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Adding Cultures into OMOP v5

vocabularies
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(Karthik) #41

Hi @mkwong and @Andrew I just wanted to follow up to see if you guys want to discuss a measure_attribute table. I think this would be the best approach.


(Charles Bailey) #42

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.

1.15 MEASUREMENT_ORGANISM

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?
(Andrew Williams) #43

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.


(Karthik) #44

Just wanted to let people know on this thread that we’ve created a proposal to handle cultures and that might also handle other clinical results. You can see the post here.


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