Provide patterns for relating absence of actionable data with assay "successfulness"
Closed this issue · 2 comments
Will elaborate later today, especially adding ID for the terms I'm using informally at this point.
If a tissue specimen is collected from a patient, the specimen is sliced and stained, and a pathologist examines it, one would hope that the pathologist can assign an AJCC histopathological grade to the tissue. That will be useful in planning future care for the patient, or for reporting the effectiveness of an investigational drug, etc. Unfortunately, grading systems frequently consist of
- an ordinal scale ranging from
- normally differentiated tissue
- to totally undifferentiated tissue, even breeching tissue boundaries
- plus some symbol like
X, meaning that the pathologist wasn't able to pick any of the ordinal levels to describe the submitted tissue specimen.
OBO has terms for explaining why the assay does not has any asserted data output. Those are about the process, where the AJCC (e.g.) grades are about the specimen. Today, we have also been discussing whether there is a legitimate way to say that an assay process was not successful. If so, we should have a pattern that relates the unsuccessful assay classification with the reason for missing data.
Sorry Mark, I didn't follow in the workshop, but now I get it. Essentially, there is an information output from a failed assay, which indicates why you don't have a measurement datum. Such as 'control failed' / 'insufficient input sample material' / 'not done'. That ties very neatly to the desire to capture some kind of outcome for a planned assay, including outcomes that did not result in measurement data.
We'll move this to the OBI tracker, and perhaps come back to COB.