added rules when value_as_concept_id, unit_concept_id, operator_concept_id can be NULL or 0 in cdm53.html and cdm54.html

This commit is contained in:
Dmitry Dymshyts 2022-10-09 13:38:45 -04:00
parent 31c7b54c2b
commit d602308dc3
2 changed files with 10 additions and 10 deletions

View File

@ -4576,7 +4576,7 @@ operator_concept_id
The meaning of Concept <a href="https://athena.ohdsi.org/search-terms/terms/4172703">4172703</a> for = is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, its important when devising analyses to not to forget testing for the content of this field for values different from =. The meaning of Concept <a href="https://athena.ohdsi.org/search-terms/terms/4172703">4172703</a> for = is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, its important when devising analyses to not to forget testing for the content of this field for values different from =.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
Operators are =, &gt; and these concepts belong to the Meas Value Operator domain. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>. Operators are =, &gt; and these concepts belong to the Meas Value Operator domain. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>. Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numerical value at all.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer
@ -4631,7 +4631,7 @@ value_as_concept_id
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 gives a categorial result for measurements those values are captured and mapped to standard concepts in the Meas Value domain.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
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 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.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer
@ -4659,7 +4659,7 @@ unit_concept_id
There is currently no recommended unit for individual measurements, i.e. it is not mandatory to represent Hemoglobin a1C measurements as a percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data. There is currently no recommended unit for individual measurements, i.e. it is not mandatory to represent Hemoglobin a1C measurements as a percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
There is no standardization requirement for units associated with MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. There is no standardization requirement for units associated with MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If the source unit is NULL (applicable to cases when there's no numerical value or when it doesn't require a unit), keep unit_concept_id NULL as well. If there's no mapping of a source unit, populate unit_concept_id with 0.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer
@ -5195,7 +5195,7 @@ value_as_concept_id
It is possible that some records destined for the Observation table have two clinical ideas represented in one source code. This is common with ICD10 codes that describe a family history of some Condition, for example. In OMOP the Vocabulary breaks these two clinical ideas into two codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the VALUE_AS_CONCEPT_ID. It is important when using the Observation table to keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID field for relevant information. It is possible that some records destined for the Observation table have two clinical ideas represented in one source code. This is common with ICD10 codes that describe a family history of some Condition, for example. In OMOP the Vocabulary breaks these two clinical ideas into two codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the VALUE_AS_CONCEPT_ID. It is important when using the Observation table to keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID field for relevant information.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
Note that the value of VALUE_AS_CONCEPT_ID may be provided through mapping from a source Concept which contains the content of the Observation. In those situations, the CONCEPT_RELATIONSHIP table in addition to the Maps to record contains a second record with the relationship_id set to Maps to value. For example, ICD10 <a href="https://athena.ohdsi.org/search-terms/terms/45581076">Z82.4</a> Family history of ischaemic heart disease and other diseases of the circulatory system has a Maps to relationship to <a href="https://athena.ohdsi.org/search-terms/terms/4167217">4167217</a> Family history of clinical finding as well as a Maps to value record to <a href="https://athena.ohdsi.org/search-terms/terms/134057">134057</a> Disorder of cardiovascular system. Note that the value of VALUE_AS_CONCEPT_ID may be provided through mapping from a source Concept which contains the content of the Observation. In those situations, the CONCEPT_RELATIONSHIP table in addition to the Maps to record contains a second record with the relationship_id set to Maps to value. For example, ICD10 <a href="https://athena.ohdsi.org/search-terms/terms/45581076">Z82.4</a> Family history of ischaemic heart disease and other diseases of the circulatory system has a Maps to relationship to <a href="https://athena.ohdsi.org/search-terms/terms/4167217">4167217</a> Family history of clinical finding as well as a Maps to value record to <a href="https://athena.ohdsi.org/search-terms/terms/134057">134057</a> Disorder of cardiovascular system. 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.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
Integer Integer
@ -5251,7 +5251,7 @@ unit_concept_id
There is currently no recommended unit for individual observation concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data. There is currently no recommended unit for individual observation concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
There is no standardization requirement for units associated with OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. There is no standardization requirement for units associated with OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If the source unit is NULL (applicable to cases when there's no numerical value or when it doesn't require a unit), keep unit_concept_id NULL as well. If there's no mapping of a source unit, populate unit_concept_id with 0.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer

View File

@ -4813,7 +4813,7 @@ operator_concept_id
The meaning of Concept <a href="https://athena.ohdsi.org/search-terms/terms/4172703">4172703</a> for = is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, its important when devising analyses to not to forget testing for the content of this field for values different from =. The meaning of Concept <a href="https://athena.ohdsi.org/search-terms/terms/4172703">4172703</a> for = is identical to omission of a OPERATOR_CONCEPT_ID value. Since the use of this field is rare, its important when devising analyses to not to forget testing for the content of this field for values different from =.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
Operators are =, &gt; and these concepts belong to the Meas Value Operator domain. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>. Operators are =, &gt; and these concepts belong to the Meas Value Operator domain. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Meas+Value+Operator&amp;standardConcept=Standard&amp;page=1&amp;pageSize=15&amp;query=">Accepted Concepts</a>. Leave it NULL if there's an exact numeric value given (instead of putting '=') or there's no numerical value at all.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer
@ -4868,7 +4868,7 @@ value_as_concept_id
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 gives a categorial result for measurements those values are captured and mapped to standard concepts in the Meas Value domain.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
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 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.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer
@ -4896,7 +4896,7 @@ unit_concept_id
There is currently no recommended unit for individual measurements, i.e. it is not mandatory to represent Hemoglobin a1C measurements as a percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data. There is currently no recommended unit for individual measurements, i.e. it is not mandatory to represent Hemoglobin a1C measurements as a percentage. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
There is no standardization requirement for units associated with MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. There is no standardization requirement for units associated with MEASUREMENT_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If the source unit is NULL (applicable to cases when there's no numerical value or when it doesn't require a unit), keep unit_concept_id NULL as well. If there's no mapping of a source unit, populate unit_concept_id with 0.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer
@ -5515,7 +5515,7 @@ value_as_concept_id
It is possible that some records destined for the Observation table have two clinical ideas represented in one source code. This is common with ICD10 codes that describe a family history of some Condition, for example. In OMOP the Vocabulary breaks these two clinical ideas into two codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the VALUE_AS_CONCEPT_ID. It is important when using the Observation table to keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID field for relevant information. It is possible that some records destined for the Observation table have two clinical ideas represented in one source code. This is common with ICD10 codes that describe a family history of some Condition, for example. In OMOP the Vocabulary breaks these two clinical ideas into two codes; one becomes the OBSERVATION_CONCEPT_ID and the other becomes the VALUE_AS_CONCEPT_ID. It is important when using the Observation table to keep this possibility in mind and to examine the VALUE_AS_CONCEPT_ID field for relevant information.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
Note that the value of VALUE_AS_CONCEPT_ID may be provided through mapping from a source Concept which contains the content of the Observation. In those situations, the CONCEPT_RELATIONSHIP table in addition to the Maps to record contains a second record with the relationship_id set to Maps to value. For example, ICD10 <a href="https://athena.ohdsi.org/search-terms/terms/45581076">Z82.4</a> Family history of ischaemic heart disease and other diseases of the circulatory system has a Maps to relationship to <a href="https://athena.ohdsi.org/search-terms/terms/4167217">4167217</a> Family history of clinical finding as well as a Maps to value record to <a href="https://athena.ohdsi.org/search-terms/terms/134057">134057</a> Disorder of cardiovascular system. Note that the value of VALUE_AS_CONCEPT_ID may be provided through mapping from a source Concept which contains the content of the Observation. In those situations, the CONCEPT_RELATIONSHIP table in addition to the Maps to record contains a second record with the relationship_id set to Maps to value. For example, ICD10 <a href="https://athena.ohdsi.org/search-terms/terms/45581076">Z82.4</a> Family history of ischaemic heart disease and other diseases of the circulatory system has a Maps to relationship to <a href="https://athena.ohdsi.org/search-terms/terms/4167217">4167217</a> Family history of clinical finding as well as a Maps to value record to <a href="https://athena.ohdsi.org/search-terms/terms/134057">134057</a> Disorder of cardiovascular system. 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.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
Integer Integer
@ -5571,7 +5571,7 @@ unit_concept_id
There is currently no recommended unit for individual observation concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data. There is currently no recommended unit for individual observation concepts. UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
There is no standardization requirement for units associated with OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. There is no standardization requirement for units associated with OBSERVATION_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If the source unit is NULL (applicable to cases when there's no numerical value or when it doesn't require a unit), keep unit_concept_id NULL as well. If there's no mapping of a source unit, populate unit_concept_id with 0.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
integer integer