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Olympians week4 #685

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Apr 29, 2024
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Olympians week4 #685

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b7e1111
closes #665
clairblacketer Apr 24, 2024
13fc598
closes #682
clairblacketer Apr 24, 2024
4869f7c
closes OHDSI/Themis #121
clairblacketer Apr 24, 2024
8ee8a7b
closes #666
clairblacketer Apr 24, 2024
51f047b
closes #653
clairblacketer Apr 24, 2024
3806428
closes #683
clairblacketer Apr 24, 2024
011f8e6
closes #679
clairblacketer Apr 24, 2024
c721007
closes #675
clairblacketer Apr 24, 2024
6eaeab4
closes #671
clairblacketer Apr 29, 2024
6d80bb3
closes #672
clairblacketer Apr 29, 2024
f2f202d
closes #684
clairblacketer Apr 29, 2024
c92b9d7
site render
clairblacketer Apr 29, 2024
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152 changes: 98 additions & 54 deletions docs/cdm53.html
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Original file line number Diff line number Diff line change
Expand Up @@ -985,7 +985,7 @@
Due to the small number of options, this tends to be zero.
</td>
<td style="text-align:left;">
If the source data codes asigned sex at birth in a non-standard

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asigned ==> assigned
vocabulary, store the concept_id here.
</td>
<td style="text-align:left;">
Expand Down Expand Up @@ -1335,7 +1335,10 @@
Choose the observation_period_type_concept_id that best represents how
the period was determined. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -1722,7 +1725,10 @@
Populate this field based on the provenance of the visit record, as in
whether it came from an EHR record or billing claim. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
Integer
Expand Down Expand Up @@ -1880,10 +1886,11 @@
admitted to the hospital from a long-term care facility, for example.
</td>
<td style="text-align:left;">
If available, map the admitted_from_source_value to a standard concept
in the visit domain. <a
If available, map the admitting_source_value to a standard concept in
the visit domain. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Visit&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. If a person was admitted from home or was self-referred,
set this to 0.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -2332,7 +2339,10 @@
Populate this field based on the provenance of the visit detail record,
as in whether it came from an EHR record or billing claim. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -2517,10 +2527,11 @@
admitted to the hospital from a long-term care facility, for example.
</td>
<td style="text-align:left;">
If available, map the admitted_from_source_value to a standard concept
in the visit domain. <a
If available, map the admitting_source_value to a standard concept in
the visit domain. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Visit&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. If a person was admitted from home or was self-referred,
set this to 0.
</td>
<td style="text-align:left;">
Integer
Expand Down Expand Up @@ -2997,7 +3008,10 @@
Choose the CONDITION_TYPE_CONCEPT_ID that best represents the provenance
of the record. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -3644,7 +3658,10 @@
the record, for example whether it came from a record of a prescription
written or physician administered drug. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -4341,7 +4358,10 @@
claim. If a procedure is recorded as an EHR encounter, the
PROCEDURE_TYPE_CONCEPT would be ‘EHR encounter record’. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -4885,7 +4905,10 @@
the record, for example whether it came from a record of a prescription
written or physician administered drug. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -5387,7 +5410,10 @@
provenance of the record, for example whether it came from an EHR record
or billing claim. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -6068,7 +6094,10 @@
provenance of the record, for example whether it came from an EHR record
or billing claim. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -6603,7 +6632,8 @@
<td style="text-align:left;">
</td>
<td style="text-align:left;">
If not available set time to midnight (00:00:00)
If you have date and time of death, populate death_datetime, otherwise
leave NULL
</td>
<td style="text-align:left;">
datetime
Expand Down Expand Up @@ -6633,9 +6663,12 @@
the same as the Visit Type, etc.
</td>
<td style="text-align:left;">
Use the type concept that be reflects the source of the death record. <a
Use the type concept that reflects the source of the death record. <a
href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -6928,7 +6961,10 @@
<td style="text-align:left;">
Put the source system of the note, as in EHR record. <a
href="https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&amp;domain=Type+Concept&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -7772,7 +7808,10 @@
<td style="text-align:left;">
Put the source of the specimen record, as in an EHR system. <a
href="https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&amp;domain=Type+Concept&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>. A more detailed explanation of each Type Concept can be
found on the <a
href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary
wiki</a>.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -8861,11 +8900,12 @@
provider_name
</td>
<td style="text-align:left;">
This field contains information that describes a healthcare provider.
</td>
<td style="text-align:left;">
This field is not necessary as it is not necessary to have the actual
identity of the Provider. Rather, the idea is to uniquely and
anonymously identify providers of care across the database.
This field is not required for identifying the Provider’s actual
identity. Instead, its purpose is to uniquely and/or anonymously
identify providers of care across the database.
</td>
<td style="text-align:left;">
varchar(255)
Expand Down Expand Up @@ -9099,15 +9139,18 @@
specialty_source_value
</td>
<td style="text-align:left;">
This is the kind of provider or specialty as it appears in the source
data. This includes physician specialties such as internal medicine,
emergency medicine, etc. and allied health professionals such as nurses,
midwives, and pharmacists.
This refers to the specific type of healthcare provider or field of
expertise listed in the source data, encompassing physician specialties
like internal medicine, emergency medicine, etc., as well as allied
health professionals such as nurses, midwives, and pharmacists. It
covers medical specialties like surgery, internal medicine, and
radiology, while other services like prosthetics, acupuncture, and
physical therapy fall under the domain of “Service.”
</td>
<td style="text-align:left;">
Put the kind of provider as it appears in the source data. This field is
up to the discretion of the ETL-er as to whether this should be the
coded value from the source or the text description of the lookup value.
The type of provider and their specialty should be entered as they
appear in the source data. The decision to use either the coded value or
the text description is left to the discretion of the ETL-er.
</td>
<td style="text-align:left;">
varchar(50)
Expand Down Expand Up @@ -9392,13 +9435,13 @@
administers care to the Person.
</td>
<td style="text-align:left;">
Map the Payer directly to a standard CONCEPT_ID. If one does not exists
please contact the vocabulary team. There is no global controlled
vocabulary available for this information. The point is to stratify on
this information and identify if Persons have the same payer, though the
name of the Payer is not necessary. <a
href="http://athena.ohdsi.org/search-terms/terms?domain=Payer&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Map the payer directly to a standard CONCEPT_ID with the domain_id of
‘Payer’ (<a
href="https://athena.ohdsi.org/search-terms/terms?domain=Payer&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>). This vocabulary is not exhaustive so if there is a value
missing, please see the <a
href="https://ohdsi.github.io/CommonDataModel/customConcepts.html">custom
concepts</a> page.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -9481,13 +9524,13 @@
enrolled in.
</td>
<td style="text-align:left;">
Map the Plan directly to a standard CONCEPT_ID. If one does not exists
please contact the vocabulary team. There is no global controlled
vocabulary available for this information. The point is to stratify on
this information and identify if Persons have the same health benefit
Plan though the name of the Plan is not necessary. <a
Map the Plan directly to a standard CONCEPT_ID in the ‘Plan’ vocabulary
(<a
href="http://athena.ohdsi.org/search-terms/terms?domain=Plan&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>). This vocabulary is not exhaustive so if there is a value
missing, please see the <a
href="https://ohdsi.github.io/CommonDataModel/customConcepts.html">custom
concepts</a> page.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -9572,13 +9615,13 @@
health plan.
</td>
<td style="text-align:left;">
Map the sponsor directly to a standard CONCEPT_ID. If one does not
exists please contact the vocabulary team. There is no global controlled
vocabulary available for this information. The point is to stratify on
this information and identify if Persons have the same sponsor though
the name of the sponsor is not necessary. <a
href="http://athena.ohdsi.org/search-terms/terms?domain=Sponsor&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Map the sponsor directly to a standard CONCEPT_ID with the domain_id of
‘Sponsor’ (<a
href="https://athena.ohdsi.org/search-terms/terms?domain=Sponsor&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>). This vocabulary is not exhaustive so if there is a value
missing, please see the <a
href="https://ohdsi.github.io/CommonDataModel/customConcepts.html">custom
concepts</a> page.
</td>
<td style="text-align:left;">
integer
Expand Down Expand Up @@ -9689,11 +9732,12 @@
This field represents the reason the Person left the Plan, if known.
</td>
<td style="text-align:left;">
Map the stop reason directly to a standard CONCEPT_ID. If one does not
exists please contact the vocabulary team. There is no global controlled
vocabulary available for this information. <a
Map the stop reason directly to a standard CONCEPT_ID with a domain of
‘Plan Stop Reason’ (<a
href="http://athena.ohdsi.org/search-terms/terms?domain=Plan+Stop+Reason&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted
Concepts</a>.
Concepts</a>). If one does not exist visit the <a
href="https://ohdsi.github.io/CommonDataModel/customConcepts.html">Custom
Concepts</a> pate for more information.
</td>
<td style="text-align:left;">
integer
Expand Down
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