Merge pull request #652 from OHDSI/olympians_week2

Olympians week2

docs/cdm53.html

@@ -5454,23 +5454,9 @@ <h3 class="tabset tabset-pills">measurement</h3>
 diastolic.
 </td>
 <td style="text-align:left;">
-If there is a negative value coming from the source, set the
-VALUE_AS_NUMBER to NULL, with the exception of the following
-Measurements (listed as LOINC codes):<br>- <a
-href="https://athena.ohdsi.org/search-terms/terms/3003396">1925-7</a>
-Base excess in Arterial blood by calculation - <a
-href="https://athena.ohdsi.org/search-terms/terms/3002032">1927-3</a>
-Base excess in Venous blood by calculation - <a
-href="https://athena.ohdsi.org/search-terms/terms/3006277">8632-2</a>
-QRS-Axis - <a
-href="https://athena.ohdsi.org/search-terms/terms/3012501">11555-0</a>
-Base excess in Blood by calculation - <a
-href="https://athena.ohdsi.org/search-terms/terms/3003129">1926-5</a>
-Base excess in Capillary blood by calculation - <a
-href="https://athena.ohdsi.org/search-terms/terms/3004959">28638-5</a>
-Base excess in Arterial cord blood by calculation <a
-href="https://athena.ohdsi.org/search-terms/terms/3007435">28639-3</a>
-Base excess in Venous cord blood by calculation
+<a
+href="https://ohdsi.github.io/Themis/negative_value_as_number.html">Convention
+for negative values</a>
 </td>
 <td style="text-align:left;">
 float

docs/cdm54.html

@@ -5788,23 +5788,9 @@ <h3 class="tabset tabset-pills">measurement</h3>
 diastolic.
 </td>
 <td style="text-align:left;">
-If there is a negative value coming from the source, set the
-VALUE_AS_NUMBER to NULL, with the exception of the following
-Measurements (listed as LOINC codes):<br>- <a
-href="https://athena.ohdsi.org/search-terms/terms/3003396">1925-7</a>
-Base excess in Arterial blood by calculation - <a
-href="https://athena.ohdsi.org/search-terms/terms/3002032">1927-3</a>
-Base excess in Venous blood by calculation - <a
-href="https://athena.ohdsi.org/search-terms/terms/3006277">8632-2</a>
-QRS-Axis - <a
-href="https://athena.ohdsi.org/search-terms/terms/3012501">11555-0</a>
-Base excess in Blood by calculation - <a
-href="https://athena.ohdsi.org/search-terms/terms/3003129">1926-5</a>
-Base excess in Capillary blood by calculation - <a
-href="https://athena.ohdsi.org/search-terms/terms/3004959">28638-5</a>
-Base excess in Arterial cord blood by calculation <a
-href="https://athena.ohdsi.org/search-terms/terms/3007435">28639-3</a>
-Base excess in Venous cord blood by calculation
+<a
+href="https://ohdsi.github.io/Themis/negative_value_as_number.html">Convention
+for negative values</a>
 </td>
 <td style="text-align:left;">
 float

inst/csv/OMOP_CDMv5.3_Field_Level.csv

@@ -148,7 +148,7 @@ measurement,measurement_datetime,No,datetime,NA,"This is not required, though it
 measurement,measurement_time,No,varchar(10),NA,This is present for backwards compatibility and will be deprecated in an upcoming version.,No,No,NA,NA,NA,NA,NA
 measurement,measurement_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Measurement record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.","Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA
 measurement,operator_concept_id,No,integer,"The meaning of Concept [4172703](https://athena.ohdsi.org/search-terms/terms/4172703) for '=' is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, it's important when devising analyses to not to forget testing for the content of this field for values different from =.","Operators are <, <=, =, >=, > and these concepts belong to the 'Meas Value Operator' domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&standardConcept=Standard&page=1&pageSize=15&query=). Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numeric value at all.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
-measurement,value_as_number,No,float,"This is the numerical value of the Result of the Measurement, if available. Note that measurements such as blood pressures will be split into their component parts i.e. one record for systolic, one record for diastolic.","If there is a negative value coming from the source, set the VALUE_AS_NUMBER to NULL, with the exception of the following Measurements (listed as LOINC codes):<br>-  [1925-7](https://athena.ohdsi.org/search-terms/terms/3003396) Base excess in Arterial blood by calculation - [1927-3](https://athena.ohdsi.org/search-terms/terms/3002032) Base excess in Venous blood by calculation - [8632-2](https://athena.ohdsi.org/search-terms/terms/3006277) QRS-Axis - [11555-0](https://athena.ohdsi.org/search-terms/terms/3012501) Base excess in Blood by calculation - [1926-5](https://athena.ohdsi.org/search-terms/terms/3003129) Base excess in Capillary blood by calculation - [28638-5](https://athena.ohdsi.org/search-terms/terms/3004959) Base excess in Arterial cord blood by calculation [28639-3](https://athena.ohdsi.org/search-terms/terms/3007435) Base excess in Venous cord blood by calculation",No,No,NA,NA,NA,NA,NA
+measurement,value_as_number,No,float,"This is the numerical value of the Result of the Measurement, if available. Note that measurements such as blood pressures will be split into their component parts i.e. one record for systolic, one record for diastolic.",[Convention for negative values](https://ohdsi.github.io/Themis/negative_value_as_number.html),No,No,NA,NA,NA,NA,NA
 measurement,value_as_concept_id,No,integer,If the raw data gives a categorial result for measurements those values are captured and mapped to standard concepts in the 'Meas Value' domain.,"If the raw data provides categorial results as well as continuous results for measurements, it is a valid ETL choice to preserve both values. The continuous value should go in the VALUE_AS_NUMBER field and the categorical value should be mapped to a standard concept in the 'Meas Value' domain and put in the VALUE_AS_CONCEPT_ID field. This is also the destination for the 'Maps to value' relationship. If there's no categorial result in a source_data, set value_as_concept_id to NULL, if there is a categorial result in a source_data but without mapping, set value_as_concept_id to 0.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
 measurement,unit_concept_id,No,integer,"At present, there isn't a prescribed unit for individual measurements, such as Hemoglobin A1C, meaning it's not obligatory to express these measurements as a percentage. UNIT_SOURCE_VALUES should be linked to a Standard Concept within the Unit domain that most accurately reflects the unit provided in the source data.","If the source data does not include units, set UNIT_CONCEPT_ID to NULL. If units are provided but not mapped, set UNIT_CONCEPT_ID to 0. Otherwise, map the units to a CONCEPT_ID. Remember that units are case-sensitive in vocabulary.",No,Yes,CONCEPT,CONCEPT_ID,Unit,NA,NA
 measurement,range_low,No,float,Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are provided by the source and should remain NULL if not given.,If reference ranges for upper and lower limit of normal as provided (typically by a laboratory) these are stored in the RANGE_HIGH and RANGE_LOW fields. This should be set to NULL if not provided.,No,No,NA,NA,NA,NA,NA

inst/csv/OMOP_CDMv5.4_Field_Level.csv

@@ -154,7 +154,7 @@ measurement,measurement_datetime,No,datetime,NA,"This is not required, though it
 measurement,measurement_time,No,varchar(10),NA,This is present for backwards compatibility and will be deprecated in an upcoming version.,No,No,NA,NA,NA,NA,NA
 measurement,measurement_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Measurement record, as in whether the measurement was from an EHR system, insurance claim, registry, or other sources.","Choose the MEASUREMENT_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=). A more detailed explanation of each Type Concept can be found on the [vocabulary wiki](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,NA,NA
 measurement,operator_concept_id,No,integer,"The meaning of Concept [4172703](https://athena.ohdsi.org/search-terms/terms/4172703) for '=' is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, it's important when devising analyses to not to forget testing for the content of this field for values different from =.","Operators are <, <=, =, >=, > and these concepts belong to the 'Meas Value Operator' domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&standardConcept=Standard&page=1&pageSize=15&query=). Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numeric value at all.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
-measurement,value_as_number,No,float,"This is the numerical value of the Result of the Measurement, if available. Note that measurements such as blood pressures will be split into their component parts i.e. one record for systolic, one record for diastolic.","If there is a negative value coming from the source, set the VALUE_AS_NUMBER to NULL, with the exception of the following Measurements (listed as LOINC codes):<br>-  [1925-7](https://athena.ohdsi.org/search-terms/terms/3003396) Base excess in Arterial blood by calculation - [1927-3](https://athena.ohdsi.org/search-terms/terms/3002032) Base excess in Venous blood by calculation - [8632-2](https://athena.ohdsi.org/search-terms/terms/3006277) QRS-Axis - [11555-0](https://athena.ohdsi.org/search-terms/terms/3012501) Base excess in Blood by calculation - [1926-5](https://athena.ohdsi.org/search-terms/terms/3003129) Base excess in Capillary blood by calculation - [28638-5](https://athena.ohdsi.org/search-terms/terms/3004959) Base excess in Arterial cord blood by calculation [28639-3](https://athena.ohdsi.org/search-terms/terms/3007435) Base excess in Venous cord blood by calculation",No,No,NA,NA,NA,NA,NA
+measurement,value_as_number,No,float,"This is the numerical value of the Result of the Measurement, if available. Note that measurements such as blood pressures will be split into their component parts i.e. one record for systolic, one record for diastolic.",[Convention for negative values](https://ohdsi.github.io/Themis/negative_value_as_number.html),No,No,NA,NA,NA,NA,NA
 measurement,value_as_concept_id,No,integer,If the raw data gives a categorial result for measurements those values are captured and mapped to standard concepts in the 'Meas Value' domain.,"If the raw data provides categorial results as well as continuous results for measurements, it is a valid ETL choice to preserve both values. The continuous value should go in the VALUE_AS_NUMBER field and the categorical value should be mapped to a standard concept in the 'Meas Value' domain and put in the VALUE_AS_CONCEPT_ID field. This is also the destination for the 'Maps to value' relationship. If there's no categorial result in a source_data, set value_as_concept_id to NULL, if there is a categorial result in a source_data but without mapping, set value_as_concept_id to 0.",No,Yes,CONCEPT,CONCEPT_ID,NA,NA,NA
 measurement,unit_concept_id,No,integer,"At present, there isn't a prescribed unit for individual measurements, such as Hemoglobin A1C, meaning it's not obligatory to express these measurements as a percentage. UNIT_SOURCE_VALUES should be linked to a Standard Concept within the Unit domain that most accurately reflects the unit provided in the source data.","If the source data does not include units, set UNIT_CONCEPT_ID to NULL. If units are provided but not mapped, set UNIT_CONCEPT_ID to 0. Otherwise, map the units to a CONCEPT_ID. Remember that units are case-sensitive in vocabulary.",No,Yes,CONCEPT,CONCEPT_ID,Unit,NA,NA
 measurement,range_low,No,float,Ranges have the same unit as the VALUE_AS_NUMBER. These ranges are provided by the source and should remain NULL if not given.,If reference ranges for upper and lower limit of normal as provided (typically by a laboratory) these are stored in the RANGE_HIGH and RANGE_LOW fields. This should be set to NULL if not provided.,No,No,NA,NA,NA,NA,NA