Html rendering
This commit is contained in:
Clair Blacketer
parent
bf37173742
commit
a7d620f199
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@ -524,7 +524,10 @@ Events should have a record nonetheless. If more than one data source
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contributes Events to the database, Persons must be reconciled, if
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possible, across the sources to create one single record per Person. The
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content of the BIRTH_DATETIME must be equivalent to the content of
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BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.</p>
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BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.<br><br>For detailed conventions
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for how to populate this table, please refer to the <a
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href="https://ohdsi.github.io/Themis/person.html">THEMIS
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repository</a>.</p>
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<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
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<thead>
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<tr>
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@ -604,7 +607,9 @@ gender identity it should be stored in the <a
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href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
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table. <a
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href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
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gender concepts</a>
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gender concepts</a>. Please refer to the <a
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href="https://ohdsi.github.io/Themis/tag_gender_concept_id.html">THEMIS
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repository</a> for detailed conventions on how to populate this field.
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</td>
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<td style="text-align:left;">
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integer
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@ -633,11 +638,12 @@ year_of_birth
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Compute age using year_of_birth.
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</td>
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<td style="text-align:left;">
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For data sources with date of birth, the year should be extracted. For
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data sources where the year of birth is not available, the approximate
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year of birth could be derived based on age group categorization, if
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available. If no year of birth is available all the person’s data should
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be dropped from the CDM instance.
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For data sources with date of birth, the year should be extracted. If no
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year of birth is available all the person’s data should be dropped from
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the CDM instance. For additional information on how to populate this
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field, please refer to the <a
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href="https://ohdsi.github.io/Themis/tag_year_of_birth.html">THEMIS
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repository</a>.
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</td>
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<td style="text-align:left;">
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integer
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@ -719,13 +725,9 @@ birth_datetime
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<td style="text-align:left;">
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This field is not required but highly encouraged. For data sources that
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provide the precise datetime of birth, that value should be stored in
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this field. If birth_datetime is not provided in the source, use the
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following logic to infer the date: If day_of_birth is null and
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month_of_birth is not null then use the first of the month in that year.
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If month_of_birth is null or if day_of_birth AND month_of_birth are both
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null and the person has records during their year of birth then use the
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date of the earliest record, otherwise use the 15th of June of that
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year. If time of birth is not given use midnight (00:00:0000).
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this field. For more information on how to populate this field, please
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refer to the <a href="https://ohdsi.github.io/Themis/person.html">THEMIS
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repository</a>.
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</td>
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<td style="text-align:left;">
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datetime
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@ -828,11 +830,10 @@ should capture the last known location of the person.
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Put the location_id from the <a
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href="https://ohdsi.github.io/CommonDataModel/cdm531.html#location">LOCATION</a>
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table here that represents the most granular location information for
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the person. This could represent anything from postal code or parts
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thereof, state, or county for example. Since many databases contain
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deidentified data, it is common that the precision of the location is
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reduced to prevent re-identification. This field should capture the last
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known location.
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the person. For additional information on how to populate this field,
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please refer to the <a
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href="https://ohdsi.github.io/Themis/populate_person_location_id.html">THEMIS
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repository</a>.
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</td>
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<td style="text-align:left;">
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integer
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@ -3311,7 +3312,10 @@ administered may have a separate meaning from quantity for prescriptions
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dispensed. If a patient has multiple records on the same day for the
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same drug or procedures the ETL should not de-dupe them unless there is
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probable reason to believe the item is a true data duplicate. Take note
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on how to handle refills for prescriptions written.</p>
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on how to handle refills for prescriptions written.<br><br>For detailed
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conventions on how to populate this table, please refer to the <a
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href="https://ohdsi.github.io/Themis/drug_exposure.html">THEMIS
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repository</a>.</p>
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<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
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<thead>
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<tr>
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@ -3545,7 +3549,10 @@ oral solution concept tells us this is oral solution. Calculate duration
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as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL)
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200*5/20 = 50 days. <a
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href="https://ohdsi.github.io/CommonDataModel/drug_dose.html">Examples
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by dose form</a>
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by dose form</a><br><br>For detailed conventions for how to populate
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this field, please see the <a
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href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS
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repository</a>.
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</td>
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<td style="text-align:left;">
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date
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@ -6509,7 +6516,9 @@ explicit record in EHR data.</p>
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<p><strong>User Guide</strong></p>
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<p>NA</p>
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<p><strong>ETL Conventions</strong></p>
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<p>NA</p>
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<p>For specific conventions on how to populate this table, please refer
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to the <a href="https://ohdsi.github.io/Themis/death.html">THEMIS
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repository</a>.</p>
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<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
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<thead>
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<tr>
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@ -6579,7 +6588,10 @@ The date the person was deceased.
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<td style="text-align:left;">
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If the precise date include day or month is not known or not allowed,
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December is used as the default month, and the last day of the month the
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default day.
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default day. For additional conventions related to this field, please
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refer to the <a
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href="https://ohdsi.github.io/Themis/tag_death_date.html">THEMIS
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repository</a>.
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</td>
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<td style="text-align:left;">
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date
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@ -8567,7 +8579,10 @@ hierarchical and business relationships between Care Sites. For example,
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wards can belong to clinics or departments, which can in turn belong to
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hospitals, which in turn can belong to hospital systems, which in turn
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can belong to HMOs.The relationships between Care Sites are defined in
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the FACT_RELATIONSHIP table.</p>
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the FACT_RELATIONSHIP table.<br><br>For additional detailed conventions
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on how to populate this table, please refer to <a
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href="https://ohdsi.github.io/Themis/care_site.html">THEMIS
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repository</a>.</p>
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<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
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<thead>
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<tr>
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@ -8670,7 +8685,10 @@ Care Site are Inpatient, then the place_of_service_concept_id should
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represent Inpatient. If information is present about a unique Care Site
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(e.g. Pharmacy) then a Care Site record should be created. <a
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href="https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=2&pageSize=15&query=">Accepted
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Concepts</a>.
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Concepts</a>. For information about how to populate this field please
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see the <a
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href="https://ohdsi.github.io/Themis/tag_place_of_service.html">THEMIS
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Conventions</a>.
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</td>
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<td style="text-align:left;">
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integer
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@ -632,7 +632,10 @@ Events should have a record nonetheless. If more than one data source
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contributes Events to the database, Persons must be reconciled, if
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possible, across the sources to create one single record per Person. The
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content of the BIRTH_DATETIME must be equivalent to the content of
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BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.</p>
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BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.<br><br>For detailed conventions
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for how to populate this table, please refer to the <a
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href="https://ohdsi.github.io/Themis/person.html">THEMIS
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repository</a>.</p>
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<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
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<thead>
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<tr>
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@ -712,7 +715,9 @@ gender identity it should be stored in the <a
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href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
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table. <a
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href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=">Accepted
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gender concepts</a>
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gender concepts</a>. Please refer to the <a
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href="https://ohdsi.github.io/Themis/tag_gender_concept_id.html">THEMIS
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repository</a> for detailed conventions on how to populate this field.
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</td>
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<td style="text-align:left;">
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integer
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@ -741,11 +746,12 @@ year_of_birth
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Compute age using year_of_birth.
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</td>
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<td style="text-align:left;">
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For data sources with date of birth, the year should be extracted. For
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data sources where the year of birth is not available, the approximate
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year of birth could be derived based on age group categorization, if
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available. If no year of birth is available all the person’s data should
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be dropped from the CDM instance.
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For data sources with date of birth, the year should be extracted. If no
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year of birth is available all the person’s data should be dropped from
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the CDM instance. For additional information on how to populate this
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field, please refer to the <a
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href="https://ohdsi.github.io/Themis/tag_year_of_birth.html">THEMIS
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repository</a>.
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</td>
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<td style="text-align:left;">
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integer
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@ -825,15 +831,11 @@ birth_datetime
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<td style="text-align:left;">
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</td>
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<td style="text-align:left;">
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This field is not required but highly encouraged for data sources that
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provide the precise datetime of birth. If birth_datetime is not provided
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in the source, use the following logic to infer the date: If
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day_of_birth is null and month_of_birth is not null then use the first
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of the month in that year. If month_of_birth is null or if day_of_birth
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AND month_of_birth are both null and the person has records during their
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year of birth then use the date of the earliest record, otherwise use
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the 15th of June of that year. If time of birth is not given use
|
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midnight (00:00:0000).
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This field is not required but highly encouraged. For data sources that
|
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provide the precise datetime of birth, that value should be stored in
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this field. For more information on how to populate this field, please
|
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refer to the <a href="https://ohdsi.github.io/Themis/person.html">THEMIS
|
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repository</a>.
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</td>
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<td style="text-align:left;">
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datetime
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@ -934,13 +936,12 @@ should capture the last known location of the person.
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</td>
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<td style="text-align:left;">
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Put the location_id from the <a
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href="https://ohdsi.github.io/CommonDataModel/cdm54.html#LOCATION">LOCATION</a>
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href="https://ohdsi.github.io/CommonDataModel/cdm531.html#location">LOCATION</a>
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table here that represents the most granular location information for
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the person. This could represent anything from postal code or parts
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thereof, state, or county for example. Since many databases contain
|
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deidentified data, it is common that the precision of the location is
|
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reduced to prevent re-identification. This field should capture the last
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known location.
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the person. For additional information on how to populate this field,
|
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please refer to the <a
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href="https://ohdsi.github.io/Themis/populate_person_location_id.html">THEMIS
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repository</a>.
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</td>
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<td style="text-align:left;">
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integer
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@ -1089,7 +1090,7 @@ gender_source_concept_id
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Due to the small number of options, this tends to be zero.
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</td>
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<td style="text-align:left;">
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If the source data codes assigned sex at birth in a non-standard
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If the source data codes asigned sex at birth in a non-standard
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vocabulary, store the concept_id here.
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</td>
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<td style="text-align:left;">
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@ -3447,7 +3448,10 @@ administered may have a separate meaning from quantity for prescriptions
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dispensed. If a patient has multiple records on the same day for the
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same drug or procedures the ETL should not de-dupe them unless there is
|
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probable reason to believe the item is a true data duplicate. Take note
|
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on how to handle refills for prescriptions written.</p>
|
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on how to handle refills for prescriptions written.<br><br>For detailed
|
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conventions on how to populate this table, please refer to the <a
|
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href="https://ohdsi.github.io/Themis/drug_exposure.html">THEMIS
|
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repository</a>.</p>
|
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<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
|
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<thead>
|
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<tr>
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|
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@ -3681,7 +3685,10 @@ oral solution concept tells us this is oral solution. Calculate duration
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as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL)
|
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200*5/20 = 50 days. <a
|
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href="https://ohdsi.github.io/CommonDataModel/drug_dose.html">Examples
|
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by dose form</a>
|
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by dose form</a><br><br>For detailed conventions for how to populate
|
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this field, please see the <a
|
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href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS
|
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repository</a>.
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</td>
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<td style="text-align:left;">
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date
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@ -7038,7 +7045,9 @@ explicit record in EHR data.</p>
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<p><strong>User Guide</strong></p>
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<p>NA</p>
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<p><strong>ETL Conventions</strong></p>
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<p>NA</p>
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<p>For specific conventions on how to populate this table, please refer
|
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to the <a href="https://ohdsi.github.io/Themis/death.html">THEMIS
|
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repository</a>.</p>
|
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<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
|
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<thead>
|
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<tr>
|
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|
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@ -7108,7 +7117,10 @@ The date the person was deceased.
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<td style="text-align:left;">
|
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If the precise date include day or month is not known or not allowed,
|
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December is used as the default month, and the last day of the month the
|
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default day.
|
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default day. For additional conventions related to this field, please
|
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refer to the <a
|
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href="https://ohdsi.github.io/Themis/tag_death_date.html">THEMIS
|
||||
repository</a>.
|
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</td>
|
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<td style="text-align:left;">
|
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date
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|
|
@ -9275,7 +9287,10 @@ hierarchical and business relationships between Care Sites. For example,
|
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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.</p>
|
||||
the FACT_RELATIONSHIP table.<br><br>For additional detailed conventions
|
||||
on how to populate this table, please refer to <a
|
||||
href="https://ohdsi.github.io/Themis/care_site.html">THEMIS
|
||||
repository</a>.</p>
|
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<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
|
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<thead>
|
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<tr>
|
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|
|
@ -9379,7 +9394,10 @@ Care Site are Inpatient, then the place_of_service_concept_id should
|
|||
represent Inpatient. If information is present about a unique Care Site
|
||||
(e.g. Pharmacy) then a Care Site record should be created. <a
|
||||
href="https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=2&pageSize=15&query=">Accepted
|
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Concepts</a>.
|
||||
Concepts</a>. For information about how to populate this field please
|
||||
see the <a
|
||||
href="https://ohdsi.github.io/Themis/tag_place_of_service.html">THEMIS
|
||||
Conventions</a>.
|
||||
</td>
|
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<td style="text-align:left;">
|
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integer
|
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|
|
|
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|
|
@ -1,6 +1,6 @@
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cdmTableName,cdmFieldName,isRequired,cdmDatatype,userGuidance,etlConventions,isPrimaryKey,isForeignKey,fkTableName,fkFieldName,fkDomain,fkClass,unique DQ identifiers
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person,person_id,Yes,integer,It is assumed that every person with a different unique identifier is in fact a different person and should be treated independently.,"Any person linkage that needs to occur to uniquely identify Persons ought to be done prior to writing this table. This identifier can be the original id from the source data provided if it is an integer, otherwise it can be an autogenerated number.",Yes,No,NA,NA,NA,NA,NA
|
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person,gender_concept_id,Yes,integer,This field is meant to capture the biological sex at birth of the Person. This field should not be used to study gender identity issues.,Use the gender or sex value present in the data under the assumption that it is the biological sex at birth. If the source data captures gender identity it should be stored in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table. [Accepted gender concepts](http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=). PLease refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_gender_concept_id.html) for detailed conventions on how to populate this field.,No,Yes,CONCEPT,CONCEPT_ID,Gender,NA,NA
|
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person,gender_concept_id,Yes,integer,This field is meant to capture the biological sex at birth of the Person. This field should not be used to study gender identity issues.,Use the gender or sex value present in the data under the assumption that it is the biological sex at birth. If the source data captures gender identity it should be stored in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table. [Accepted gender concepts](http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=). Please refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_gender_concept_id.html) for detailed conventions on how to populate this field.,No,Yes,CONCEPT,CONCEPT_ID,Gender,NA,NA
|
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person,year_of_birth,Yes,integer,Compute age using year_of_birth.,"For data sources with date of birth, the year should be extracted. If no year of birth is available all the person's data should be dropped from the CDM instance. For additional information on how to populate this field, please refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_year_of_birth.html).",No,No,NA,NA,NA,NA,NA
|
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person,month_of_birth,No,integer,NA,"For data sources that provide the precise date of birth, the month should be extracted and stored in this field.",No,No,NA,NA,NA,NA,NA
|
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person,day_of_birth,No,integer,NA,"For data sources that provide the precise date of birth, the day should be extracted and stored in this field.",No,No,NA,NA,NA,NA,NA
|
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|
|
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|
|
|
@ -1,6 +1,6 @@
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cdmTableName,cdmFieldName,isRequired,cdmDatatype,userGuidance,etlConventions,isPrimaryKey,isForeignKey,fkTableName,fkFieldName,fkDomain,fkClass,unique DQ identifiers
|
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person,person_id,Yes,integer,It is assumed that every person with a different unique identifier is in fact a different person and should be treated independently.,"Any person linkage that needs to occur to uniquely identify Persons ought to be done prior to writing this table. This identifier can be the original id from the source data provided if it is an integer, otherwise it can be an autogenerated number.",Yes,No,NA,NA,NA,NA,NA
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person,gender_concept_id,Yes,integer,This field is meant to capture the biological sex at birth of the Person. This field should not be used to study gender identity issues.,Use the gender or sex value present in the data under the assumption that it is the biological sex at birth. If the source data captures gender identity it should be stored in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table. [Accepted gender concepts](http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=). PLease refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_gender_concept_id.html) for detailed conventions on how to populate this field.,No,Yes,CONCEPT,CONCEPT_ID,Gender,NA,NA
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person,gender_concept_id,Yes,integer,This field is meant to capture the biological sex at birth of the Person. This field should not be used to study gender identity issues.,Use the gender or sex value present in the data under the assumption that it is the biological sex at birth. If the source data captures gender identity it should be stored in the [OBSERVATION](https://ohdsi.github.io/CommonDataModel/cdm531.html#observation) table. [Accepted gender concepts](http://athena.ohdsi.org/search-terms/terms?domain=Gender&standardConcept=Standard&page=1&pageSize=15&query=). Please refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_gender_concept_id.html) for detailed conventions on how to populate this field.,No,Yes,CONCEPT,CONCEPT_ID,Gender,NA,NA
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person,year_of_birth,Yes,integer,Compute age using year_of_birth.,"For data sources with date of birth, the year should be extracted. If no year of birth is available all the person's data should be dropped from the CDM instance. For additional information on how to populate this field, please refer to the [THEMIS repository](https://ohdsi.github.io/Themis/tag_year_of_birth.html).",No,No,NA,NA,NA,NA,NA
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person,month_of_birth,No,integer,NA,"For data sources that provide the precise date of birth, the month should be extracted and stored in this field.",No,No,NA,NA,NA,NA,NA
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person,day_of_birth,No,integer,NA,"For data sources that provide the precise date of birth, the day should be extracted and stored in this field.",No,No,NA,NA,NA,NA,NA
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Reference in New Issue