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).",
"$ref": "../common/commonDefinitions.json#/definitions/Gender"
},
"Gender": {
"description": "Sex of the individual. Value from NCIT General Qualifier (NCIT:C27993): 'unknown' (not assessed or not available) (NCIT:C17998), 'female' (NCIT:C16576), or 'male', (NCIT:C20197).",
"$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:
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.
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
(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:
Naming of the property: I concur that we can name the definition as "Sex" and the conflct should be away.
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.
The
Individual
property is calledsex
, with a description of:The values are then defined in the
Gender
property in common:This needs to be fixed:
sex
andgender
. They can both be used in parallel if necessary, although for the general purposes here thesex
definition would seem to take precedence. In any case a property should not be defined by using a conflicting term.... or strictly go for the
genotypic_sex
classes