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OMOP
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Hack-a-thon updates 

Closes #81, #387, #239, #412, #391, #330, #408, #365, #306, #264
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Clair Blacketer 2021-08-19 14:42:18 -04:00
parent d73a0f426d
commit 7067be34ac
4 changed files with 462 additions and 444 deletions
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inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -167,6 +167,8 @@ MEASUREMENT,measurement_source_concept_id,No,integer,"This is the concept repres
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,,,,,
MEASUREMENT,measurement_event_id,No,bigint,"If the Measurement record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here. ",No,No,,,,,
MEASUREMENT,meas_event_field_concept_id,No,integer,"If the Measurement record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. ",Put the CONCEPT_ID that identifies which table and field the MEASUREMENT_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,,,
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,,,
@ -186,6 +188,8 @@ OBSERVATION,observation_source_concept_id,No,integer,"This is the concept repres
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,,,,,
OBSERVATION,observation_event_id,No,bigint,"If the Observation record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here. See the [ETL Conventions for the OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm60.html#observation) table for more details.",No,No,,,,,
OBSERVATION,obs_event_field_concept_id,No,integer,"If the Observation record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. ",Put the CONCEPT_ID that identifies which table and field the OBSERVATION_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,,,
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,,,,,
@ -195,6 +199,8 @@ DEATH,cause_source_value,No,varchar(50),,"If available, put the source code repr
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_event_id,No,bigint,"If the Note record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here.",No,No,,,,,
NOTE,note_event_field_concept_id,No,integer,"If the Note record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. ",Put the CONCEPT_ID that identifies which table and field the NOTE_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_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,,
@ -260,7 +266,7 @@ LOCATION,location_id,Yes,integer,The unique key given to a unique Location.,Each
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,state,No,varchar(2),Please see the user guide for the location table for clarification on what this field represents in locations outside of the US.,,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,,,,,
@ -361,6 +367,22 @@ Condition.",,No,No,,,,,
CONDITION_ERA,condition_occurrence_count,No,integer,"The number of individual Condition
Occurrences used to construct the
condition era.",,No,No,,,,,
EPISODE,episode_id,Yes,bigint,A unique identifier for each Episode.,,Yes,No,,,,,
EPISODE,person_id,Yes,bigint,The PERSON_ID of the PERSON for whom the episode is recorded.,,No,Yes,PERSON,PERSON_ID,,,
EPISODE,episode_concept_id,Yes,integer,"The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.","Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see [article] for cancers and [article] for non-cancers describing how these are defined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=)",No,Yes,,,Episode,,
EPISODE,episode_start_date,Yes,date,The date when the Episode beings. ,Please see [article] for how to define an Episode start date.,No,No,,,,,
EPISODE,episode_start_datetime,No,datetime,The date and time when the Episode begins.,,No,No,,,,,
EPISODE,episode_end_date,No,date,The date when the instance of the Episode is considered to have ended.,Please see [article] for how to define an Episode end date.,,,,,,,
EPISODE,episode_end_datetime,No,datetime,The date when the instance of the Episode is considered to have ended.,,No,No,,,,,
EPISODE,episode_parent_id,No,bigint,Use this field to find the Episode that subsumes the given Episode record. This is used in the case that an Episode are nested into each other.,"If there are multiple nested levels to how Episodes are represented, the EPISODE_PARENT_ID can be used to record this relationship. ",No,No,,,,,
EPISODE,episode_number,No,integer,"For sequences of episodes, this is used to indicate the order the episodes occurred. For example, lines of treatment could be indicated here. ",Please see [article] for the details of how to count episodes.,No,No,,,,,
EPISODE,episode_object_concept_id,Yes,integer,"A Standard Concept representing the disease phase, outcome, or other abstraction of which the episode consists. For example, if the EPISODE_CONCEPT_ID is [treatment regimen](https://athena.ohdsi.org/search-terms/terms/32531) then the EPISODE_OBJECT_CONCEPT_ID should contain the chemotherapy regimen concept, like [Afatinib monotherapy](https://athena.ohdsi.org/search-terms/terms/35804392). ",Episode entries from the 'Disease Episode' concept class should have an episode_object_concept_id that comes from the Condition domain. Episode entries from the 'Treatment Episode' concept class should have an episode_object_concept_id that scome from the 'Procedure' domain or 'Regimen' concept class.,No,Yes,CONCEPT,CONCEPT_ID,,,
EPISODE,episode_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Episode record, as in whether the episode was from an EHR system, insurance claim, registry, or other sources.",Choose the EPISODE_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,,
EPISODE,episode_source_value,No,varchar(50),The source code for the Episdoe as it appears in the source data. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,,No,No,,,,,
EPISODE,episode_source_concept_id,No,integer,A foreign key to a Episode Concept that refers to the code used in the source.,Given that the Episodes are user-defined it is unlikely that there will be a Source Concept available. If that is the case then set this field to zero. ,No,Yes,CONCEPT,CONCEPT_ID,,,
EPISODE_EVENT,episode_id,Yes,bigint,Use this field to link the EPISODE_EVENT record to its EPISODE.,Put the EPISODE_ID that subsumes the EPISODE_EVENT record here.,No,Yes,EPISODE,EPISODE_ID,,,
EPISODE_EVENT,event_id,Yes,bigint,"This field is the primary key of the linked record in the database. For example, if the Episode Event is a Condition Occurrence, then the CONDITION_OCCURRENCE_ID of the linked record goes in this field. ",Put the primary key of the linked record here. ,No,No,,,,,
EPISODE_EVENT,episode_event_field_concept_id,Yes,integer,This field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. ,Put the CONCEPT_ID that identifies which table and field the EVENT_ID came from. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?vocabulary=CDM&conceptClass=Field&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,Metadata,,
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,,,

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
167 OBSERVATION provider_id qualifier_concept_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. This field contains all attributes specifying the clinical fact further, such as as degrees, severities, drug-drug interaction alerts etc. 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. 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 PROVIDER CONCEPT PROVIDER_ID CONCEPT_ID
168 OBSERVATION visit_occurrence_id unit_concept_id No integer The visit during which the Observation occurred. 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. 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. 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 VISIT_OCCURRENCE CONCEPT VISIT_OCCURRENCE_ID CONCEPT_ID Unit
169 OBSERVATION visit_detail_id provider_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. The provider associated with the observation record, e.g. the provider who ordered the test or the provider who recorded the result. Same rules apply as for the VISIT_OCCURRENCE_ID. 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 VISIT_DETAIL PROVIDER VISIT_DETAIL_ID PROVIDER_ID
170 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
171 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
172 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
173 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
174 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
188 NOTE note_type_concept_id note_event_id Yes No integer bigint The provenance of the note. Most likely this will be EHR. If the Note record is related to another record in the database, this field is the primary key of the linked record. 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=). Put the primary key of the linked record, if applicable, here. No Yes No CONCEPT CONCEPT_ID Type Concept
189 NOTE note_class_concept_id note_event_field_concept_id Yes No integer A Standard Concept Id representing the HL7 LOINC Document Type Vocabulary classification of the note. If the Note record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. 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). Put the CONCEPT_ID that identifies which table and field the NOTE_EVENT_ID came from. No Yes CONCEPT CONCEPT_ID
190 NOTE note_title note_date No Yes varchar(250) date The title of the note. The date the note was recorded. No No
191 NOTE note_datetime No datetime If time is not given set the time to midnight. No No
192 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
193 NOTE note_text note_class_concept_id Yes varchar(MAX) integer The content of the note. 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 No Yes CONCEPT CONCEPT_ID
194 NOTE encoding_concept_id note_title Yes No integer varchar(250) This is the Concept representing the character encoding type. The title of the note. 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 No CONCEPT CONCEPT_ID
195 NOTE language_concept_id note_text Yes integer varchar(MAX) The language of the note. The content of the note. Use Concepts that are descendants of the concept [4182347](https://athena.ohdsi.org/search-terms/terms/4182347) (World Languages). No Yes No CONCEPT CONCEPT_ID
199 NOTE note_source_value visit_occurrence_id No varchar(50) integer The Visit during which the note was written. The source value mapped to the NOTE_CLASS_CONCEPT_ID. No No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID
200 NOTE_NLP NOTE note_nlp_id visit_detail_id Yes No integer A unique identifier for the NLP record. The Visit Detail during which the note was written. Yes No No Yes VISIT_DETAIL VISIT_DETAIL_ID
201 NOTE_NLP NOTE note_id note_source_value Yes No integer varchar(50) This is the NOTE_ID for the NOTE record the NLP record is associated to. The source value mapped to the NOTE_CLASS_CONCEPT_ID. No No
202 NOTE_NLP note_nlp_id Yes integer A unique identifier for the NLP record. Yes No
203 NOTE_NLP note_id Yes integer This is the NOTE_ID for the NOTE record the NLP record is associated to. No No
204 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
205 NOTE_NLP snippet No varchar(250) A small window of text surrounding the term No No
206 NOTE_NLP offset No varchar(50) Character offset of the extracted term in the input note No No
266 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
267 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
268 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
269 PAYER_PLAN_PERIOD payer_plan_period_start_date Yes date Start date of Plan coverage. No No
270 PAYER_PLAN_PERIOD payer_plan_period_end_date Yes date End date of Plan coverage. No No
271 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
272 PAYER_PLAN_PERIOD payer_source_value No varchar(50) This is the Payer as it appears in the source data. No No
367 CONCEPT_RELATIONSHIP CONCEPT concept_id_1 standard_concept Yes No integer 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 Yes No CONCEPT CONCEPT_ID
368 CONCEPT_RELATIONSHIP CONCEPT concept_id_2 concept_code Yes integer 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 Yes No CONCEPT CONCEPT_ID
369 CONCEPT_RELATIONSHIP CONCEPT relationship_id valid_start_date Yes varchar(20) date 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. 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 Yes No RELATIONSHIP RELATIONSHIP_ID
370 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
371 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
372 VOCABULARY vocabulary_id Yes varchar(20) A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. Yes No
373 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
374 VOCABULARY vocabulary_reference Yes varchar(255) External reference to documentation or available download of the about the vocabulary. No No
375 VOCABULARY vocabulary_version No varchar(255) Version of the Vocabulary as indicated in the source. No No
376 VOCABULARY vocabulary_concept_id Yes integer A Concept that represents the Vocabulary the VOCABULARY record belongs to. No Yes CONCEPT CONCEPT_ID
377 DOMAIN domain_id Yes varchar(20) A unique key for each domain. Yes No
378 DOMAIN domain_name Yes varchar(255) The name describing the Domain, e.g. Condition, Procedure, Measurement etc. No No
379 DOMAIN domain_concept_id Yes integer A Concept representing the Domain Concept the DOMAIN record belongs to. No Yes CONCEPT CONCEPT_ID
380 CONCEPT_CLASS concept_class_id Yes varchar(20) A unique key for each class. Yes No
381 CONCEPT_CLASS concept_class_name Yes varchar(255) The name describing the Concept Class, e.g. Clinical Finding, Ingredient, etc. No No
382 CONCEPT_CLASS concept_class_concept_id Yes integer A Concept that represents the Concept Class. No Yes CONCEPT CONCEPT_ID
383 CONCEPT_RELATIONSHIP concept_id_1 Yes integer No Yes CONCEPT CONCEPT_ID
384 CONCEPT_RELATIONSHIP concept_id_2 Yes integer No Yes CONCEPT CONCEPT_ID
385 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
386 CONCEPT_RELATIONSHIP valid_start_date Yes date The date when the relationship is first recorded. No No
387 CONCEPT_RELATIONSHIP valid_end_date Yes date The date when the relationship is invalidated. No No
388 CONCEPT_RELATIONSHIP invalid_reason No varchar(1) Reason the relationship was invalidated. Possible values are 'D' (deleted), 'U' (updated) or NULL. No No

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inst/csv/OMOP_CDMv5.4_Table_Level.csv
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@ -40,7 +40,7 @@ SPECIMEN,CDM,No,SPECIMEN_,Yes,0,,The specimen domain contains the records identi
FACT_RELATIONSHIP,CDM,No,,No,,,"The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain, or different domains. Examples of Fact Relationships include: [Person relationships](https://athena.ohdsi.org/search-terms/terms?domain=Relationship&standardConcept=Standard&page=2&pageSize=15&query=) (parent-child), care site relationships (hierarchical organizational structure of facilities within a health system), indication relationship (between drug exposures and associated conditions), usage relationships (of devices during the course of an associated procedure), or facts derived from one another (measurements derived from an associated specimen).",,"All relationships are directional, and each relationship is represented twice symmetrically within the FACT_RELATIONSHIP table. For example, two persons if person_id = 1 is the mother of person_id = 2 two records are in the FACT_RELATIONSHIP table (all strings in fact concept_id records in the Concept table:
- Person, 1, Person, 2, parent of
- Person, 2, Person, 1, child of"
LOCATION,CDM,No,,No,,,The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites.,,"Each address or Location is unique and is present only once in the table. Locations do not contain names, such as the name of a hospital. In order to construct a full address that can be used in the postal service, the address information from the Location needs to be combined with information from the Care Site."
LOCATION,CDM,No,,No,,,The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites.,"The current iteration of the LOCATION table is US centric. Until a major release to correct this, certain fields can be used to represent different international values. <br><br> - STATE can also be used for province or district<br>- ZIP is also the postal code or postcode","Each address or Location is unique and is present only once in the table. Locations do not contain names, such as the name of a hospital. In order to construct a full address that can be used in the postal service, the address information from the Location needs to be combined with information from the Care Site."
CARE_SITE,CDM,No,,No,,,"The CARE_SITE table contains a list of uniquely identified institutional (physical or organizational) units where healthcare delivery is practiced (offices, wards, hospitals, clinics, etc.).",,"Care site is a unique combination of location_id and place_of_service_source_value. Care site does not take into account the provider (human) information such a specialty. Many source data do not make a distinction between individual and institutional providers. The CARE_SITE table contains the institutional providers. If the source, instead of uniquely identifying individual Care Sites, only provides limited information such as Place of Service, generic or ""pooled"" Care Site records are listed in the CARE_SITE table. There can be hierarchical and business relationships between Care Sites. For example, wards can belong to clinics or departments, which can in turn belong to hospitals, which in turn can belong to hospital systems, which in turn can belong to HMOs.The relationships between Care Sites are defined in the FACT_RELATIONSHIP table."
PROVIDER,CDM,No,,No,,,"The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on healthcare to patients, such as physicians, nurses, midwives, physical therapists etc.","Many sources do not make a distinction between individual and institutional providers. The PROVIDER table contains the individual providers. If the source, instead of uniquely identifying individual providers, only provides limited information such as specialty, generic or 'pooled' Provider records are listed in the PROVIDER table.",
PAYER_PLAN_PERIOD,CDM,No,,Yes,0,,"The PAYER_PLAN_PERIOD table captures details of the period of time that a Person is continuously enrolled under a specific health Plan benefit structure from a given Payer. Each Person receiving healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or directly provides, the care. These benefit plans are provided by payers, such as health insurances or state or government agencies. In each plan the details of the health benefits are defined for the Person or her family, and the health benefit Plan might change over time typically with increasing utilization (reaching certain cost thresholds such as deductibles), plan availability and purchasing choices of the Person. The unique combinations of Payer organizations, health benefit Plans and time periods in which they are valid for a Person are recorded in this table.","A Person can have multiple, overlapping, Payer_Plan_Periods in this table. For example, medical and drug coverage in the US can be represented by two Payer_Plan_Periods. The details of the benefit structure of the Plan is rarely known, the idea is just to identify that the Plans are different.",

1 cdmTableName schema isRequired conceptPrefix measurePersonCompleteness measurePersonCompletenessThreshold validation tableDescription userGuidance etlConventions
40 COHORT_DEFINITION RESULTS No No The COHORT_DEFINITION table contains records defining a Cohort derived from the data through the associated description and syntax and upon instantiation (execution of the algorithm) placed into the COHORT table. Cohorts are a set of subjects that satisfy a given combination of inclusion criteria for a duration of time. The COHORT_DEFINITION table provides a standardized structure for maintaining the rules governing the inclusion of a subject into a cohort, and can store operational programming code to instantiate the cohort within the OMOP Common Data Model.
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inst/csv/OMOP_CDMv6.0_Field_Level.csv
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@ -118,7 +118,7 @@ PROCEDURE_OCCURRENCE,procedure_concept_id,Yes,integer,"The PROCEDURE_CONCEPT_ID
PROCEDURE_OCCURRENCE,procedure_date,No,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,Yes,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,Yes,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. If not available, set to 0. [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,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. If not available, set to 0. [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,bigint,"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,bigint,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,,,
@ -210,7 +210,7 @@ NOTE_NLP,note_nlp_id,Yes,bigint,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,"\""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,,,
@ -334,33 +334,29 @@ PAYER_PLAN_PERIOD,family_source_value,No,varchar(50),The common identifier for a
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,bigint,,,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,bigint,,,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,,,,,
COST,cost_id,Yes,bigint,A unique identifier for each COST record.,,Yes,No,,,,,
COST,person_id,Yes,bigint,,,No,No,,,,,
COST,cost_event_id,Yes,bigint,"If the Cost record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here.",No,No,,,,,
COST,cost_event_field_concept_id,Yes,integer,"If the Cost record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. ",Put the CONCEPT_ID that identifies which table and field the COST_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,,,
COST,cost_concept_id,No,integer,A foreign key that refers to a Standard Cost Concept identifier in the Standardized Vocabularies belonging to the 'Cost' vocabulary.,,No,Yes,CONCEPT,CONCEPT_ID,,,
COST,cost_type_concept_id,No,integer,A foreign key identifier to a concept in the CONCEPT table for the provenance or the source of the COST data and belonging to the 'Type Concept' vocabulary,,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
COST,cost_source_concept_id,No,integer,A foreign key to a Cost Concept that refers to the code used in the source.,,No,Yes,CONCEPT,CONCEPT_ID,,,
COST,cost_source_value,No,varchar(50),The source value for the cost as it appears in the source data,,No,No,,,,,
COST,currency_concept_id,No,integer,"A foreign key identifier to the concept representing the 3-letter code used to delineate international currencies, such as USD for US Dollar. These belong to the 'Currency' vocabulary",,No,No,CONCEPT,CONCEPT_ID,,,
COST,cost,No,float,The actual financial cost amount,,No,No,,,,,
COST,incurred_date,No,date,"The first date of service of the clinical event corresponding to the cost as in table capturing the information (e.g. date of visit, date of procedure, date of condition, date of drug etc).",,No,No,,,,,
COST,billed_date,No,date,The date a bill was generated for a service or encounter,,No,No,,,,,
COST,paid_date,No,date,The date payment was received for a service or encounter,,No,No,,,,,
COST,revenue_code_concept_id,No,integer,A foreign key referring to a Standard Concept ID in the Standardized Vocabularies for Revenue codes belonging to the 'Revenue Code' vocabulary.,,No,Yes,CONCEPT,CONCEPT_ID,,,
COST,drg_concept_id,No,integer,A foreign key referring to a Standard Concept ID in the Standardized Vocabularies for DRG codes belonging to the 'DRG' vocabulary.,,No,Yes,CONCEPT,CONCEPT_ID,,,
COST,revenue_code_source_value,No,varchar(50),"The source value for the Revenue code as it appears in the source data, stored here for reference.",,No,No,,,,,
COST,drg_source_value,No,varchar(50),"The source value for the 3-digit DRG source code as it appears in the source data, stored here for reference.",,No,No,,,,,
COST,payer_plan_period_id,No,bigint,"A foreign key to the PAYER_PLAN_PERIOD table, where the details of the Payer, Plan and Family are stored. Record the payer_plan_id that relates to the payer who contributed to the paid_by_payer field.",,No,No,,,,,
DRUG_ERA,drug_era_id,Yes,bigint,,,Yes,No,,,,,
DRUG_ERA,person_id,Yes,bigint,,,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:
DRUG_ERA,drug_era_start_datetime,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_datetime,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,,,,,
@ -371,18 +367,18 @@ DOSE_ERA,person_id,Yes,bigint,,,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,,,,,
DOSE_ERA,dose_era_start_datetime,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_datetime,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,bigint,,,Yes,No,,,,,
CONDITION_ERA,person_id,Yes,bigint,,,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
CONDITION_ERA,condition_era_start_datetime,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,,,,,
CONDITION_ERA,condition_era_end_date,Yes,datetime,"The end date for the Condition Era
CONDITION_ERA,condition_era_end_datetime,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
@ -538,7 +534,7 @@ 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_DEFINITION,cohort_definition_id,Yes,integer,"This is the identifier given to the cohort, usually by the ATLAS application",,No,No,,,,,
COHORT_DEFINITION,cohort_definition_id,Yes,bigint,"This is the identifier given to the cohort, usually by the ATLAS application",,No,No,,,,,
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,,,

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
118 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
119 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
120 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
121 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
122 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. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). 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. No Yes CONCEPT CONCEPT_ID Type Concept
123 DEVICE_EXPOSURE unique_device_id No varchar(50) This is the Unique Device Identification number for devices regulated by the FDA, if given. For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field. No No
124 DEVICE_EXPOSURE quantity No integer No No
210 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
211 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
212 SPECIMEN specimen_date Yes date The date the specimen was collected. No No
213 SPECIMEN specimen_datetime No datetime No No
214 SPECIMEN quantity No float The amount of specimen collected from the person. No No
215 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
216 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
334 DRUG_ERA DOSE_ERA drug_era_end_date person_id Yes datetime bigint 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 Yes PERSON PERSON_ID
335 DRUG_ERA DOSE_ERA drug_exposure_count drug_concept_id No Yes integer The Concept Id representing the specific drug ingredient. No No Yes CONCEPT CONCEPT_ID Drug Ingredient
336 DRUG_ERA DOSE_ERA gap_days unit_concept_id No Yes integer The Concept Id representing the unit of the specific drug ingredient. 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 Yes CONCEPT CONCEPT_ID Unit
337 DOSE_ERA dose_era_id dose_value Yes bigint float The numeric value of the dosage of the drug_ingredient. Yes No No
338 DOSE_ERA person_id dose_era_start_datetime Yes bigint datetime The date the Person started on the specific dosage, with at least 31 days since any prior exposure. No Yes No PERSON PERSON_ID
339 DOSE_ERA drug_concept_id dose_era_end_datetime Yes integer datetime The Concept Id representing the specific drug ingredient. 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 Yes No CONCEPT CONCEPT_ID Drug Ingredient
340 DOSE_ERA CONDITION_ERA unit_concept_id condition_era_id Yes integer bigint The Concept Id representing the unit of the specific drug ingredient. No Yes Yes No CONCEPT CONCEPT_ID Unit
341 DOSE_ERA CONDITION_ERA dose_value person_id Yes float bigint The numeric value of the dosage of the drug_ingredient. No No PERSON PERSON_ID
342 DOSE_ERA CONDITION_ERA dose_era_start_date condition_concept_id Yes datetime integer The date the Person started on the specific dosage, with at least 31 days since any prior exposure. The Concept Id representing the Condition. No No Yes CONCEPT CONCEPT_ID Condition
343 DOSE_ERA CONDITION_ERA dose_era_end_date condition_era_start_datetime 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. 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
344 CONDITION_ERA condition_era_id condition_era_end_datetime Yes integer 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. Yes No No
345 CONDITION_ERA person_id condition_occurrence_count Yes No bigint integer The number of individual Condition Occurrences used to construct the condition era. No No PERSON PERSON_ID
346 CONDITION_ERA METADATA condition_concept_id metadata_concept_id Yes integer The Concept Id representing the Condition. No Yes CONCEPT CONCEPT_ID Condition
347 CONDITION_ERA METADATA condition_era_start_date metadata_type_concept_id Yes datetime integer 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 Yes CONCEPT CONCEPT_ID
348 CONDITION_ERA METADATA condition_era_end_date name Yes datetime varchar(250) 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
349 CONDITION_ERA METADATA condition_occurrence_count value_as_string No integer varchar(250) The number of individual Condition Occurrences used to construct the condition era. No No
350 METADATA metadata_concept_id value_as_concept_id Yes No integer No Yes CONCEPT CONCEPT_ID
351 METADATA metadata_type_concept_id metadata_date Yes No integer date No Yes No CONCEPT CONCEPT_ID
352 METADATA name metadata_datetime Yes No varchar(250) datetime No No
353 METADATA CDM_SOURCE value_as_string cdm_source_name No Yes varchar(250) varchar(255) The name of the CDM instance. No No
354 METADATA CDM_SOURCE value_as_concept_id cdm_source_abbreviation No integer varchar(25) The abbreviation of the CDM instance. No Yes No 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 No varchar(25) The abbreviation of the CDM instance. No No
355 CDM_SOURCE cdm_holder No varchar(255) The holder of the CDM instance. No No
356 CDM_SOURCE source_description No varchar(MAX) The description of the CDM instance. No No
357 CDM_SOURCE source_documentation_reference No varchar(255) No No
358 CDM_SOURCE cdm_etl_reference No varchar(255) Put the link to the CDM version used. No No
359 CDM_SOURCE source_release_date No date The release date of the source data. No No
360 CDM_SOURCE cdm_release_date No date The release data of the CDM instance. No No
361 CDM_SOURCE cdm_version No varchar(10) No No
362 CDM_SOURCE vocabulary_version No varchar(20) No No
367 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
368 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
369 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
370 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
371 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
372 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
373 VOCABULARY vocabulary_id Yes varchar(20) A unique identifier for each Vocabulary, such as ICD9CM, SNOMED, Visit. Yes No
374 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
375 VOCABULARY vocabulary_reference Yes varchar(255) External reference to documentation or available download of the about the vocabulary. No No
376 VOCABULARY vocabulary_version No varchar(255) Version of the Vocabulary as indicated in the source. No No
377 VOCABULARY vocabulary_concept_id Yes integer A Concept that represents the Vocabulary the VOCABULARY record belongs to. No Yes CONCEPT CONCEPT_ID
378 DOMAIN domain_id Yes varchar(20) A unique key for each domain. Yes No
379 DOMAIN domain_name Yes varchar(255) The name describing the Domain, e.g. Condition, Procedure, Measurement etc. No No
380 DOMAIN domain_concept_id Yes integer A Concept representing the Domain Concept the DOMAIN record belongs to. No Yes CONCEPT CONCEPT_ID
381 CONCEPT_CLASS concept_class_id Yes varchar(20) A unique key for each class. Yes No
382 CONCEPT_CLASS concept_class_name Yes varchar(255) The name describing the Concept Class, e.g. Clinical Finding, Ingredient, etc. No No
383 CONCEPT_CLASS concept_class_concept_id Yes integer A Concept that represents the Concept Class. No Yes CONCEPT CONCEPT_ID
384 CONCEPT_RELATIONSHIP concept_id_1 Yes integer No Yes CONCEPT CONCEPT_ID
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