct the -condition era.",,No,No,,,,, -METADATA,metadata_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -METADATA,metadata_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -METADATA,name,Yes,varchar(250),,,No,No,,,,, -METADATA,value_as_string,No,varchar(250),,,No,No,,,,, -METADATA,value_as_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -METADATA,metadata_date,No,date,,,No,No,,,,, -METADATA,metadata_datetime,No,datetime,,,No,No,,,,, -CDM_SOURCE,cdm_source_name,Yes,varchar(255),The name of the CDM instance.,,No,No,,,,, -CDM_SOURCE,cdm_source_abbreviation,Yes,varchar(25),The abbreviation of the CDM instance.,,No,No,,,,, -CDM_SOURCE,cdm_holder,Yes,varchar(255),The holder of the CDM instance.,,No,No,,,,, -CDM_SOURCE,source_description,No,varchar(MAX),The description of the CDM instance.,,No,No,,,,, -CDM_SOURCE,source_documentation_reference,No,varchar(255),,,No,No,,,,, -CDM_SOURCE,cdm_etl_reference,No,varchar(255),,Put the link to the CDM version used.,No,No,,,,, -CDM_SOURCE,source_release_date,Yes,date,The release date of the source data.,,No,No,,,,, -CDM_SOURCE,cdm_release_date,Yes,date,The release data of the CDM instance.,,No,No,,,,, -CDM_SOURCE,cdm_version,No,varchar(10),,,No,No,,,,, -CDM_SOURCE,cdm_version_concept_id,Yes,integer,The Concept Id representing the version of the CDM.,,,,,,,, -CDM_SOURCE,vocabulary_version,Yes,varchar(20),,,No,No,,,,, -CONCEPT,concept_id,Yes,integer,A unique identifier for each Concept across all domains.,,Yes,No,,,,, -CONCEPT,concept_name,Yes,varchar(255),"An unambiguous, meaningful and descriptive name for the Concept.",,No,No,,,,, -CONCEPT,domain_id,Yes,varchar(20),A foreign key to the [DOMAIN](https://ohdsi.github.io/CommonDataModel/cdm531.html#domain) table the Concept belongs to.,,No,Yes,DOMAIN,DOMAIN_ID,,, +condition era.",,No,No,,,,, +METADATA,metadata_id,Yes,integer,The unique key given to a Metadata record.,Attribute value is auto-generated,Yes,No,,,,, +METADATA,metadata_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +METADATA,metadata_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +METADATA,name,Yes,varchar(250),,,No,No,,,,, +METADATA,value_as_string,No,varchar(250),,,No,No,,,,, +METADATA,value_as_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +METADATA,value_as_number,No,float,"This is the numerical value of the Result of the Metadata, if applicable and available. It is not expected that all Metadata will have numeric results, rather, this field is here to house values should they exist. ",,No,No,,,,, +METADATA,metadata_date,No,date,,,No,No,,,,, +METADATA,metadata_datetime,No,datetime,,,No,No,,,,, +CDM_SOURCE,cdm_source_name,Yes,varchar(255),The name of the CDM instance.,,No,No,,,,, +CDM_SOURCE,cdm_source_abbreviation,Yes,varchar(25),The abbreviation of the CDM instance.,,No,No,,,,, +CDM_SOURCE,cdm_holder,Yes,varchar(255),The holder of the CDM instance.,,No,No,,,,, +CDM_SOURCE,source_description,No,varchar(MAX),The description of the CDM instance.,,No,No,,,,, +CDM_SOURCE,source_documentation_reference,No,varchar(255),,,No,No,,,,, +CDM_SOURCE,cdm_etl_reference,No,varchar(255),,Put the link to the CDM version used.,No,No,,,,, +CDM_SOURCE,source_release_date,Yes,date,The release date of the source data.,,No,No,,,,, +CDM_SOURCE,cdm_release_date,Yes,date,The release data of the CDM instance.,,No,No,,,,, +CDM_SOURCE,cdm_version,No,varchar(10),,,No,No,,,,, +CDM_SOURCE,cdm_version_concept_id,Yes,integer,The Concept Id representing the version of the CDM.,,,,,,,, +CDM_SOURCE,vocabulary_version,Yes,varchar(20),,,No,No,,,,, +CONCEPT,concept_id,Yes,integer,A unique identifier for each Concept across all domains.,,Yes,No,,,,, +CONCEPT,concept_name,Yes,varchar(255),"An unambiguous, meaningful and descriptive name for the Concept.",,No,No,,,,, +CONCEPT,domain_id,Yes,varchar(20),A foreign key to the [DOMAIN](https://ohdsi.github.io/CommonDataModel/cdm531.html#domain) table the Concept belongs to.,,No,Yes,DOMAIN,DOMAIN_ID,,, CONCEPT,vocabulary_id,Yes,varchar(20),"A foreign key to the [VOCABULARY](https://ohdsi.github.io/CommonDataModel/cdm531.html#vocabulary) table indicating from which source the -Concept has been adapted.",,No,Yes,VOCABULARY,VOCABULARY_ID,,, +Concept has been adapted.",,No,Yes,VOCABULARY,VOCABULARY_ID,,, CONCEPT,concept_class_id,Yes,varchar(20),"The attribute or concept class of the Concept. Examples are 'Clinical Drug', -'Ingredient', 'Clinical Finding' etc.",,No,Yes,CONCEPT_CLASS,CONCEPT_CLASS_ID,,, +'Ingredient', 'Clinical Finding' etc.",,No,Yes,CONCEPT_CLASS,CONCEPT_CLASS_ID,,, CONCEPT,standard_concept,No,varchar(1),"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.",,No,No,,,,, +Concept), otherwise the content is NULL.",,No,No,,,,, CONCEPT,concept_code,Yes,varchar(50),"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.",,No,No,,,,, +codes are not unique across vocabularies.",,No,No,,,,, CONCEPT,valid_start_date,Yes,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.",,No,No,,,,, +(known) date of inception.",,No,No,,,,, CONCEPT,valid_end_date,Yes,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.",,No,No,,,,, +becomes deprecated.",,No,No,,,,, CONCEPT,invalid_reason,No,varchar(1),"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.",,No,No,,,,, +valid_end_date has the default value.",,No,No,,,,, VOCABULARY,vocabulary_id,Yes,varchar(20),"A unique identifier for each Vocabulary, such -as ICD9CM, SNOMED, Visit.",,Yes,No,,,,, +as ICD9CM, SNOMED, Visit.",,Yes,No,,,,, VOCABULARY,vocabulary_name,Yes,varchar(255),"The name describing the vocabulary, for example, International Classification of Diseases, Ninth Revision, Clinical -Modification, Volume 1 and 2 (NCHS) etc.",,No,No,,,,, +Modification, Volume 1 and 2 (NCHS) etc.",,No,No,,,,, VOCABULARY,vocabulary_reference,Yes,varchar(255),"External reference to documentation or available download of the about the -vocabulary.",,No,No,,,,, +vocabulary.",,No,No,,,,, VOCABULARY,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in -the source.",,No,No,,,,, -VOCABULARY,vocabulary_concept_id,Yes,integer,A Concept that represents the Vocabulary the VOCABULARY record belongs to.,,No,Yes,CONCEPT,CONCEPT_ID,,, -DOMAIN,domain_id,Yes,varchar(20),A unique key for each domain.,,Yes,No,,,,, +the source.",,No,No,,,,, +VOCABULARY,vocabulary_concept_id,Yes,integer,A Concept that represents the Vocabulary the VOCABULARY record belongs to.,,No,Yes,CONCEPT,CONCEPT_ID,,, +DOMAIN,domain_id,Yes,varchar(20),A unique key for each domain.,,Yes,No,,,,, DOMAIN,domain_name,Yes,varchar(255),"The name describing the Domain, e.g. Condition, Procedure, Measurement -etc.",,No,No,,,,, -DOMAIN,domain_concept_id,Yes,integer,A Concept representing the Domain Concept the DOMAIN record belongs to.,,No,Yes,CONCEPT,CONCEPT_ID,,, -CONCEPT_CLASS,concept_class_id,Yes,varchar(20),A unique key for each class.,,Yes,No,,,,, +etc.",,No,No,,,,, +DOMAIN,domain_concept_id,Yes,integer,A Concept representing the Domain Concept the DOMAIN record belongs to.,,No,Yes,CONCEPT,CONCEPT_ID,,, +CONCEPT_CLASS,concept_class_id,Yes,varchar(20),A unique key for each class.,,Yes,No,,,,, CONCEPT_CLASS,concept_class_name,Yes,varchar(255),"The name describing the Concept Class, e.g. -Clinical Finding, Ingredient, etc.",,No,No,,,,, -CONCEPT_CLASS,concept_class_concept_id,Yes,integer,A Concept that represents the Concept Class.,,No,Yes,CONCEPT,CONCEPT_ID,,, -CONCEPT_RELATIONSHIP,concept_id_1,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -CONCEPT_RELATIONSHIP,concept_id_2,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -CONCEPT_RELATIONSHIP,relationship_id,Yes,varchar(20),The relationship between CONCEPT_ID_1 and CONCEPT_ID_2. Please see the [Vocabulary Conventions](https://ohdsi.github.io/CommonDataModel/dataModelConventions.html#concept_relationships). for more information. ,,No,Yes,RELATIONSHIP,RELATIONSHIP_ID,,, -CONCEPT_RELATIONSHIP,valid_start_date,Yes,date,The date when the relationship is first recorded.,,No,No,,,,, -CONCEPT_RELATIONSHIP,valid_end_date,Yes,date,The date when the relationship is invalidated.,,No,No,,,,, -CONCEPT_RELATIONSHIP,invalid_reason,No,varchar(1),"Reason the relationship was invalidated. Possible values are 'D' (deleted), 'U' (updated) or NULL. ",,No,No,,,,, +Clinical Finding, Ingredient, etc.",,No,No,,,,, +CONCEPT_CLASS,concept_class_concept_id,Yes,integer,A Concept that represents the Concept Class.,,No,Yes,CONCEPT,CONCEPT_ID,,, +CONCEPT_RELATIONSHIP,concept_id_1,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +CONCEPT_RELATIONSHIP,concept_id_2,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +CONCEPT_RELATIONSHIP,relationship_id,Yes,varchar(20),The relationship between CONCEPT_ID_1 and CONCEPT_ID_2. Please see the [Vocabulary Conventions](https://ohdsi.github.io/CommonDataModel/dataModelConventions.html#concept_relationships). for more information. ,,No,Yes,RELATIONSHIP,RELATIONSHIP_ID,,, +CONCEPT_RELATIONSHIP,valid_start_date,Yes,date,The date when the relationship is first recorded.,,No,No,,,,, +CONCEPT_RELATIONSHIP,valid_end_date,Yes,date,The date when the relationship is invalidated.,,No,No,,,,, +CONCEPT_RELATIONSHIP,invalid_reason,No,varchar(1),"Reason the relationship was invalidated. Possible values are 'D' (deleted), 'U' (updated) or NULL. ",,No,No,,,,, RELATIONSHIP,relationship_id,Yes,varchar(20),"The type of relationship captured by the -relationship record.",,Yes,No,,,,, -RELATIONSHIP,relationship_name,Yes,varchar(255),,,No,No,,,,, +relationship record.",,Yes,No,,,,, +RELATIONSHIP,relationship_name,Yes,varchar(255),,,No,No,,,,, RELATIONSHIP,is_hierarchical,Yes,varchar(1),"Defines whether a relationship defines concepts into classes or hierarchies. Values -are 1 for hierarchical relationship or 0 if not.",,No,No,,,,, +are 1 for hierarchical relationship or 0 if not.",,No,No,,,,, RELATIONSHIP,defines_ancestry,Yes,varchar(1),"Defines whether a hierarchical relationship contributes to the concept_ancestor table. These are subsets of the hierarchical -relationships. Valid values are 1 or 0.",,No,No,,,,, +relationships. Valid values are 1 or 0.",,No,No,,,,, RELATIONSHIP,reverse_relationship_id,Yes,varchar(20),"The identifier for the relationship used to define the reverse relationship between two -concepts.",,No,No,,,,, +concepts.",,No,No,,,,, RELATIONSHIP,relationship_concept_id,Yes,integer,"A foreign key that refers to an identifier in the [CONCEPT](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept) table for the unique -relationship concept.",,No,Yes,CONCEPT,CONCEPT_ID,,, -CONCEPT_SYNONYM,concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, -CONCEPT_SYNONYM,concept_synonym_name,Yes,varchar(1000),,,No,No,,,,, -CONCEPT_SYNONYM,language_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +relationship concept.",,No,Yes,CONCEPT,CONCEPT_ID,,, +CONCEPT_SYNONYM,concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, +CONCEPT_SYNONYM,concept_synonym_name,Yes,varchar(1000),,,No,No,,,,, +CONCEPT_SYNONYM,language_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,, CONCEPT_ANCESTOR,ancestor_concept_id,Yes,integer,"The Concept Id for the higher-level concept -that forms the ancestor in the relationship.",,No,Yes,CONCEPT,CONCEPT_ID,,, +that forms the ancestor in the relationship.",,No,Yes,CONCEPT,CONCEPT_ID,,, CONCEPT_ANCESTOR,descendant_concept_id,Yes,integer,"The Concept Id for the lower-level concept that forms the descendant in the -relationship.",,No,Yes,CONCEPT,CONCEPT_ID,,, +relationship.",,No,Yes,CONCEPT,CONCEPT_ID,,, CONCEPT_ANCESTOR,min_levels_of_separation,Yes,integer,"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.",,No,No,,,,, +that is used to simplify hierarchic analysis.",,No,No,,,,, CONCEPT_ANCESTOR,max_levels_of_separation,Yes,integer,"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.",,No,No,,,,, +that is used to simplify hierarchic analysis.",,No,No,,,,, SOURCE_TO_CONCEPT_MAP,source_code,Yes,varchar(50),"The source code being translated -into a Standard Concept.",,No,No,,,,, +into a Standard Concept.",,No,No,,,,, SOURCE_TO_CONCEPT_MAP,source_concept_id,Yes,integer,"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. ",No,Yes,CONCEPT,CONCEPT_ID,,, +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. ",No,Yes,CONCEPT,CONCEPT_ID,,, SOURCE_TO_CONCEPT_MAP,source_vocabulary_id,Yes,varchar(20),"A foreign key to the VOCABULARY table defining the vocabulary of the source code that is being translated to a Standard -Concept.",,No,No,,,,, +Concept.",,No,No,,,,, SOURCE_TO_CONCEPT_MAP,source_code_description,No,varchar(255),"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.",,No,No,,,,, +the name of the concept.",,No,No,,,,, SOURCE_TO_CONCEPT_MAP,target_concept_id,Yes,integer,"The target Concept to which the source code is being -mapped.",,No,Yes,CONCEPT,CONCEPT_ID,,, -SOURCE_TO_CONCEPT_MAP,target_vocabulary_id,Yes,varchar(20),The Vocabulary of the target Concept.,,No,Yes,VOCABULARY,VOCABULARY_ID,,, +mapped.",,No,Yes,CONCEPT,CONCEPT_ID,,, +SOURCE_TO_CONCEPT_MAP,target_vocabulary_id,Yes,varchar(20),The Vocabulary of the target Concept.,,No,Yes,VOCABULARY,VOCABULARY_ID,,, SOURCE_TO_CONCEPT_MAP,valid_start_date,Yes,date,"The date when the mapping -instance was first recorded.",,No,No,,,,, +instance was first recorded.",,No,No,,,,, SOURCE_TO_CONCEPT_MAP,valid_end_date,Yes,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.",,No,No,,,,, -SOURCE_TO_CONCEPT_MAP,invalid_reason,No,varchar(1),"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.",,No,No,,,,, -DRUG_STRENGTH,drug_concept_id,Yes,integer,The Concept representing the Branded Drug or Clinical Drug Product.,,No,Yes,CONCEPT,CONCEPT_ID,,, -DRUG_STRENGTH,ingredient_concept_id,Yes,integer,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.",No,Yes,CONCEPT,CONCEPT_ID,,, -DRUG_STRENGTH,amount_value,No,float,The numeric value or the amount of active ingredient contained within the drug product.,,No,No,,,,, -DRUG_STRENGTH,amount_unit_concept_id,No,integer,The Concept representing the Unit of measure for the amount of active ingredient contained within the drug product. ,,No,Yes,CONCEPT,CONCEPT_ID,,, -DRUG_STRENGTH,numerator_value,No,float,The concentration of the active ingredient contained within the drug product.,,No,No,,,,, -DRUG_STRENGTH,numerator_unit_concept_id,No,integer,The Concept representing the Unit of measure for the concentration of active ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,,, -DRUG_STRENGTH,denominator_value,No,float,"The amount of total liquid (or other divisible product, such as ointment, gel, spray, etc.).",,No,No,,,,, -DRUG_STRENGTH,denominator_unit_concept_id,No,integer,The Concept representing the denominator unit for the concentration of active ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,,, -DRUG_STRENGTH,box_size,No,integer,The number of units of Clinical Branded Drug or Quantified Clinical or Branded Drug contained in a box as dispensed to the patient.,,No,No,,,,, +Default value is 31-Dec-2099.",,No,No,,,,, +SOURCE_TO_CONCEPT_MAP,invalid_reason,No,varchar(1),"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.",,No,No,,,,, +DRUG_STRENGTH,drug_concept_id,Yes,integer,The Concept representing the Branded Drug or Clinical Drug Product.,,No,Yes,CONCEPT,CONCEPT_ID,,, +DRUG_STRENGTH,ingredient_concept_id,Yes,integer,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.",No,Yes,CONCEPT,CONCEPT_ID,,, +DRUG_STRENGTH,amount_value,No,float,The numeric value or the amount of active ingredient contained within the drug product.,,No,No,,,,, +DRUG_STRENGTH,amount_unit_concept_id,No,integer,The Concept representing the Unit of measure for the amount of active ingredient contained within the drug product. ,,No,Yes,CONCEPT,CONCEPT_ID,,, +DRUG_STRENGTH,numerator_value,No,float,The concentration of the active ingredient contained within the drug product.,,No,No,,,,, +DRUG_STRENGTH,numerator_unit_concept_id,No,integer,The Concept representing the Unit of measure for the concentration of active ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,,, +DRUG_STRENGTH,denominator_value,No,float,"The amount of total liquid (or other divisible product, such as ointment, gel, spray, etc.).",,No,No,,,,, +DRUG_STRENGTH,denominator_unit_concept_id,No,integer,The Concept representing the denominator unit for the concentration of active ingredient.,,No,Yes,CONCEPT,CONCEPT_ID,,, +DRUG_STRENGTH,box_size,No,integer,The number of units of Clinical Branded Drug or Quantified Clinical or Branded Drug contained in a box as dispensed to the patient.,,No,No,,,,, DRUG_STRENGTH,valid_start_date,Yes,date,"The date when the Concept was first recorded. The default value is -1-Jan-1970.",,No,No,,,,, -DRUG_STRENGTH,valid_end_date,Yes,date,The date when then Concept became invalid.,,No,No,,,,, -DRUG_STRENGTH,invalid_reason,No,varchar(1),"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.",,No,No,,,,, -COHORT,cohort_definition_id,Yes,integer,,,No,No,,,,, -COHORT,subject_id,Yes,integer,,,No,No,,,,, -COHORT,cohort_start_date,Yes,date,,,No,No,,,,, -COHORT,cohort_end_date,Yes,date,,,No,No,,,,, -COHORT_DEFINITION,cohort_definition_id,Yes,integer,"This is the identifier given to the cohort, usually by the ATLAS application",,No,No,COHORT,COHORT_DEFINITION_ID,,, -COHORT_DEFINITION,cohort_definition_name,Yes,varchar(255),A short description of the cohort,,No,No,,,,, -COHORT_DEFINITION,cohort_definition_description,No,varchar(MAX),A complete description of the cohort.,,No,No,,,,, -COHORT_DEFINITION,definition_type_concept_id,Yes,integer,Type defining what kind of Cohort Definition the record represents and how the syntax may be executed.,,No,Yes,CONCEPT,CONCEPT_ID,,, -COHORT_DEFINITION,cohort_definition_syntax,No,varchar(MAX),Syntax or code to operationalize the Cohort Definition.,,No,No,,,,, -COHORT_DEFINITION,subject_concept_id,Yes,integer,"This field contains a Concept that represents the domain of the subjects that are members of the cohort (e.g., Person, Provider, Visit).",,No,Yes,CONCEPT,CONCEPT_ID,,, +1-Jan-1970.",,No,No,,,,, +DRUG_STRENGTH,valid_end_date,Yes,date,The date when then Concept became invalid.,,No,No,,,,, +DRUG_STRENGTH,invalid_reason,No,varchar(1),"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.",,No,No,,,,, +COHORT,cohort_definition_id,Yes,integer,,,No,No,,,,, +COHORT,subject_id,Yes,integer,,,No,No,,,,, +COHORT,cohort_start_date,Yes,date,,,No,No,,,,, +COHORT,cohort_end_date,Yes,date,,,No,No,,,,, +COHORT_DEFINITION,cohort_definition_id,Yes,integer,"This is the identifier given to the cohort, usually by the ATLAS application",,No,No,COHORT,COHORT_DEFINITION_ID,,, +COHORT_DEFINITION,cohort_definition_name,Yes,varchar(255),A short description of the cohort,,No,No,,,,, +COHORT_DEFINITION,cohort_definition_description,No,varchar(MAX),A complete description of the cohort.,,No,No,,,,, +COHORT_DEFINITION,definition_type_concept_id,Yes,integer,Type defining what kind of Cohort Definition the record represents and how the syntax may be executed.,,No,Yes,CONCEPT,CONCEPT_ID,,, +COHORT_DEFINITION,cohort_definition_syntax,No,varchar(MAX),Syntax or code to operationalize the Cohort Definition.,,No,No,,,,, +COHORT_DEFINITION,subject_concept_id,Yes,integer,"This field contains a Concept that represents the domain of the subjects that are members of the cohort (e.g., Person, Provider, Visit).",,No,Yes,CONCEPT,CONCEPT_ID,,, COHORT_DEFINITION,cohort_initiation_date,No,date,A date to indicate when the Cohort was initiated in the COHORT table.,,No,No,,,,, \ No newline at end of file diff --git a/rmd/_site.yml b/rmd/_site.yml index 387b8be..2ad5c78 100644 --- a/rmd/_site.yml +++ b/rmd/_site.yml @@ -27,10 +27,10 @@ navbar: menu: - text: "CDM v3.0" href: cdm30.html - - text: "CDM v5.3.1" - href: cdm531.html + - text: "CDM v5.3" + href: cdm53.html - text: "CDM v5.4" - href: cdm531.html + href: cdm54.html - text: "CDM v6.0" href: cdm60.html - text: "Proposals" diff --git a/rmd/cdm53.Rmd b/rmd/cdm53.Rmd new file mode 100644 index 0000000..e7d234b --- /dev/null +++ b/rmd/cdm53.Rmd @@ -0,0 +1,109 @@ +--- +output: + # pdf_document: + # toc: yes + # toc_depth: '5' + html_document: + toc: yes + toc_depth: 5 + toc_float: yes +--- + +```{r setup, include=FALSE, eval=TRUE} + +#todo figure out how to get the document dynamically without specifying the name +library(rmarkdown) +library(knitr) +library(kableExtra) +library(magrittr) +library(dplyr) +library(stringr) + +``` + +# **OMOP CDM v5.3** + +Below is the specification document for the OMOP Common Data Model, v5.3 (previously v5.3.1). Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page. + +*__Special Note__ This documentation previously referenced v5.3.1. During the OHDSI/CommonDataModel Hack-A-Thon that occurred on August 18, 2021 the decision was made to align documentation with the minor releases. Hot fixes and minor.minor release can be found through the searching of tags.* + +--after regeneration of DDLs +link to csv of cdm +link to pdf of cdm documentation +link to forum on doc page + +```{r docLoop53, echo=FALSE, results='asis'} +tableSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3_Table_Level.csv", stringsAsFactors = FALSE) +cdmSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3_Field_Level.csv", stringsAsFactors = FALSE) + +tables <- tableSpecs$cdmTableName + +cdmSpecsClean <- cdmSpecs %>% + dplyr::select(`CDM Table` = cdmTableName, + `CDM Field` = cdmFieldName, + `User Guide` = userGuidance, + `ETL Conventions` = etlConventions, + `Datatype` = cdmDatatype, + `Required` = isRequired, + `Primary Key` = isPrimaryKey, + `Foreign Key` = isForeignKey, + `FK Table` = fkTableName, + `FK Domain` = fkDomain + ) + +cdmSpecsClean[is.na(cdmSpecsClean)] <- "" + +for(tb in tables) { + + if(tb == 'PERSON'){ + cat("## **Clinical Data Tables**\n\n") + } + + if(tb == 'LOCATION'){ + cat("## **Health System Data Tables**\n\n") + } + + if(tb == 'PAYER_PLAN_PERIOD'){ + cat("## **Health Economics Data Tables**\n\n") + } + + if(tb == 'DRUG_ERA'){ + cat("## **Standardized Derived Elements**\n\n") + } + + if(tb == 'METADATA'){ + cat("## **Metadata Tables**\n\n") + } + if(tb == 'CONCEPT'){ + cat("## **Vocabulary Tables**\n\n") + } + + cat("###", tb, "{.tabset .tabset-pills} \n\n") + + tableInfo <- subset(tableSpecs, cdmTableName == tb) + cat("**Table Description**\n\n",tableInfo[,"tableDescription"], "\n\n") + + if(!isTRUE(tableInfo[,"userGuidance"]=="")){ + cat("**User Guide**\n\n",tableInfo[,"userGuidance"],"\n\n") + } + + if(!isTRUE(tableInfo[,"etlConventions"]=="")){ + cat("**ETL Conventions**\n\n",tableInfo[,"etlConventions"],"\n\n") + } + + loopTable <- subset(cdmSpecsClean, `CDM Table` == tb) + loopTable <- subset(loopTable, select = -c(1)) + + print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html", escape = FALSE) %>% + column_spec(1, bold = T) %>% + column_spec(2, width = "3in", include_thead = T) %>% + column_spec(3, width = "4in", include_thead = T) %>% + column_spec(4:9, width = "1in", include_thead = T) %>% + kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13)) + + + } + + + +``` diff --git a/rmd/cdm531.Rmd b/rmd/cdm54.Rmd similarity index 78% rename from rmd/cdm531.Rmd rename to rmd/cdm54.Rmd index 9d75990..2cbcfda 100644 --- a/rmd/cdm531.Rmd +++ b/rmd/cdm54.Rmd @@ -1,107 +1,107 @@ ---- -output: - # pdf_document: - # toc: yes - # toc_depth: '5' - html_document: - toc: yes - toc_depth: 5 - toc_float: yes ---- - -```{r setup, include=FALSE, eval=TRUE} - -#todo figure out how to get the document dynamically without specifying the name -library(rmarkdown) -library(knitr) -library(kableExtra) -library(magrittr) -library(dplyr) -library(stringr) - -``` - -# **OMOP CDM v5.3.1** - -Below is the specification document for the OMOP Common Data Model, v5.3.1. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page. - ---after regeneration of DDLs -link to csv of cdm -link to pdf of cdm documentation -link to forum on doc page - -```{r docLoop53, echo=FALSE, results='asis'} -tableSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3.1_Table_Level.csv", stringsAsFactors = FALSE) -cdmSpecs <- read.csv("../inst/csv/OMOP_CDMv5.3.1_Field_Level.csv", stringsAsFactors = FALSE) - -tables <- tableSpecs$cdmTableName - -cdmSpecsClean <- cdmSpecs %>% - dplyr::select(`CDM Table` = cdmTableName, - `CDM Field` = cdmFieldName, - `User Guide` = userGuidance, - `ETL Conventions` = etlConventions, - `Datatype` = cdmDatatype, - `Required` = isRequired, - `Primary Key` = isPrimaryKey, - `Foreign Key` = isForeignKey, - `FK Table` = fkTableName, - `FK Domain` = fkDomain - ) - -cdmSpecsClean[is.na(cdmSpecsClean)] <- "" - -for(tb in tables) { - - if(tb == 'PERSON'){ - cat("## **Clinical Data Tables**\n\n") - } - - if(tb == 'LOCATION'){ - cat("## **Health System Data Tables**\n\n") - } - - if(tb == 'PAYER_PLAN_PERIOD'){ - cat("## **Health Economics Data Tables**\n\n") - } - - if(tb == 'DRUG_ERA'){ - cat("## **Standardized Derived Elements**\n\n") - } - - if(tb == 'METADATA'){ - cat("## **Metadata Tables**\n\n") - } - if(tb == 'CONCEPT'){ - cat("## **Vocabulary Tables**\n\n") - } - - cat("###", tb, "{.tabset .tabset-pills} \n\n") - - tableInfo <- subset(tableSpecs, cdmTableName == tb) - cat("**Table Description**\n\n",tableInfo[,"tableDescription"], "\n\n") - - if(!isTRUE(tableInfo[,"userGuidance"]=="")){ - cat("**User Guide**\n\n",tableInfo[,"userGuidance"],"\n\n") - } - - if(!isTRUE(tableInfo[,"etlConventions"]=="")){ - cat("**ETL Conventions**\n\n",tableInfo[,"etlConventions"],"\n\n") - } - - loopTable <- subset(cdmSpecsClean, `CDM Table` == tb) - loopTable <- subset(loopTable, select = -c(1)) - - print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html", escape = FALSE) %>% - column_spec(1, bold = T) %>% - column_spec(2, width = "3in", include_thead = T) %>% - column_spec(3, width = "4in", include_thead = T) %>% - column_spec(4:9, width = "1in", include_thead = T) %>% - kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13)) - - - } - - - -``` +--- +output: + # pdf_document: + # toc: yes + # toc_depth: '5' + html_document: + toc: yes + toc_depth: 5 + toc_float: yes +--- + +```{r setup, include=FALSE, eval=TRUE} + +#todo figure out how to get the document dynamically without specifying the name +library(rmarkdown) +library(knitr) +library(kableExtra) +library(magrittr) +library(dplyr) +library(stringr) + +``` + +# **OMOP CDM v5.4** + +Below is the specification document for the OMOP Common Data Model, v5.4. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page. + +--after regeneration of DDLs +link to csv of cdm +link to pdf of cdm documentation +link to forum on doc page + +```{r docLoop53, echo=FALSE, results='asis'} +tableSpecs <- read.csv("../inst/csv/OMOP_CDMv5.4_Table_Level.csv", stringsAsFactors = FALSE) +cdmSpecs <- read.csv("../inst/csv/OMOP_CDMv5.4_Field_Level.csv", stringsAsFactors = FALSE) + +tables <- tableSpecs$cdmTableName + +cdmSpecsClean <- cdmSpecs %>% + dplyr::select(`CDM Table` = cdmTableName, + `CDM Field` = cdmFieldName, + `User Guide` = userGuidance, + `ETL Conventions` = etlConventions, + `Datatype` = cdmDatatype, + `Required` = isRequired, + `Primary Key` = isPrimaryKey, + `Foreign Key` = isForeignKey, + `FK Table` = fkTableName, + `FK Domain` = fkDomain + ) + +cdmSpecsClean[is.na(cdmSpecsClean)] <- "" + +for(tb in tables) { + + if(tb == 'PERSON'){ + cat("## **Clinical Data Tables**\n\n") + } + + if(tb == 'LOCATION'){ + cat("## **Health System Data Tables**\n\n") + } + + if(tb == 'PAYER_PLAN_PERIOD'){ + cat("## **Health Economics Data Tables**\n\n") + } + + if(tb == 'DRUG_ERA'){ + cat("## **Standardized Derived Elements**\n\n") + } + + if(tb == 'METADATA'){ + cat("## **Metadata Tables**\n\n") + } + if(tb == 'CONCEPT'){ + cat("## **Vocabulary Tables**\n\n") + } + + cat("###", tb, "{.tabset .tabset-pills} \n\n") + + tableInfo <- subset(tableSpecs, cdmTableName == tb) + cat("**Table Description**\n\n",tableInfo[,"tableDescription"], "\n\n") + + if(!isTRUE(tableInfo[,"userGuidance"]=="")){ + cat("**User Guide**\n\n",tableInfo[,"userGuidance"],"\n\n") + } + + if(!isTRUE(tableInfo[,"etlConventions"]=="")){ + cat("**ETL Conventions**\n\n",tableInfo[,"etlConventions"],"\n\n") + } + + loopTable <- subset(cdmSpecsClean, `CDM Table` == tb) + loopTable <- subset(loopTable, select = -c(1)) + + print(kable(x = loopTable, align = "l", row.names = FALSE, format = "html", escape = FALSE) %>% + column_spec(1, bold = T) %>% + column_spec(2, width = "3in", include_thead = T) %>% + column_spec(3, width = "4in", include_thead = T) %>% + column_spec(4:9, width = "1in", include_thead = T) %>% + kable_styling(c("condensed","hover"), position = "center", full_width = T, font_size = 13)) + + + } + + + +``` diff --git a/rmd/indices-primary-foreign.Rmd b/rmd/indices-primary-foreign.Rmd new file mode 100644 index 0000000..f0a1272 --- /dev/null +++ b/rmd/indices-primary-foreign.Rmd @@ -0,0 +1,48 @@ +--- +title: "Indices, Primary Keys and Foreign Key Constraints" +output: + html_document: + toc: true + toc_depth: 5 + toc_float: true +--- + +## Overview +Database indices improve the performance of queries against a database by organizing the data in a way that increase query execution. + +This article was written to provide guidance on the setting of indices, primary and foreign keys for data that has been transformed into the Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM). The community that supports the design and development of the OHDSI/CommonDataModel Github repository is a diverse collaborative of healthcare and technical profesisonals whom have limited data base adminstrative (DBA) experience. As a result, the comments below should be interpreted as suggestions and recommendations to help increase performance. Your teams needs may call for a modified configuration. + +## General Recommendations +Should your database of choice support indexing, the OMOP CDM Working Group recommends + +* Indexing on all columns containing an "_id" (e.g. condition_occurrence_id, drug_exposure_id, measurement_id, procedure_occurrence_id, etc.) +* Indexing on primary and foreign keys + +For all databases, regardless of custom indice support, primary and foreign keys should be set. This is a step towards ensuring data integrity. Information on what table level attributes should be set as primary and foreign keys can be found within the *_Field_Level.csv file(s) located in the [INST/CSV directory](https://github.com/OHDSI/CommonDataModel/tree/v5.4/inst/csv) + +## Database support +The OHDSI/CommonDataModel package leverages OHDSI/SQLRender and as a result is only capable of supporting sources that are supported by OHDSI/SQLRender. The following databases are currently supported. + +### Microsoft SQL Server +### Oracle +### PostgreSQL + +### Amazon Redshift +On AWS Redshift it is important to ensure that your data is properly distributed and sorted across nodes. Compression on certain columns may also help. The designed DDL does set DISTKEYS in an effort to optimize performance. This configuration can be seen within the [Redshift-specific DDL](https://github.com/OHDSI/CommonDataModel/blob/v5.4/ddl/5.4/redshift/OMOPCDM_redshift_5.4_ddl.sql). + +### Impala +### IBM Netezza +### Google BigQuery +Google BigQuery does not require manual optimization and/or sizing. Google BigQuery does massive parallel full table scans and intensive caching, all under the hood. +[Reference](https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2) + +### Microsoft Parallel Data Warehouse (PDW) +### SQLite + +### Databricks +This database type is not yet supported but is actively being worked on by a number of collaborators. For more informtion, please contact Ajit Londhe of Amgen. + +## References + +[ISO Best Practices of CDM Indexing](https://forums.ohdsi.org/t/iso-best-practices-of-cdm-indexing/10939/2) +