Html rendering

2024-04-12 13:03:53 -04:00 · 2024-04-12 13:03:53 -04:00 · a7d620f199
parent bf37173742
commit a7d620f199
4 changed files with 92 additions and 56 deletions
--- a/docs/cdm53.html
+++ b/docs/cdm53.html
@ -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
+For data sources with date of birth, the year should be extracted. If no
-data sources where the year of birth is not available, the approximate
+year of birth is available all the person’s data should be dropped from
-year of birth could be derived based on age group categorization, if
+the CDM instance. For additional information on how to populate this
-available. If no year of birth is available all the person’s data should
+field, please refer to the <a
-be dropped from the CDM instance.
+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
+this field. For more information on how to populate this field, please
-following logic to infer the date: If day_of_birth is null and
+refer to the <a href="https://ohdsi.github.io/Themis/person.html">THEMIS
-month_of_birth is not null then use the first of the month in that year.
+repository</a>.
 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).
 </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
+the person. For additional information on how to populate this field,
-thereof, state, or county for example. Since many databases contain
+please refer to the <a
-deidentified data, it is common that the precision of the location is
+href="https://ohdsi.github.io/Themis/populate_person_location_id.html">THEMIS
-reduced to prevent re-identification. This field should capture the last
+repository</a>.
 known location.
 </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
--- a/docs/cdm54.html
+++ b/docs/cdm54.html
@ -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
+For data sources with date of birth, the year should be extracted. If no
-data sources where the year of birth is not available, the approximate
+year of birth is available all the person’s data should be dropped from
-year of birth could be derived based on age group categorization, if
+the CDM instance. For additional information on how to populate this
-available. If no year of birth is available all the person’s data should
+field, please refer to the <a
-be dropped from the CDM instance.
+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
+This field is not required but highly encouraged. For data sources that
-provide the precise datetime of birth. If birth_datetime is not provided
+provide the precise datetime of birth, that value should be stored in
-in the source, use the following logic to infer the date: If
+this field. For more information on how to populate this field, please
-day_of_birth is null and month_of_birth is not null then use the first
+refer to the <a href="https://ohdsi.github.io/Themis/person.html">THEMIS
-of the month in that year. If month_of_birth is null or if day_of_birth
+repository</a>.
 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).
 </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
+the person. For additional information on how to populate this field,
-thereof, state, or county for example. Since many databases contain
+please refer to the <a
-deidentified data, it is common that the precision of the location is
+href="https://ohdsi.github.io/Themis/populate_person_location_id.html">THEMIS
-reduced to prevent re-identification. This field should capture the last
+repository</a>.
 known location.
 </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
--- a/inst/csv/OMOP_CDMv5.3_Field_Level.csv
+++ b/inst/csv/OMOP_CDMv5.3_Field_Level.csv
@ -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
--- a/inst/csv/OMOP_CDMv5.4_Field_Level.csv
+++ b/inst/csv/OMOP_CDMv5.4_Field_Level.csv
@ -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