Specification for laboratory tests for disease and genetic conditions

[cookeac]

Proposal or request provided by an ICAR ADE specification user:

I am trying to determine the appropriate ICAR API schemas to use for genomic test results and disease test results.

I can see how we can use the diagnoses schema for milk culture result entry. However, for disease testing, users tend to want to set a permanent flag on animals showing their status. This is used especially for those needing to export a report for traceability upon shipping the animal to another location.

The standard data fields are: Date of test Test type Result (positive, negative, or inconclusive) Result Value (numeric) I can also see the need to include values for the source of the result and test method.

[cookeac]

Discussed 2024-08-08 We could see a few options for this:

1. Implement one of the existing clinical laboratory or testing laboratory data standards. These already exist (often in XML, but are transferrable). They are likely more complex than our requirements but the tools exist to specify a concrete subset.
2. Implement a test result event that captured the animal/location/date, laboratory identifier, sample Id, and then an array of results (for instance Andrew's team had implemented one with an array of these items).
3. Implement a test result event as above, but have it contain an array of icarDiagnosisType.

We ask all members to talk to their teams who deal with test results or geneticists who deal with genetic tests whether they have sample data and/or what data fields they capture. This would help us decide on an approach.

[cvigorsICBF]

Some things to consider:

Test type - Assuming this is the kind of test carried out, e.g. mystatinV1, mystatinV2, micro satellites, BVD (Virus) Elisa etc. This is likely to be an ever changing list. Suggest renaming to 'Test Name' Sample type - e.g. blood, hair, ear punch etc. Result - possibly too simple with just 3 fields. BVD lab test, for example could be "positive" or "dam positive" and more. Might be better as a string, suggest rename to 'Interpreted result', or something similar? Result value - possible scenario where the value is not numeric is a genetic test on animal coat colour. Lab - Identifier for the lab carrying out the test. Lab reference number.

Suggestion is to get some sample scenarios of laboratory tests for disease and genetic conditions that need to be handled by this feature.

A lot of the fields in this does seem more applicable, especially the inclusion of unit.