Add slot: host_disease_stat

[bmeluch]

"host_disease_stat" is listed in the MIxS "Plant-Associated" extension but I could not find it in the NMDC schema documentation or mixs.yaml, is there a reason it did not get imported?

host_disease_stat
List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org/, non-human host diseases are free text
Expected_value: disease name or Disease Ontology term

This is an EMSL metadata field, adding to the schema to support EMSL users in the submission portal.

[bmeluch]

@turbomam @mslarae13 any guidance or thoughts on this slot/importing this slot from MIxS?

[turbomam]

There is a long complicated story about how MIxS terms have been imported into the nmdc-schema, and that's about to change with

• DO NOT MERGE YET change MIxS import to 6.2 #1386

For now, I have tied this issue to a branch, which will turn into a PR very shortly. It imports the definition of host_disease_stat into src/schema/mixs.yaml and makes host_disease_stat available to the Biosample class.

[turbomam]

https://github.com/microbiomedata/nmdc-schema/pull/1408/files

[bmeluch]

Thank you @turbomam for context + dealing with the complicated import issue!

[turbomam]

reopening because this PR hasn't been merged yet:

• DO NOT MERGE YET change MIxS import to 6.2 #1386

So main doesn't build right now!

[turbomam]

https://github.com/GenomicsStandardsConsortium/mixs/blob/885b4544edd68ce42d9a55df217033bb3eee200d/src/mixs/schema/mixs.yaml#L8224-L8240

  host_disease_stat:
    annotations:
      Expected_value:
        tag: Expected_value
        value: disease name or Disease Ontology term
    description: List of diseases with which the host has been diagnosed; can include
      multiple diagnoses. The value of the field depends on host; for humans the terms
      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
      non-human host diseases are free text
    title: host disease status
    in_subset:
      - nucleic acid sequence source
    keywords:
      - disease
      - host
      - host.
      - status
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000031