Is "Sex" correctly labelled in the Pedigree example and Sex documentation

Hi @julesjacobsen

Is Sex correctly labelled in the Pedigree/Sex schemas?

In genetics/genomics, we usually use "1" for male, and "2" for female (easy to remember as equivalent to the normal number of X chromosomes per sex), but in the documentation and the examples for the Pedigree (https://phenopacket-schema.readthedocs.io/en/latest/pedigree.html) and Sex fields (https://phenopacket-schema.readthedocs.io/en/latest/sex.html#rstsex), it indicates that females should be encoded as 1 and males as 2.

Unfortunately the NICT links on the Sex page didn't work for me, so I can't check if they do have F1 and M2. However, if this is the case, then there is an inconsistency between NICT and what is defined in PLINK, so a choice needs to be made, as the documentation is inconsistent. Personally, I would suggest we stick with PLINK.

This may seem trivial, but obviously could lead to a lot of miscoding that will be a pain for users to rectify later.

Review the Pedigree and Sex documentation pages, along with the referenced NICT and PLINK conventions, to establish which sex encoding the project should use. Done means the convention is decided and the documentation and examples consistently reflect it.