Add genetic diversity fields

[arschat]

For which schema is a change/update being suggested?

I would like to request updates to the human_specific.json& the medical_history.json schema.

What should the change/update be?

I would like to add 4 current residence/ 4 place of birth/ 2 ethnicity/ 2 language fields to the human_specific.json schema and 4 reproduction and 1 diet field to the medical_history.json schema to allow data contributors to record those new genetic diversity fields.

This update constitutes a minor change to the schema(s) it affects.

What new field(s) need to be changed/added?

Ethnicity

1. Field name: ethnicity_question
   • Description: Question and response options posed to donors for collecting metadata on donor self-reported ethnicity and/or tribe and/or dialect group and/or race etc.
   • Type: string
   • Required: no
   • Examples: "What is your ethnicity?; Are you Hispanic/Latino?; Which categories describe you? Select all that apply from the following"
2. Field name: ethnicity_parents
   • Description: Ethnicity(-ies) of the donor's parents.
   • Type: ethnicity ontology
   • Required: no
   • Examples: "Chinese; Malay"

Genetic ancestry

Removed - to be added when other bionetwork requests as well

1. field name: ancestry_genetic
   • Description: A quantitative measure of genetic ancestry. Report coordinates in principal component analysis (PCA) space relative to reference datasets.
   • Type: array of strings
   • Required: no
   • Examples: "PCA1: 0.1234; PCA2: -0.5678" or "CENTRAL_SOUTH_ASIA: 0.0505; AMERICA: -0.1234"
2. field name: ancestry_genetic_datatype
   • Description: Data type (genotyping array, whole-genome sequence, single-cell genomics data) used for inference of genetic
   • Type: string
   • Required: no
   • Examples: singlecellFASTQ; IlluminaGSAv3; WGS
3. field name: ancestry_genetic_pipeline
   • Description: Name of pipeline used for inference of genetic ancestry.
   • Type: string
   • Required: no
   • Examples: scadmix; HCA; local

Language

1. Field name: primary_language
   • Description: Primary language(s) spoken by the donor. Can include dialects (for example, Hokkien).
   • Type: string
   • Required: no
2. Field name: mother_father_language
   • Description: Ancestral language(s) spoken by parents (“mother tongue” and/or “father tongue”) and/or grandparents. Can include dialects (for example, Hokkien).
   • Type: string
   • Required: no

Location - current residence

1. Field name: current_residence_location_country
   • Description: Country and state of donor's current residence at time of sample collection.
   • Type: string
   • Required: no
2. Field name: current_residence_location_granular
   • Description: Nearest city, town, or village to location of donor's current residence at time of sample collection.
   • Type: string
   • Required: no
3. Field name: current_residence_duration
   • Description: Duration of residence, in years, rounded up to the nearest whole number, at time of sample collection.
   • Type: string
   • Required: no
4. Field name: current_residence_urbanrural
   • Description: Urban, suburban, or rural descriptor of current residence.
   • Type: string
   • Required: no
   • CV or enum: "urban; suburban; rural"

Location - place of birth

1. Field name: place_of_birth_location_country
   • Description: Country and state of place of birth.
   • Type: string
   • Required: no
2. Field name: place_of_birth_location_granular
   • Description: Nearest city, town, or village to location of place of birth.
   • Type: string
   • Required: no
3. Field name: place_of_birth_duration
   • Description: Duration of residence, in years, rounded up to the nearest whole number.
   • Type: string
   • Required: no
4. Field name: place_of_birth_urbanrural
   • Description: Urban, suburban, or rural descriptor of place of birth.
   • Type: string
   • Required: no
   • CV or enum: "urban; suburban; rural"

Reproduction

1. Field name: parity
   • Description: Number of children (full-term pregnancies) the donor has given birth to at time of sample collection.
   • Type: integer
   • Required: no
2. Field name: gravidity
   • Description: Number of pregnancies the donor has had at time of sample collection.
   • Type: integer
   • Required: no
3. Field name: menarche_age
   • Description: Age at menarche, rounded to nearest whole number.
   • Type: integer
   • Required: no
4. Field name: menopause_status
   • Description: Menopausal status of donor at time of sample collection.
   • Type: integer
   • Required: no
   • CV or enum: "pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced)"

Diet

1. Field name: diet_meat
   • Description: Dietary patterns of donor - meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet - at time of sample collection.
   • Type: string
   • Required: no
   • CV or enum: "gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore."

Why is the change requested?

Genetic diversity network has requested those fields that could be grouped in the human specific and medical_history modules