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Clair Blacketer 2024-04-12 13:03:53 -04:00
parent bf37173742
commit a7d620f199
4 changed files with 92 additions and 56 deletions
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68
docs/cdm53.html
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@ -524,7 +524,10 @@ Events should have a record nonetheless. If more than one data source
contributes Events to the database, Persons must be reconciled, if
possible, across the sources to create one single record per Person. The
content of the BIRTH_DATETIME must be equivalent to the content of
BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.</p>
BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.<br><br>For detailed conventions
for how to populate this table, please refer to the <a
href="https://ohdsi.github.io/Themis/person.html">THEMIS
repository</a>.</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
@ -604,7 +607,9 @@ gender identity it should be stored in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
table. <a
href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
gender concepts</a>
gender concepts</a>. Please refer to the <a
href="https://ohdsi.github.io/Themis/tag_gender_concept_id.html">THEMIS
repository</a> for detailed conventions on how to populate this field.
</td>
<td style="text-align:left;">
integer
@ -633,11 +638,12 @@ year_of_birth
Compute age using year_of_birth.
</td>
<td style="text-align:left;">
For data sources with date of birth, the year should be extracted. For
data sources where the year of birth is not available, the approximate
year of birth could be derived based on age group categorization, if
available. If no year of birth is available all the person’s data should
be dropped from the CDM instance.
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 <a
href="https://ohdsi.github.io/Themis/tag_year_of_birth.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
integer
@ -719,13 +725,9 @@ birth_datetime
<td style="text-align:left;">
This field is not required but highly encouraged. For data sources that
provide the precise datetime of birth, that value should be stored in
this field. If birth_datetime is not provided in the source, use the
following logic to infer the date: If day_of_birth is null and
month_of_birth is not null then use the first of the month in that year.
If month_of_birth is null or if day_of_birth AND month_of_birth are both
null and the person has records during their year of birth then use the
date of the earliest record, otherwise use the 15th of June of that
year. If time of birth is not given use midnight (00:00:0000).
this field. For more information on how to populate this field, please
refer to the <a href="https://ohdsi.github.io/Themis/person.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
datetime
@ -828,11 +830,10 @@ should capture the last known location of the person.
Put the location_id from the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#location">LOCATION</a>
table here that represents the most granular location information for
the person. This could represent anything from postal code or parts
thereof, state, or county for example. Since many databases contain
deidentified data, it is common that the precision of the location is
reduced to prevent re-identification. This field should capture the last
known location.
the person. For additional information on how to populate this field,
please refer to the <a
href="https://ohdsi.github.io/Themis/populate_person_location_id.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
integer
@ -3311,7 +3312,10 @@ administered may have a separate meaning from quantity for prescriptions
dispensed. If a patient has multiple records on the same day for the
same drug or procedures the ETL should not de-dupe them unless there is
probable reason to believe the item is a true data duplicate. Take note
on how to handle refills for prescriptions written.</p>
on how to handle refills for prescriptions written.<br><br>For detailed
conventions on how to populate this table, please refer to the <a
href="https://ohdsi.github.io/Themis/drug_exposure.html">THEMIS
repository</a>.</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
@ -3545,7 +3549,10 @@ oral solution concept tells us this is oral solution. Calculate duration
as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL)
200*5/20 = 50 days. <a
href="https://ohdsi.github.io/CommonDataModel/drug_dose.html">Examples
by dose form</a>
by dose form</a><br><br>For detailed conventions for how to populate
this field, please see the <a
href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
date
@ -6509,7 +6516,9 @@ explicit record in EHR data.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<p>For specific conventions on how to populate this table, please refer
to the <a href="https://ohdsi.github.io/Themis/death.html">THEMIS
repository</a>.</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
@ -6579,7 +6588,10 @@ The date the person was deceased.
<td style="text-align:left;">
If the precise date include day or month is not known or not allowed,
December is used as the default month, and the last day of the month the
default day.
default day. For additional conventions related to this field, please
refer to the <a
href="https://ohdsi.github.io/Themis/tag_death_date.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
date
@ -8567,7 +8579,10 @@ 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.</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>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
@ -8670,7 +8685,10 @@ 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&amp;standardConcept=Standard&amp;page=2&amp;pageSize=15&amp;query=">Accepted
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>
<td style="text-align:left;">
integer

76
docs/cdm54.html
View File

@ -632,7 +632,10 @@ Events should have a record nonetheless. If more than one data source
contributes Events to the database, Persons must be reconciled, if
possible, across the sources to create one single record per Person. The
content of the BIRTH_DATETIME must be equivalent to the content of
BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.</p>
BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.<br><br>For detailed conventions
for how to populate this table, please refer to the <a
href="https://ohdsi.github.io/Themis/person.html">THEMIS
repository</a>.</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
@ -712,7 +715,9 @@ gender identity it should be stored in the <a
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
table. <a
href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
gender concepts</a>
gender concepts</a>. Please refer to the <a
href="https://ohdsi.github.io/Themis/tag_gender_concept_id.html">THEMIS
repository</a> for detailed conventions on how to populate this field.
</td>
<td style="text-align:left;">
integer
@ -741,11 +746,12 @@ year_of_birth
Compute age using year_of_birth.
</td>
<td style="text-align:left;">
For data sources with date of birth, the year should be extracted. For
data sources where the year of birth is not available, the approximate
year of birth could be derived based on age group categorization, if
available. If no year of birth is available all the person’s data should
be dropped from the CDM instance.
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 <a
href="https://ohdsi.github.io/Themis/tag_year_of_birth.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
integer
@ -825,15 +831,11 @@ birth_datetime
<td style="text-align:left;">
</td>
<td style="text-align:left;">
This field is not required but highly encouraged for data sources that
provide the precise datetime of birth. If birth_datetime is not provided
in the source, use the following logic to infer the date: If
day_of_birth is null and month_of_birth is not null then use the first
of the month in that year. If month_of_birth is null or if day_of_birth
AND month_of_birth are both null and the person has records during their
year of birth then use the date of the earliest record, otherwise use
the 15th of June of that year. If time of birth is not given use
midnight (00:00:0000).
This field is not required but highly encouraged. For data sources that
provide the precise datetime of birth, that value should be stored in
this field. For more information on how to populate this field, please
refer to the <a href="https://ohdsi.github.io/Themis/person.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
datetime
@ -934,13 +936,12 @@ should capture the last known location of the person.
</td>
<td style="text-align:left;">
Put the location_id from the <a
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#LOCATION">LOCATION</a>
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#location">LOCATION</a>
table here that represents the most granular location information for
the person. This could represent anything from postal code or parts
thereof, state, or county for example. Since many databases contain
deidentified data, it is common that the precision of the location is
reduced to prevent re-identification. This field should capture the last
known location.
the person. For additional information on how to populate this field,
please refer to the <a
href="https://ohdsi.github.io/Themis/populate_person_location_id.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
integer
@ -1089,7 +1090,7 @@ gender_source_concept_id
Due to the small number of options, this tends to be zero.
</td>
<td style="text-align:left;">
If the source data codes assigned sex at birth in a non-standard
If the source data codes asigned sex at birth in a non-standard
vocabulary, store the concept_id here.
</td>
<td style="text-align:left;">
@ -3447,7 +3448,10 @@ administered may have a separate meaning from quantity for prescriptions
dispensed. If a patient has multiple records on the same day for the
same drug or procedures the ETL should not de-dupe them unless there is
probable reason to believe the item is a true data duplicate. Take note
on how to handle refills for prescriptions written.</p>
on how to handle refills for prescriptions written.<br><br>For detailed
conventions on how to populate this table, please refer to the <a
href="https://ohdsi.github.io/Themis/drug_exposure.html">THEMIS
repository</a>.</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
@ -3681,7 +3685,10 @@ oral solution concept tells us this is oral solution. Calculate duration
as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL)
200*5/20 = 50 days. <a
href="https://ohdsi.github.io/CommonDataModel/drug_dose.html">Examples
by dose form</a>
by dose form</a><br><br>For detailed conventions for how to populate
this field, please see the <a
href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
date
@ -7038,7 +7045,9 @@ explicit record in EHR data.</p>
<p><strong>User Guide</strong></p>
<p>NA</p>
<p><strong>ETL Conventions</strong></p>
<p>NA</p>
<p>For specific conventions on how to populate this table, please refer
to the <a href="https://ohdsi.github.io/Themis/death.html">THEMIS
repository</a>.</p>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
@ -7108,7 +7117,10 @@ The date the person was deceased.
<td style="text-align:left;">
If the precise date include day or month is not known or not allowed,
December is used as the default month, and the last day of the month the
default day.
default day. For additional conventions related to this field, please
refer to the <a
href="https://ohdsi.github.io/Themis/tag_death_date.html">THEMIS
repository</a>.
</td>
<td style="text-align:left;">
date
@ -9275,7 +9287,10 @@ 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.</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>
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
<thead>
<tr>
@ -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&amp;standardConcept=Standard&amp;page=2&amp;pageSize=15&amp;query=">Accepted
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>
<td style="text-align:left;">
integer

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

@ -1,6 +1,6 @@
cdmTableName,cdmFieldName,isRequired,cdmDatatype,userGuidance,etlConventions,isPrimaryKey,isForeignKey,fkTableName,fkFieldName,fkDomain,fkClass,unique DQ identifiers
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
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
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
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
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
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

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
2 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
3 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. 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
4 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
5 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
6 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

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

@ -1,6 +1,6 @@
cdmTableName,cdmFieldName,isRequired,cdmDatatype,userGuidance,etlConventions,isPrimaryKey,isForeignKey,fkTableName,fkFieldName,fkDomain,fkClass,unique DQ identifiers
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
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
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
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
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
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

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
2 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
3 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. 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
4 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
5 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
6 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