Skip to content

Commit a7d620f

Browse files
clairblacketerclairblacketer
committed
Html rendering
1 parent bf37173 commit a7d620f

File tree

4 files changed

+92
-56
lines changed

4 files changed

+92
-56
lines changed

‎docs/cdm53.html

+43-25
Original file line numberDiff line numberDiff line change
@@ -524,7 +524,10 @@ <h3 class="tabset tabset-pills">person</h3>
524524
contributes Events to the database, Persons must be reconciled, if
525525
possible, across the sources to create one single record per Person. The
526526
content of the BIRTH_DATETIME must be equivalent to the content of
527-
BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.</p>
527+
BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.<br><br>For detailed conventions
528+
for how to populate this table, please refer to the <a
529+
href="https://ohdsi.github.io/Themis/person.html">THEMIS
530+
repository</a>.</p>
528531
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
529532
<thead>
530533
<tr>
@@ -604,7 +607,9 @@ <h3 class="tabset tabset-pills">person</h3>
604607
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
605608
table. <a
606609
href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
607-
gender concepts</a>
610+
gender concepts</a>. Please refer to the <a
611+
href="https://ohdsi.github.io/Themis/tag_gender_concept_id.html">THEMIS
612+
repository</a> for detailed conventions on how to populate this field.
608613
</td>
609614
<td style="text-align:left;">
610615
integer
@@ -633,11 +638,12 @@ <h3 class="tabset tabset-pills">person</h3>
633638
Compute age using year_of_birth.
634639
</td>
635640
<td style="text-align:left;">
636-
For data sources with date of birth, the year should be extracted. For
637-
data sources where the year of birth is not available, the approximate
638-
year of birth could be derived based on age group categorization, if
639-
available. If no year of birth is available all the person’s data should
640-
be dropped from the CDM instance.
641+
For data sources with date of birth, the year should be extracted. If no
642+
year of birth is available all the person’s data should be dropped from
643+
the CDM instance. For additional information on how to populate this
644+
field, please refer to the <a
645+
href="https://ohdsi.github.io/Themis/tag_year_of_birth.html">THEMIS
646+
repository</a>.
641647
</td>
642648
<td style="text-align:left;">
643649
integer
@@ -719,13 +725,9 @@ <h3 class="tabset tabset-pills">person</h3>
719725
<td style="text-align:left;">
720726
This field is not required but highly encouraged. For data sources that
721727
provide the precise datetime of birth, that value should be stored in
722-
this field. If birth_datetime is not provided in the source, use the
723-
following logic to infer the date: If day_of_birth is null and
724-
month_of_birth is not null then use the first of the month in that year.
725-
If month_of_birth is null or if day_of_birth AND month_of_birth are both
726-
null and the person has records during their year of birth then use the
727-
date of the earliest record, otherwise use the 15th of June of that
728-
year. If time of birth is not given use midnight (00:00:0000).
728+
this field. For more information on how to populate this field, please
729+
refer to the <a href="https://ohdsi.github.io/Themis/person.html">THEMIS
730+
repository</a>.
729731
</td>
730732
<td style="text-align:left;">
731733
datetime
@@ -828,11 +830,10 @@ <h3 class="tabset tabset-pills">person</h3>
828830
Put the location_id from the <a
829831
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#location">LOCATION</a>
830832
table here that represents the most granular location information for
831-
the person. This could represent anything from postal code or parts
832-
thereof, state, or county for example. Since many databases contain
833-
deidentified data, it is common that the precision of the location is
834-
reduced to prevent re-identification. This field should capture the last
835-
known location.
833+
the person. For additional information on how to populate this field,
834+
please refer to the <a
835+
href="https://ohdsi.github.io/Themis/populate_person_location_id.html">THEMIS
836+
repository</a>.
836837
</td>
837838
<td style="text-align:left;">
838839
integer
@@ -3311,7 +3312,10 @@ <h3 class="tabset tabset-pills">drug_exposure</h3>
33113312
dispensed. If a patient has multiple records on the same day for the
33123313
same drug or procedures the ETL should not de-dupe them unless there is
33133314
probable reason to believe the item is a true data duplicate. Take note
3314-
on how to handle refills for prescriptions written.</p>
3315+
on how to handle refills for prescriptions written.<br><br>For detailed
3316+
conventions on how to populate this table, please refer to the <a
3317+
href="https://ohdsi.github.io/Themis/drug_exposure.html">THEMIS
3318+
repository</a>.</p>
33153319
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
33163320
<thead>
33173321
<tr>
@@ -3545,7 +3549,10 @@ <h3 class="tabset tabset-pills">drug_exposure</h3>
35453549
as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL)
35463550
200*5/20 = 50 days. <a
35473551
href="https://ohdsi.github.io/CommonDataModel/drug_dose.html">Examples
3548-
by dose form</a>
3552+
by dose form</a><br><br>For detailed conventions for how to populate
3553+
this field, please see the <a
3554+
href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS
3555+
repository</a>.
35493556
</td>
35503557
<td style="text-align:left;">
35513558
date
@@ -6509,7 +6516,9 @@ <h3 class="tabset tabset-pills">death</h3>
65096516
<p><strong>User Guide</strong></p>
65106517
<p>NA</p>
65116518
<p><strong>ETL Conventions</strong></p>
6512-
<p>NA</p>
6519+
<p>For specific conventions on how to populate this table, please refer
6520+
to the <a href="https://ohdsi.github.io/Themis/death.html">THEMIS
6521+
repository</a>.</p>
65136522
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
65146523
<thead>
65156524
<tr>
@@ -6579,7 +6588,10 @@ <h3 class="tabset tabset-pills">death</h3>
65796588
<td style="text-align:left;">
65806589
If the precise date include day or month is not known or not allowed,
65816590
December is used as the default month, and the last day of the month the
6582-
default day.
6591+
default day. For additional conventions related to this field, please
6592+
refer to the <a
6593+
href="https://ohdsi.github.io/Themis/tag_death_date.html">THEMIS
6594+
repository</a>.
65836595
</td>
65846596
<td style="text-align:left;">
65856597
date
@@ -8567,7 +8579,10 @@ <h3 class="tabset tabset-pills">care_site</h3>
85678579
wards can belong to clinics or departments, which can in turn belong to
85688580
hospitals, which in turn can belong to hospital systems, which in turn
85698581
can belong to HMOs.The relationships between Care Sites are defined in
8570-
the FACT_RELATIONSHIP table.</p>
8582+
the FACT_RELATIONSHIP table.<br><br>For additional detailed conventions
8583+
on how to populate this table, please refer to <a
8584+
href="https://ohdsi.github.io/Themis/care_site.html">THEMIS
8585+
repository</a>.</p>
85718586
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
85728587
<thead>
85738588
<tr>
@@ -8670,7 +8685,10 @@ <h3 class="tabset tabset-pills">care_site</h3>
86708685
represent Inpatient. If information is present about a unique Care Site
86718686
(e.g. Pharmacy) then a Care Site record should be created. <a
86728687
href="https://athena.ohdsi.org/search-terms/terms?domain=Visit&amp;standardConcept=Standard&amp;page=2&amp;pageSize=15&amp;query=">Accepted
8673-
Concepts</a>.
8688+
Concepts</a>. For information about how to populate this field please
8689+
see the <a
8690+
href="https://ohdsi.github.io/Themis/tag_place_of_service.html">THEMIS
8691+
Conventions</a>.
86748692
</td>
86758693
<td style="text-align:left;">
86768694
integer

‎docs/cdm54.html

+47-29
Original file line numberDiff line numberDiff line change
@@ -632,7 +632,10 @@ <h3 class="tabset tabset-pills">person</h3>
632632
contributes Events to the database, Persons must be reconciled, if
633633
possible, across the sources to create one single record per Person. The
634634
content of the BIRTH_DATETIME must be equivalent to the content of
635-
BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.</p>
635+
BIRTH_DAY, BIRTH_MONTH and BIRTH_YEAR.<br><br>For detailed conventions
636+
for how to populate this table, please refer to the <a
637+
href="https://ohdsi.github.io/Themis/person.html">THEMIS
638+
repository</a>.</p>
636639
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
637640
<thead>
638641
<tr>
@@ -712,7 +715,9 @@ <h3 class="tabset tabset-pills">person</h3>
712715
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#observation">OBSERVATION</a>
713716
table. <a
714717
href="http://athena.ohdsi.org/search-terms/terms?domain=Gender&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
715-
gender concepts</a>
718+
gender concepts</a>. Please refer to the <a
719+
href="https://ohdsi.github.io/Themis/tag_gender_concept_id.html">THEMIS
720+
repository</a> for detailed conventions on how to populate this field.
716721
</td>
717722
<td style="text-align:left;">
718723
integer
@@ -741,11 +746,12 @@ <h3 class="tabset tabset-pills">person</h3>
741746
Compute age using year_of_birth.
742747
</td>
743748
<td style="text-align:left;">
744-
For data sources with date of birth, the year should be extracted. For
745-
data sources where the year of birth is not available, the approximate
746-
year of birth could be derived based on age group categorization, if
747-
available. If no year of birth is available all the person’s data should
748-
be dropped from the CDM instance.
749+
For data sources with date of birth, the year should be extracted. If no
750+
year of birth is available all the person’s data should be dropped from
751+
the CDM instance. For additional information on how to populate this
752+
field, please refer to the <a
753+
href="https://ohdsi.github.io/Themis/tag_year_of_birth.html">THEMIS
754+
repository</a>.
749755
</td>
750756
<td style="text-align:left;">
751757
integer
@@ -825,15 +831,11 @@ <h3 class="tabset tabset-pills">person</h3>
825831
<td style="text-align:left;">
826832
</td>
827833
<td style="text-align:left;">
828-
This field is not required but highly encouraged for data sources that
829-
provide the precise datetime of birth. If birth_datetime is not provided
830-
in the source, use the following logic to infer the date: If
831-
day_of_birth is null and month_of_birth is not null then use the first
832-
of the month in that year. If month_of_birth is null or if day_of_birth
833-
AND month_of_birth are both null and the person has records during their
834-
year of birth then use the date of the earliest record, otherwise use
835-
the 15th of June of that year. If time of birth is not given use
836-
midnight (00:00:0000).
834+
This field is not required but highly encouraged. For data sources that
835+
provide the precise datetime of birth, that value should be stored in
836+
this field. For more information on how to populate this field, please
837+
refer to the <a href="https://ohdsi.github.io/Themis/person.html">THEMIS
838+
repository</a>.
837839
</td>
838840
<td style="text-align:left;">
839841
datetime
@@ -934,13 +936,12 @@ <h3 class="tabset tabset-pills">person</h3>
934936
</td>
935937
<td style="text-align:left;">
936938
Put the location_id from the <a
937-
href="https://ohdsi.github.io/CommonDataModel/cdm54.html#LOCATION">LOCATION</a>
939+
href="https://ohdsi.github.io/CommonDataModel/cdm531.html#location">LOCATION</a>
938940
table here that represents the most granular location information for
939-
the person. This could represent anything from postal code or parts
940-
thereof, state, or county for example. Since many databases contain
941-
deidentified data, it is common that the precision of the location is
942-
reduced to prevent re-identification. This field should capture the last
943-
known location.
941+
the person. For additional information on how to populate this field,
942+
please refer to the <a
943+
href="https://ohdsi.github.io/Themis/populate_person_location_id.html">THEMIS
944+
repository</a>.
944945
</td>
945946
<td style="text-align:left;">
946947
integer
@@ -1089,7 +1090,7 @@ <h3 class="tabset tabset-pills">person</h3>
10891090
Due to the small number of options, this tends to be zero.
10901091
</td>
10911092
<td style="text-align:left;">
1092-
If the source data codes assigned sex at birth in a non-standard
1093+
If the source data codes asigned sex at birth in a non-standard
10931094
vocabulary, store the concept_id here.
10941095
</td>
10951096
<td style="text-align:left;">
@@ -3447,7 +3448,10 @@ <h3 class="tabset tabset-pills">drug_exposure</h3>
34473448
dispensed. If a patient has multiple records on the same day for the
34483449
same drug or procedures the ETL should not de-dupe them unless there is
34493450
probable reason to believe the item is a true data duplicate. Take note
3450-
on how to handle refills for prescriptions written.</p>
3451+
on how to handle refills for prescriptions written.<br><br>For detailed
3452+
conventions on how to populate this table, please refer to the <a
3453+
href="https://ohdsi.github.io/Themis/drug_exposure.html">THEMIS
3454+
repository</a>.</p>
34513455
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
34523456
<thead>
34533457
<tr>
@@ -3681,7 +3685,10 @@ <h3 class="tabset tabset-pills">drug_exposure</h3>
36813685
as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL)
36823686
200*5/20 = 50 days. <a
36833687
href="https://ohdsi.github.io/CommonDataModel/drug_dose.html">Examples
3684-
by dose form</a>
3688+
by dose form</a><br><br>For detailed conventions for how to populate
3689+
this field, please see the <a
3690+
href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS
3691+
repository</a>.
36853692
</td>
36863693
<td style="text-align:left;">
36873694
date
@@ -7038,7 +7045,9 @@ <h3 class="tabset tabset-pills">death</h3>
70387045
<p><strong>User Guide</strong></p>
70397046
<p>NA</p>
70407047
<p><strong>ETL Conventions</strong></p>
7041-
<p>NA</p>
7048+
<p>For specific conventions on how to populate this table, please refer
7049+
to the <a href="https://ohdsi.github.io/Themis/death.html">THEMIS
7050+
repository</a>.</p>
70427051
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
70437052
<thead>
70447053
<tr>
@@ -7108,7 +7117,10 @@ <h3 class="tabset tabset-pills">death</h3>
71087117
<td style="text-align:left;">
71097118
If the precise date include day or month is not known or not allowed,
71107119
December is used as the default month, and the last day of the month the
7111-
default day.
7120+
default day. For additional conventions related to this field, please
7121+
refer to the <a
7122+
href="https://ohdsi.github.io/Themis/tag_death_date.html">THEMIS
7123+
repository</a>.
71127124
</td>
71137125
<td style="text-align:left;">
71147126
date
@@ -9275,7 +9287,10 @@ <h3 class="tabset tabset-pills">care_site</h3>
92759287
wards can belong to clinics or departments, which can in turn belong to
92769288
hospitals, which in turn can belong to hospital systems, which in turn
92779289
can belong to HMOs.The relationships between Care Sites are defined in
9278-
the FACT_RELATIONSHIP table.</p>
9290+
the FACT_RELATIONSHIP table.<br><br>For additional detailed conventions
9291+
on how to populate this table, please refer to <a
9292+
href="https://ohdsi.github.io/Themis/care_site.html">THEMIS
9293+
repository</a>.</p>
92799294
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
92809295
<thead>
92819296
<tr>
@@ -9379,7 +9394,10 @@ <h3 class="tabset tabset-pills">care_site</h3>
93799394
represent Inpatient. If information is present about a unique Care Site
93809395
(e.g. Pharmacy) then a Care Site record should be created. <a
93819396
href="https://athena.ohdsi.org/search-terms/terms?domain=Visit&amp;standardConcept=Standard&amp;page=2&amp;pageSize=15&amp;query=">Accepted
9382-
Concepts</a>.
9397+
Concepts</a>. For information about how to populate this field please
9398+
see the <a
9399+
href="https://ohdsi.github.io/Themis/tag_place_of_service.html">THEMIS
9400+
Conventions</a>.
93839401
</td>
93849402
<td style="text-align:left;">
93859403
integer

‎inst/csv/OMOP_CDMv5.3_Field_Level.csv

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
cdmTableName,cdmFieldName,isRequired,cdmDatatype,userGuidance,etlConventions,isPrimaryKey,isForeignKey,fkTableName,fkFieldName,fkDomain,fkClass,unique DQ identifiers
22
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.,No,Yes,CONCEPT,CONCEPT_ID,Gender,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.,No,Yes,CONCEPT,CONCEPT_ID,Gender,NA,NA
44
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
55
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
66
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

0 commit comments

Comments
 (0)