Thanks for getting the discussion going again!
Not as a final recommendation, but just to provide an inadequate straw person, here's what we currently use for
measure_organism (apologies for format; I can't figure out tables in the forums). Basically just a specialized attribute with links back to most-used entities.
The measurement organism table contains organism information related to laboratory culture results in the measurement table. This table is CUSTOM to Pedsnet.
Note 1: There can be multiple organisms for a single culture laboratory result.
Field |NOT Null Constraint |Network Requirement |Data Type | Description | PEDSnet Conventions
--- | --- | --- | --- | ---| ---
meas_organism_id | Yes |Yes| Integer |A system-generated unique identifier for each organism culture relationship. | This is not a value found in the EHR. Sites may choose to use a sequential value for this field.
measurement_id | Yes |Yes| Integer | A foreign key to the lab result in the measurement table where the organism was observed.
person_id| Yes |Yes| Integer| A foreign key identifier to the person who the measurement is being documented for. The demographic details of that person are stored in the person table.|
visit_occurrence_id| No |Provide When Available| Integer | A foreign key to the visit where the culture lab was ordered|
organism_concept_id| Yes |Yes| Integer| A foreign key to a standard concept identifier for the organism in the Vocabulary.|
Please include valid concept ids (consistent with OMOP CDMv5). Predefined value set (valid concept_ids found in CONCEPT table where vocabulary_id = SNOMED and concept_class_id= Organism and standard_concept=S)
select * from concept where vocabulary_id ='SNOMED' and concept_class_id='Organism' and standard_concept='S' yields 33039 valid concept_ids.
organism_source_value | Yes |Yes| Varchar | The organism value as it appears in the source.
positivity_datetime| No| Optional | Datetime| The estimated date and time of initial growth as reported in the source.|
If a field marked as "Provide when available" for the network requirement is not available at your site, please relay this information to the DCC
1.15.1 Additional Notes
- The time to positivity field is marked as optional. Please inform the DCC in the provenance files if this data is available at your site.