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Fixes mismatches in data types (removes bigints) 

closes #453
This commit is contained in:
Clair Blacketer 2022-01-13 12:34:30 -05:00
parent 4d77b93fe7
commit 09fe23fd44
1 changed files with 8 additions and 8 deletions
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16
inst/csv/OMOP_CDMv5.4_Field_Level.csv
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@ -167,7 +167,7 @@ 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,measurement_event_id,No,integer,"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,,,
@ -188,7 +188,7 @@ 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,observation_event_id,No,integer,"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,,,,,
@ -212,7 +212,7 @@ NOTE,provider_id,No,integer,The Provider who wrote the note.,The ETL may need to
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,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_id,No,integer,"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_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,,,,,
@ -367,21 +367,21 @@ 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_id,Yes,integer,A unique identifier for each Episode.,,Yes,No,,,,,
EPISODE,person_id,Yes,integer,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,CONCEPT,CONCEPT_ID,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.,No,No,,,,,
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_parent_id,No,integer,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,"Procedure, Regimen",,
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=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). ,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_id,Yes,integer,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,integer,"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,,,

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
167 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
168 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
169 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
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
188 NOTE note_date Yes date The date the note was recorded. No No
189 NOTE note_datetime No datetime If time is not given set the time to midnight. No No
190 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=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT). No Yes CONCEPT CONCEPT_ID Type Concept
191 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
192 NOTE note_title No varchar(250) The title of the note. No No
193 NOTE note_text Yes varchar(MAX) The content of the note. No No
194 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
212 NOTE_NLP nlp_datetime No datetime The date and time of the note processing. No No
213 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] 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
214 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:<br><br> - History = true - Concept_date = anything before the time of the report No No
215 NOTE_NLP term_modifiers No varchar(2000) For the modifiers that are there, they would have to have these values:<br><br> - Negation = false - Subject = patient - Conditional = false - Rule_out = false - Uncertain = true or high or moderate or even low (could argue about low). Term_modifiers will concatenate all modifiers for different types of entities (conditions, drugs, labs etc) into one string. Lab values will be saved as one of the modifiers. No No
216 SPECIMEN specimen_id Yes integer Unique identifier for each specimen. Yes No
217 SPECIMEN person_id Yes integer The person from whom the specimen is collected. No Yes PERSON PERSON_ID
218 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
367 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
368 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
369 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
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 No 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