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.
Antibiotic resistance data?
Hi @cukarthik, I’m so sorry for missing this when you posted it. I was in transition to a new institution and my attention to most things OHDSI flagged for a few weeks. I will ping @mkwong, @rtmill, @bailey and @Rijnbeek about this to get their input on pushing it forward.