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:
- A Specimen record that contains specimen and anatomic site.
- A Measurement record that contains microbiology test and test result and point to the first Specimen record.
- 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
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</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.
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>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:
The above source data will become following:
Record 1
<style> </style>Record 2
<style> </style>Record 3
<style> </style>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.