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Repository for OMOP CDM conventions as defined by THEMIS. These can be reference lists of concepts, pieces of standardized code for data generation or quality certification, and debates.
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How to store Microbiology Susceptibility data into OMOP CDM #172

Open crabcakeworld opened 7 months ago

crabcakeworld commented 7 months ago

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): <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

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 <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

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

Record 2 <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

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 <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

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.

MelaniePhilofsky commented 1 month ago

We will discuss this in the CDM WG 2025. This is a big issue with many different use cases.

don-torok commented 1 month ago

The relationships Specimen to Susceptibility then Susceptibility to Organism seems wrong. I think the relationship should be Specimen to Organism then Organism to Susceptibility. So that the Organism record will point back to the specimen and the susceptibility record will point to the organism.

crabcakeworld commented 1 day ago

The relationships Specimen to Susceptibility then Susceptibility to Organism seems wrong. I think the relationship should be Specimen to Organism then Organism to Susceptibility. So that the Organism record will point back to the specimen and the susceptibility record will point to the organism.

Yes, @don-torok. You are correct!. I have modified my design according your comment.

crabcakeworld commented 1 day ago

Here is the microbiology data model consolidation file. We can discuss it during our next Themis meeting. Microbiology data models consolidation.xlsx