Merge pull request #685 from OHDSI/olympians_week4

Olympians week4

docs/cdm53.html

@@ -1335,7 +1335,10 @@ <h3 class="tabset tabset-pills">observation_period</h3>
 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
@@ -1722,7 +1725,10 @@ <h3 class="tabset tabset-pills">visit_occurrence</h3>
 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
@@ -1880,10 +1886,11 @@ <h3 class="tabset tabset-pills">visit_occurrence</h3>
 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
@@ -2332,7 +2339,10 @@ <h3 class="tabset tabset-pills">visit_detail</h3>
 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
@@ -2517,10 +2527,11 @@ <h3 class="tabset tabset-pills">visit_detail</h3>
 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
@@ -2997,7 +3008,10 @@ <h3 class="tabset tabset-pills">condition_occurrence</h3>
 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
@@ -3644,7 +3658,10 @@ <h3 class="tabset tabset-pills">drug_exposure</h3>
 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
@@ -4341,7 +4358,10 @@ <h3 class="tabset tabset-pills">procedure_occurrence</h3>
 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
@@ -4885,7 +4905,10 @@ <h3 class="tabset tabset-pills">device_exposure</h3>
 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
@@ -5387,7 +5410,10 @@ <h3 class="tabset tabset-pills">measurement</h3>
 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
@@ -6068,7 +6094,10 @@ <h3 class="tabset tabset-pills">observation</h3>
 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
@@ -6603,7 +6632,8 @@ <h3 class="tabset tabset-pills">death</h3>
 <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
@@ -6633,9 +6663,12 @@ <h3 class="tabset tabset-pills">death</h3>
 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
@@ -6928,7 +6961,10 @@ <h3 class="tabset tabset-pills">note</h3>
 <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
@@ -7772,7 +7808,10 @@ <h3 class="tabset tabset-pills">specimen</h3>
 <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
@@ -8861,11 +8900,12 @@ <h3 class="tabset tabset-pills">provider</h3>
 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)
@@ -9099,15 +9139,18 @@ <h3 class="tabset tabset-pills">provider</h3>
 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)
@@ -9392,13 +9435,13 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 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
@@ -9481,13 +9524,13 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 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
@@ -9572,13 +9615,13 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 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
@@ -9689,11 +9732,12 @@ <h3 class="tabset tabset-pills">payer_plan_period</h3>
 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