Provide patterns for relating absence of actionable data with assay "successfulness"

[turbomam]

If a specimen, OBI:0001479, is collected from a human with a patient role, that specimen is sliced and stained, and a pathologist examines it, one would hope that the pathologist can assign an AJCC histopathological stage to the tissue. That would be useful in planning future care for the patient, or for reporting the effectiveness of an investigational drug, etc. Unfortunately, pathological staging systems often include

• an ordinal scale ranging from
  • no tumor detected
  • tumor detected, but localized in situ
  • tumors with greater size or extent
• plus some symbol like TX, meaning that the pathologist wasn't able to pick any of the ordinal levels to describe the tumor size or extent in the specimen.

OBI implements AJCC TX as a subclass of OBI:0002199 'reason for lack of data item'

One term currently under consideration for COB is 'completely executed planned process', COB:0000035, which would be an intermediate between planned process and assay.

So, in the anecdote above, if the pathologist was operating under an implicit objective of reporting an AJCC stage value specification, does that mean that no assay occurred?

Can we axiomatically say that a planned process that does not have a datum or value specification output can not be an assay, and vice versa?

This issue was created in the "Core Ontology for Biology and Biomedicine" repo and migrated here because of its investigation focus. See https://github.com/OBOFoundry/COB/issues/110

[DanBerrios]

Discussed on OBI Dev Call 09/14/20. Assays are understood and asserted to have been completed planned processes.

[turbomam]

@turbomam will reread the COB slides to ensure that the proposal meets this use case... looks promising

[ddooley]

Issue is "intends to implement" is not an object property yet in OBI or COB. Consensus is to add NTR for this to COB.