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Merge pull request #686 from OHDSI/olympians_week4 

Olympians week4
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clairblacketer 2024-04-29 17:07:30 -04:00 committed by GitHub
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15
docs/cdm53.html
View File

@ -1600,7 +1600,8 @@ 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.
the patient-provider interaction. If this information is not available
the record should be dropped.
</td>
<td style="text-align:left;">
date
@ -4966,6 +4967,8 @@ quantity
<td style="text-align:left;">
</td>
<td style="text-align:left;">
If there is a record of device exposure in the source but no quantity
value, then set to 1.
</td>
<td style="text-align:left;">
integer
@ -8822,14 +8825,14 @@ No
<h3 class="tabset tabset-pills">provider</h3>
<p><strong>Table Description</strong></p>
<p>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.</p>
providers; duplication is not allowed. These are individuals providing
hands-on healthcare to patients, such as physicians, nurses, midwives,
physical therapists etc.</p>
<p><strong>User Guide</strong></p>
<p>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
providers. If the source only provides limited information such as
specialty instead of uniquely identifying individual providers, generic
or ‘pooled’ Provider records are listed in the PROVIDER table.</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>

15
docs/cdm54.html
View File

@ -1708,7 +1708,8 @@ 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.
the patient-provider interaction. If this information is not available
the record should be dropped.
</td>
<td style="text-align:left;">
date
@ -5171,6 +5172,8 @@ quantity
<td style="text-align:left;">
</td>
<td style="text-align:left;">
If there is a record of device exposure in the source but no quantity
value, then set to 1.
</td>
<td style="text-align:left;">
integer
@ -9495,14 +9498,14 @@ No
<h3 class="tabset tabset-pills">provider</h3>
<p><strong>Table Description</strong></p>
<p>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.</p>
providers; duplication is not allowed. These are individuals providing
hands-on healthcare to patients, such as physicians, nurses, midwives,
physical therapists etc.</p>
<p><strong>User Guide</strong></p>
<p>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
providers. If the source only provides limited information such as
specialty instead of uniquely identifying individual providers, generic
or ‘pooled’ Provider records are listed in the PROVIDER table.</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>

4
inst/csv/OMOP_CDMv5.3_Field_Level.csv
View File

@ -25,7 +25,7 @@ observation_period,period_type_concept_id,Yes,integer,"This field can be used to
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,NA,NA,NA,NA,NA
visit_occurrence,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA
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,NA,NA
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,NA,NA,NA,NA,NA
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. If this information is not available the record should be dropped.",No,No,NA,NA,NA,NA,NA
visit_occurrence,visit_start_datetime,No,datetime,NA,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,NA,NA,NA,NA,NA
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
@ -134,7 +134,7 @@ device_exposure,device_exposure_end_date,No,date,"The DEVICE_EXPOSURE_END_DATE d
device_exposure,device_exposure_end_datetime,No,datetime,NA,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,NA,NA,NA,NA,NA
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=). 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,NA,NA
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,NA,NA,NA,NA,NA
device_exposure,quantity,No,integer,NA,NA,No,No,NA,NA,NA,NA,NA
device_exposure,quantity,No,integer,NA,"If there is a record of device exposure in the source but no quantity value, then set to 1.",No,No,NA,NA,NA,NA,NA
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,NA,NA,NA
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,NA,NA,NA
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,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
25 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 NA NA NA NA NA
26 visit_occurrence person_id Yes integer NA NA No Yes PERSON PERSON_ID NA NA NA
27 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 NA NA
28 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. 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. If this information is not available the record should be dropped. No No NA NA NA NA NA
29 visit_occurrence visit_start_datetime No datetime NA If no time is given for the start date of a visit, set it to midnight (00:00:0000). No No NA NA NA NA NA
30 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 NA NA NA NA NA
31 visit_occurrence visit_end_datetime No datetime NA If no time is given for the end date of a visit, set it to midnight (00:00:0000). No No NA NA NA NA NA
134 measurement measurement_time No varchar(10) NA This is present for backwards compatibility and will be deprecated in an upcoming version. No No NA NA NA NA NA
135 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=). 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 NA NA
136 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=). Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numeric value at all. No Yes CONCEPT CONCEPT_ID NA NA NA
137 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. [Convention for negative values](https://ohdsi.github.io/Themis/negative_value_as_number.html) No No NA NA NA NA NA
138 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 there is no categorial result in the source data, set VALUE_AS_CONCEPT_ID to NULL, if there is a categorial result in a source data but without mapping, set VALUE_AS_CONCEPT_ID to 0, else map to a CONCEPT_ID. No Yes CONCEPT CONCEPT_ID NA NA NA
139 measurement unit_concept_id No integer At present, there isn't a prescribed unit for individual measurements, such as Hemoglobin A1C, meaning it's not obligatory to express these measurements as a percentage. UNIT_SOURCE_VALUES should be linked to a Standard Concept within the Unit domain that most accurately reflects the unit provided in the source data. If the source data does not include units, set UNIT_CONCEPT_ID to NULL. If units are provided but not mapped, set UNIT_CONCEPT_ID to 0. Otherwise, map the units to a CONCEPT_ID. Remember that units are case-sensitive in vocabulary. No Yes CONCEPT CONCEPT_ID Unit NA NA
140 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 NA NA NA NA NA

2
inst/csv/OMOP_CDMv5.3_Table_Level.csv
View File

@ -42,7 +42,7 @@ fact_relationship,CDM,No,NA,No,NA,NA,"The FACT_RELATIONSHIP table contains recor
- Person, 2, Person, 1, child of"
location,CDM,No,NA,No,NA,NA,The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites.,NA,"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,NA,No,NA,NA,"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.).",NA,"Care site is a unique combination of location_id and nature of the site - the latter could be the place of service, name, or another characteristic in your source data. 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.<br><br>For additional detailed conventions on how to populate this table, please refer to [THEMIS repository](https://ohdsi.github.io/Themis/care_site.html)."
provider,CDM,No,NA,No,NA,NA,"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.",NA
provider,CDM,No,NA,No,NA,NA,"The PROVIDER table contains a list of uniquely identified healthcare providers; duplication is not allowed. 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 only provides limited information such as specialty instead of uniquely identifying individual providers, generic or 'pooled' Provider records are listed in the PROVIDER table.",NA
payer_plan_period,CDM,No,NA,Yes,0,NA,"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.",NA
cost,CDM,No,NA,No,NA,NA,"The COST table captures records containing the cost of any medical event recorded in one of the OMOP clinical event tables such as DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, VISIT_DETAIL, DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT.

1 cdmTableName schema isRequired conceptPrefix measurePersonCompleteness measurePersonCompletenessThreshold validation tableDescription userGuidance etlConventions
42
43
44
45
46
47
48

4
inst/csv/OMOP_CDMv5.4_Field_Level.csv
View File

@ -25,7 +25,7 @@ observation_period,period_type_concept_id,Yes,integer,"This field can be used to
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,NA,NA,NA,NA,NA
visit_occurrence,person_id,Yes,integer,NA,NA,No,Yes,PERSON,PERSON_ID,NA,NA,NA
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,NA,NA
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,NA,NA,NA,NA,NA
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. If this information is not available the record should be dropped.",No,No,NA,NA,NA,NA,NA
visit_occurrence,visit_start_datetime,No,datetime,NA,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,NA,NA,NA,NA,NA
visit_occurrence,visit_end_date,Yes,date,"For inpatient visits the end date is typically the discharge date. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull.","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
@ -137,7 +137,7 @@ device_exposure,device_exposure_end_datetime,No,datetime,NA,If a source does not
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=). 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,NA,NA
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,NA,NA,NA,NA,NA
device_exposure,production_id,No,varchar(255),This is the Production Identifier (UDI-PI) portion of the Unique Device Identification.,NA,No,No,NA,NA,NA,NA,NA
device_exposure,quantity,No,integer,NA,NA,No,No,NA,NA,NA,NA,NA
device_exposure,quantity,No,integer,NA,"If there is a record of device exposure in the source but no quantity value, then set to 1.",No,No,NA,NA,NA,NA,NA
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,NA,NA,NA
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,NA,NA,NA
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,NA,NA,NA

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
25 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 NA NA NA NA NA
26 visit_occurrence person_id Yes integer NA NA No Yes PERSON PERSON_ID NA NA NA
27 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 NA NA
28 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. 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. If this information is not available the record should be dropped. No No NA NA NA NA NA
29 visit_occurrence visit_start_datetime No datetime NA If no time is given for the start date of a visit, set it to midnight (00:00:0000). No No NA NA NA NA NA
30 visit_occurrence visit_end_date Yes date For inpatient visits the end date is typically the discharge date. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull. 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 NA NA NA NA NA
31 visit_occurrence visit_end_datetime No datetime If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_datetime, then set the visit_end_datetime to the datetime of the data pull. If no time is given for the end date of a visit, set it to midnight (00:00:0000). No No NA NA NA NA NA
137 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. This is the standard concept mapped from the source value which represents a measurement. The CONCEPT_ID that the MEASUREMENT_SOURCE_VALUE maps to. Only records whose source values map to concepts with a domain of Measurement should go in this table. No Yes CONCEPT CONCEPT_ID Measurement NA NA
138 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 NA NA NA NA NA
139 measurement measurement_datetime No datetime NA 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 NA NA NA NA NA
140 measurement measurement_time No varchar(10) NA This is present for backwards compatibility and will be deprecated in an upcoming version. No No NA NA NA NA NA
141 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=). 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 NA NA
142 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=). Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numeric value at all. No Yes CONCEPT CONCEPT_ID NA NA NA
143 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. [Convention for negative values](https://ohdsi.github.io/Themis/negative_value_as_number.html) No No NA NA NA NA NA

2
inst/csv/OMOP_CDMv5.4_Table_Level.csv
View File

@ -42,7 +42,7 @@ fact_relationship,CDM,No,NA,No,NA,NA,"The FACT_RELATIONSHIP table contains recor
- Person, 2, Person, 1, child of"
location,CDM,No,NA,No,NA,NA,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 <br>- COUNTY can also be used to represent region","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,NA,No,NA,NA,"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.).",NA,"Care site is a unique combination of location_id and nature of the site - the latter could be the place of service, name, or another characteristic in your source data. 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.<br><br>For additional detailed conventions on how to populate this table, please refer to [THEMIS repository](https://ohdsi.github.io/Themis/care_site.html)."
provider,CDM,No,NA,No,NA,NA,"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.",NA
provider,CDM,No,NA,No,NA,NA,"The PROVIDER table contains a list of uniquely identified healthcare providers; duplication is not allowed. 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 only provides limited information such as specialty instead of uniquely identifying individual providers, generic or 'pooled' Provider records are listed in the PROVIDER table.",NA
payer_plan_period,CDM,No,NA,Yes,0,NA,"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.",NA
cost,CDM,No,NA,No,NA,NA,"The COST table captures records containing the cost of any medical event recorded in one of the OMOP clinical event tables such as DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, VISIT_DETAIL, DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT.

1 cdmTableName schema isRequired conceptPrefix measurePersonCompleteness measurePersonCompletenessThreshold validation tableDescription userGuidance etlConventions
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