Documentation, inconsistencies in TNM use

[mbaudis]

The v2 documentation provides different options for TNM findings:

• clinical_tnm_finding in Disease, with the description "child terms of NCIT:C48232 (Cancer TNM Finding)" and examples in the documentation (but partially using the prefixes for pathological TNM)

  clinicalTnmFinding:
  - id: "NCIT:C48766"
    label: "pT2b Stage Finding"
  - id: "NCIT:C48750"
    label: "pN2 Stage Finding"

• pathological_tnm_finding in Biosample w/o example in the documentation (so far) but inline notes in the .proto

  // ARGO mapping specimen::pathological_t_category 
  // ARGO mapping specimen::pathological_n_category
  // ARGO mapping specimen::pathological_m_category

While I assume the duality between clinical and pathological for the different scopes of subject.diseases and biosample reflects different optional uses,

• it is not clear if e.g. for all TNM annotations NCIT:C48232 should be used (probably?)
• that there is a need for "clinical" versus "pathological" categories, since e.g. pN2 indicates a pathological finding

I would suggest to keep (if needed) TNM properties in disease and biosample, but w/o explicit designation of clin/path. In this case also different observations (clinical. patho) can be collected (e.g. a patient may have pre- and post-OP stages but no specific biosample data etc.). Also, the ARGO references may be informative but should be secondary to term usage documentation (or moved to extended documentation).