Merge pull request #686 from OHDSI/olympians_week4

Olympians week4

docs/cdm53.html

@@ -1600,7 +1600,8 @@ <h3 class="tabset tabset-pills">visit_occurrence</h3>
 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 @@ <h3 class="tabset tabset-pills">device_exposure</h3>
 <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 @@ <h3 class="tabset tabset-pills">care_site</h3>
 <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>

docs/cdm54.html

@@ -1708,7 +1708,8 @@ <h3 class="tabset tabset-pills">visit_occurrence</h3>
 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 @@ <h3 class="tabset tabset-pills">device_exposure</h3>
 <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 @@ <h3 class="tabset tabset-pills">care_site</h3>
 <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>

inst/csv/OMOP_CDMv5.3_Field_Level.csv

@@ -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

inst/csv/OMOP_CDMv5.3_Table_Level.csv

@@ -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.
 

inst/csv/OMOP_CDMv5.4_Field_Level.csv

@@ -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