CDM or THEMIS convention?

THEMIS

Table or Field level?

Table

Is this a general convention?

Applies to multiple fields

Summary of issues

Below is taken from a real EHR data (PHI removed):

<style> </style>

mio_src	mio_body_site	cm_organism	specimen	antibiotic	result	result_description	lab test LOINC code
Abscess	Hand, Right	Staphylococcus aureus	Abscess	Moxifloxacin	<=0.25	Sensitive	31039-1

How to put these information into OMOP CDM?

Summary of answer

This has not been rectified.

When taking above data into OMOP CDM, it will load into 3 records as follows:

1. A Specimen record that contains specimen and anatomic site.
2. A Measurement record that contains microbiology test and test result and point to the first Specimen record.
3. A Measurement record that contains the organism that is being tested and point to the 2nd Measurement record.

The above source data will become following:

Record 1

<style> </style>

specimen_id	specimen_concept_id	anatomic_site_concept_id	disease_status_concept_id
34567890	34567890	4124271 (Abscess swab)	4302584 (Structure of right hand)

Record 2

<style> </style>

measurement_id	measurement_concept_id	value_as_Concept_id	value_as_number	unit_concept_id	measurement_source_value	measurement_event_id	meas_event_field_concept_id
12345678	3037708 (Moxifloxacin [Susceptibility])	4307105 (Sensitive)	0.25	8859 (microgram per milliliter)	31039-1 (Moxifloxacin [Susceptibility])	34567890	1147049 (specimen.specimen_id)

Record 3

<style> </style>

measurement_id	measurement_concept_id	value_as_Concept_id	value_as_number	unit_concept_id	measurement_source_value	measurement_event_id	meas_event_field_concept_id
23456789	4189544 (Microbial culture)	4149419 (Staphylococcus aureus)				12345678	1147729 (measurement.measurement_id)

Related links

https://forums.ohdsi.org/t/mapping-microbiology-susceptibility-into-omop-cdm4-observations/167/57

Other comments/notes

The above solution has a problem. In the 3rd record, the value_as_concept_id field only allows concept_id of "Meas Value" domain. But the organism concept_id, 4149419 (Staphylococcus aureus) belongs to Observation domain. There might be other solutions out there. But the above solution is the presiding idea.