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render cdm specs

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Maxim Moinat 2024-06-14 16:11:28 +02:00
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19
docs/cdm53.html
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@ -3552,23 +3552,8 @@ the patient.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
If this information is not explicitly available in the data, infer the If this information is not explicitly available in the data, infer the
end date using the following methods:<br><br> 1. Start first with end date from start date and duration.<br>For detailed conventions for
duration or days supply using the calculation drug start date + days how to populate this field, please see the <a
supply -1 day. 2. Use quantity divided by daily dose that you may obtain
from the sig or a source field (or assumed daily dose of 1) for solid,
indivisibile, drug products. If quantity represents ingredient amount,
quantity divided by daily dose * concentration (from drug_strength) drug
concept id tells you the dose form. 3. If it is an administration
record, set drug end date equal to drug start date. If the record is a
written prescription then set end date to start date + 29. If the record
is a mail-order prescription set end date to start date + 89. The end
date must be equal to or greater than the start date. Ibuprofen 20mg/mL
oral solution concept tells us this is oral solution. Calculate duration
as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL)
200*5/20 = 50 days. <a
href="https://ohdsi.github.io/CommonDataModel/drug_dose.html">Examples
by dose form</a><br><br>For detailed conventions for how to populate
this field, please see the <a
href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS
repository</a>. repository</a>.
</td> </td>

19
docs/cdm54.html
View File

@ -3676,23 +3676,8 @@ the patient.
</td> </td>
<td style="text-align:left;"> <td style="text-align:left;">
If this information is not explicitly available in the data, infer the If this information is not explicitly available in the data, infer the
end date using the following methods:<br><br> 1. Start first with end date from start date and duration.<br>For detailed conventions for
duration or days supply using the calculation drug start date + days how to populate this field, please see the <a
supply -1 day. 2. Use quantity divided by daily dose that you may obtain
from the sig or a source field (or assumed daily dose of 1) for solid,
indivisibile, drug products. If quantity represents ingredient amount,
quantity divided by daily dose * concentration (from drug_strength) drug
concept id tells you the dose form. 3. If it is an administration
record, set drug end date equal to drug start date. If the record is a
written prescription then set end date to start date + 29. If the record
is a mail-order prescription set end date to start date + 89. The end
date must be equal to or greater than the start date. Ibuprofen 20mg/mL
oral solution concept tells us this is oral solution. Calculate duration
as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL)
200*5/20 = 50 days. <a
href="https://ohdsi.github.io/CommonDataModel/drug_dose.html">Examples
by dose form</a><br><br>For detailed conventions for how to populate
this field, please see the <a
href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS href="https://ohdsi.github.io/Themis/tag_drug_exposure.html">THEMIS
repository</a>. repository</a>.
</td> </td>

2
inst/csv/OMOP_CDMv6.0_Field_Level.csv
View File

@ -92,7 +92,7 @@ drug_exposure,person_id,Yes,bigint,The PERSON_ID of the PERSON for whom the drug
drug_exposure,drug_concept_id,Yes,integer,"The DRUG_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download.","The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the Concept and are recorded in the following order of precedence: 'Branded Pack', 'Clinical Pack', 'Branded Drug', 'Clinical Drug', 'Branded Drug Component', 'Clinical Drug Component', 'Branded Drug Form', 'Clinical Drug Form', and only if no other information is available 'Ingredient'. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,NA,NA drug_exposure,drug_concept_id,Yes,integer,"The DRUG_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a drug product or molecule otherwise introduced to the body. The drug concepts can have a varying degree of information about drug strength and dose. This information is relevant in the context of quantity and administration information in the subsequent fields plus strength information from the DRUG_STRENGTH table, provided as part of the standard vocabulary download.","The CONCEPT_ID that the DRUG_SOURCE_VALUE maps to. The concept id should be derived either from mapping from the source concept id or by picking the drug concept representing the most amount of detail you have. Records whose source values map to standard concepts with a domain of Drug should go in this table. When the Drug Source Value of the code cannot be translated into Standard Drug Concept IDs, a Drug exposure entry is stored with only the corresponding SOURCE_CONCEPT_ID and DRUG_SOURCE_VALUE and a DRUG_CONCEPT_ID of 0. The Drug Concept with the most detailed content of information is preferred during the mapping process. These are indicated in the CONCEPT_CLASS_ID field of the Concept and are recorded in the following order of precedence: 'Branded Pack', 'Clinical Pack', 'Branded Drug', 'Clinical Drug', 'Branded Drug Component', 'Clinical Drug Component', 'Branded Drug Form', 'Clinical Drug Form', and only if no other information is available 'Ingredient'. Note: If only the drug class is known, the DRUG_CONCEPT_ID field should contain 0. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Drug&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Drug,NA,NA
drug_exposure,drug_exposure_start_date,Yes,date,Use this date to determine the start date of the drug record.,"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE.",No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_start_date,Yes,date,Use this date to determine the start date of the drug record.,"Valid entries include a start date of a prescription, the date a prescription was filled, or the date on which a Drug administration was recorded. It is a valid ETL choice to use the date the drug was ordered as the DRUG_EXPOSURE_START_DATE.",No,No,NA,NA,NA,NA,NA
drug_exposure,drug_exposure_start_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_start_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA
drug_exposure,drug_exposure_end_date,Yes,date,The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient.,"If this information is not explicitly available in the data, infer the end date using the following methods:/n/n 1. Start first with duration or days supply using the calculation drug start date + days supply -1 day. 2. Use quantity divided by daily dose that you may obtain from the sig or a source field (or assumed daily dose of 1) for solid, indivisibile, drug products. If quantity represents ingredient amount, quantity divided by daily dose * concentration (from drug_strength) drug concept id tells you the dose form. 3. If it is an administration record, set drug end date equal to drug start date. If the record is a written prescription then set end date to start date + 29. If the record is a mail-order prescription set end date to start date + 89. The end date must be equal to or greater than the start date. Ibuprofen 20mg/mL oral solution concept tells us this is oral solution. Calculate duration as quantity (200 example) * daily dose (5mL) /concentration (20mg/mL) 200*5/20 = 50 days. [Examples by dose form](https://ohdsi.github.io/CommonDataModel/drug_dose.html)",No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_end_date,Yes,date,The DRUG_EXPOSURE_END_DATE denotes the day the drug exposure ended for the patient.,"If this information is not explicitly available in the data, infer the end date from start date and duration.<br>For detailed conventions for how to populate this field, please see the [THEMIS repository](https://ohdsi.github.io/Themis/tag_drug_exposure.html).",No,No,NA,NA,NA,NA,NA
drug_exposure,drug_exposure_end_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA drug_exposure,drug_exposure_end_datetime,No,datetime,NA,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,NA,NA,NA,NA,NA
drug_exposure,verbatim_end_date,No,date,"This is the end date of the drug exposure as it appears in the source data, if it is given",Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable.,No,No,NA,NA,NA,NA,NA drug_exposure,verbatim_end_date,No,date,"This is the end date of the drug exposure as it appears in the source data, if it is given",Put the end date or discontinuation date as it appears from the source data or leave blank if unavailable.,No,No,NA,NA,NA,NA,NA
drug_exposure,drug_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to delineate between prescriptions written vs. prescriptions dispensed vs. medication history vs. patient-reported exposure, etc.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [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 drug_exposure,drug_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to delineate between prescriptions written vs. prescriptions dispensed vs. medication history vs. patient-reported exposure, etc.","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [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

1 cdmTableName cdmFieldName isRequired cdmDatatype userGuidance etlConventions isPrimaryKey isForeignKey fkTableName fkFieldName fkDomain fkClass unique DQ identifiers
92 drug_exposure route_concept_id No integer NA The standard CONCEPT_ID that the ROUTE_SOURCE_VALUE maps to in the route domain. No Yes CONCEPT CONCEPT_ID Route NA NA
93 drug_exposure lot_number No varchar(50) NA NA No No NA NA NA NA NA
94 drug_exposure provider_id No bigint The Provider associated with drug record, e.g. the provider who wrote the prescription or the provider who administered the drug. The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record, for example the ordering vs administering physician on an EHR record. No Yes PROVIDER PROVIDER_ID NA NA NA
95 drug_exposure visit_occurrence_id No bigint The Visit during which the drug was prescribed, administered or dispensed. To populate this field drug exposures must be explicitly initiated in the visit. No Yes VISIT_OCCURRENCE VISIT_OCCURRENCE_ID NA NA NA
96 drug_exposure visit_detail_id No bigint The VISIT_DETAIL record during which the drug exposure occurred. For example, if the person was in the ICU at the time of the drug administration the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit. Same rules apply as for the VISIT_OCCURRENCE_ID. No Yes VISIT_DETAIL VISIT_DETAIL_ID NA NA NA
97 drug_exposure drug_source_value No varchar(50) This field houses the verbatim value from the source data representing the drug exposure that occurred. For example, this could be an NDC or Gemscript code. This code is mapped to a Standard Drug Concept in the Standardized Vocabularies and the original code is stored here for reference. No No NA NA NA NA NA
98 drug_exposure drug_source_concept_id Yes integer This is the concept representing the drug source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Drug necessary for a given analytic use case. Consider using DRUG_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network. If the DRUG_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. If unavailable, set to 0. No Yes CONCEPT CONCEPT_ID NA NA NA