Sex / Gender to be normalized

[mbaudis]

The Individual property is called sex, with a description of:

"sex": {
  "description": "Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993): 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576), or 'male', (NCIT:C20197).",
  "$ref": "../common/commonDefinitions.json#/definitions/Gender"
},

The values are then defined in the Gender property in common:

"Gender": {
      "description": "Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993): 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576), or 'male', (NCIT:C20197).",
      "$ref": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-framework-v2/main/common/ontologyTerm.json",
      "examples": [
        { "id": "NCIT:C16576", "label": "female" },
        { "id": "NCIT:C20197", "label": "male" },
        { "id": "NCIT:C1799", "label": "unknown" }
      ]
    },

This needs to be fixed:

1. There is a fundamental difference between the use of sex and gender. They can both be used in parallel if necessary, although for the general purposes here the sex definition would seem to take precedence. In any case a property should not be defined by using a conflicting term.
2. While several terms are available for this we should either follow the Phenopackets use
   • female sex. Maps to NCIT:C46113
   • male sex. Maps to NCIT:C46112
   • Not assessed or not available. Maps to NCIT:C17998
   • It is not possible to accurately assess the applicability of MALE/FEMALE. Maps to NCIT:C45908

... or strictly go for the genotypic_sex classes

[jrambla]

(Sorry, I've answered this issue or one very similar some days ago, but I'm realizing that the response is not in the thread) You are pointing to two different issues here:

1. Naming of the property: I concur that we can name the definition as "Sex" and the conflct should be away.
2. What is the concept described in the property. I have prioritized a generic attribute, where the Beacon is saying "male" w/o having to indicate if that is phenotypic, genotypic or any other consideration to it. Therefore, I'd opted for the ancestor term vs the ones that imply a more specific determination.

Is this clearer now?