Added genetic diversity fields - Fixes #1610

docs/jsonBrowser/module.md

@@ -432,6 +432,21 @@ Property name | Description | Type | Required? | Object reference? | User friend
 --- | --- | --- | --- | --- | --- | --- | --- 
 body_mass_index | The body mass index of the donor. | number | no |  | Body mass index |  | 36.4
 ethnicity | Ethnicity of the donor. | array | no | [See module  ethnicity_ontology](module.md#ethnicity-ontology) | Ethnicity |  | 
+ethnicity_question | 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. | string | no |  | Ethnicity question |  | What is your ethnicity?; Are you Hispanic/Latino?; Which categories describe you? Select all that apply. Note You may select more than one group. 1. American Indian or Alaska Native (for example, Aztec, Blackfeet Tribe, Mayan, Navajo Nation, Native Village of Barrow (Utqiagvik) Inupiat Traditional Government, Nome Eskimo Community, etc.), 2 - Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.), 3 - Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.), 4 - Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.), 5 - Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.), 6 - Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.), 7 - White (for example, English, European, French, German, Irish, Italian, Polish, etc.), 8 - None of these fully describe me (optional free text answer), 9 - Prefer not to answer
+ethnicity_parents | Ethnicity(-ies) of the donor's parents. | array | no | [See module  ethnicity_ontology](module.md#ethnicity-ontology) | Parents ethnicity |  | 
+ancestry_genetic | A quantitative measure of genetic ancestry. For instance Establish common coordinates across all studies, based on a reference comprising the 1000 Genomes Project and Human Genome Diversity Project datasets. Project donor data (genotype data, single-cell genomics data) against reference datasets. Report coordinates in principal component analysis (PCA) space relative to reference datasets. | array | no |  | Genetic ancestry |  | PCA1: 0.1234; PCA2: -0.5678 or CENTRAL_SOUTH_ASIA: 0.0505; AMERICA: -0.1234
+ancestry_genetic_datatype | Data type (genotyping array, whole-genome sequence, single-cell genomics data) used for inference of genetic ancestry. | string | no |  | Genetic ancestry datatype |  | singlecellFASTQ; IlluminaGSAv3; WGS
+ancestry_genetic_pipeline | Pipeline name used for inference of genetic ancestry. | string | no |  | Genetic ancestry pipeline |  | scadmix; HCA; local
+primary_language | Primary language(s), spoken by donor. Can include dialects (for example, Hokkien). | array | no |  | Donor primary language |  | Mandarin Chinese; Hokkien; Bahasa Melayu
+mother_father_language | Ancestral language(s), spoken by parents (“mother tongue” and / or “father tongue”) and / or grandparents. Can include dialects (for example, Hokkien). | array | no |  | Mother/ Father Tongue |  | Mandarin Chinese; Hokkien; Bahasa Melayu
+current_residence_location_country | Country and state of donor's current residence at time of sample collection. | string | no |  | Country of current residence |  | Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Nassau Bahamas
+current_residence_location_granular | Nearest city, town, or village to location of donor's current residence at time of sample collection. | string | no |  | Location of current residence |  | Singapore; Cambridge; Boston; Kingston
+current_residence_duration | Duration of residence, in years, rounded up to the nearest whole number, at time of sample collection. | string | no |  | Duration of current residence |  | 20; 45-65
+current_residence_urbanrural | Urban, suburban, or rural descriptor of current residence. | string | no |  | Area type of current residence | urban, suburban, rural | urban; suburban; rural
+place_of_birth_location_country | Country and state of place of birth. | string | no |  | Country of birth |  | Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Nassau Bahamas
+place_of_birth_location_granular | Nearest city, town, or village to location of place of birth. | string | no |  | Location of birth |  | Singapore; Cambridge; Boston; Kingston
+place_of_birth_duration | Duration of residence, in years, rounded up to the nearest whole number. | string | no |  | Duration in place of birth |  | 20; 45-65
+place_of_birth_urbanrural | Urban, suburban, or rural descriptor of place of birth. | string | no |  | Area type of place of birth | urban, suburban, rural | urban; suburban; rural
 
 ## Growth conditions<a name='Growth conditions'></a>
 _Information relating to how a biomaterial was grown and/or maintained in a laboratory setting._
@@ -558,6 +573,11 @@ smoking_status | Whether the individual is actively, was formerly or never consu
 smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking. | number | no |  | Smoking pack years |  | 4.55
 years_since_smoking_cessation | If smoking status is 'former', specify the number of years since smoking cessation. | integer | no |  | Years since smoking cessation |  | 12
 nutritional_state | Nutritional state of individual at time of biomaterial collection. | string | no |  | Nutritional state | normal, fasting, feeding tube removed | Should be one of: normal, fasting, or feeding tube removed.
+diet_meat_consumption | Dietary patterns of donor – meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet – at time of sample collection. Fill yes if donor consumes meat or no if donor does not consumes meat. | boolean | no |  | Meat consumption |  | Should be one of: yes; no.
+menarche_age | Age at menarche, rounded to nearest whole number. | integer | no |  | Menarche age |  | 10; 11;, 15
+menopause_status | Menopausal status of donor at time of sample collection. | string | no |  | Menopause status | pre-menopausal, peri-menopausal, post-menopausal, post-menopausal (induced) | pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced)
+parity | Number of children (full-term pregnancies) the donor has given birth to at time of sample collection. | integer | no |  | Pregnancy - parity |  | 0; 3, 7
+gravidity | Number of pregnancies the donor has had at time of sample collection. | integer | no |  | Pregnancy - gravidity |  | 0; 3, 7
 test_results | Results from medical tests performed on the individual. | string | no |  | Test results |  | lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative
 treatment | Treatments the individual has undergone prior to biomaterial collection. | string | no |  | Treatments |  | Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer
 

json_schema/module/biomaterial/human_specific.json

@@ -2,6 +2,17 @@
     "$schema": "http://json-schema.org/draft-07/schema#",
     "description": "Information specific to a donor that is a human (Homo sapiens).",
     "additionalProperties": false,
+    "dependencies": {
+      "ethnicity_question": [
+        "ethnicity"
+        ],
+      "ancestry_genetic_datatype": [
+        "ancestry_genetic"
+        ],
+      "ancestry_genetic_pipeline": [
+        "ancestry_genetic"
+        ]
+      },
     "title": "Human-specific",
     "name": "human_specific",
     "type": "object",
@@ -33,6 +44,142 @@
             },
             "user_friendly": "Ethnicity",
             "guidelines": "Enter one or more ethnicities, separated by a comma."
+        },
+        "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",
+            "user_friendly": "Ethnicity question",
+            "example": "What is your ethnicity?; Are you Hispanic/Latino?; Which categories describe you? Select all that apply. Note You may select more than one group. 1. American Indian or Alaska Native (for example, Aztec, Blackfeet Tribe, Mayan, Navajo Nation, Native Village of Barrow (Utqiagvik) Inupiat Traditional Government, Nome Eskimo Community, etc.), 2 - Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.), 3 - Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.), 4 - Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.), 5 - Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.), 6 - Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.), 7 - White (for example, English, European, French, German, Irish, Italian, Polish, etc.), 8 - None of these fully describe me (optional free text answer), 9 - Prefer not to answer",
+            "bionetworks": ["genetic diversity"]
+        },
+        "ethnicity_parents": {
+            "description": "Ethnicity(-ies) of the donor's parents.",
+            "type": "array",
+            "items": {
+                "$ref": "module/ontology/ethnicity_ontology.json"
+            },
+            "user_friendly": "Parents ethnicity",
+            "guidelines": "Enter one or more ethnicities, separated by a comma.",
+            "bionetworks": ["genetic diversity"]
+        },
+        "ancestry_genetic": {
+            "description": "A quantitative measure of genetic ancestry. For instance Establish common coordinates across all studies, based on a reference comprising the 1000 Genomes Project and Human Genome Diversity Project datasets. Project donor data (genotype data, single-cell genomics data) against reference datasets. Report coordinates in principal component analysis (PCA) space relative to reference datasets.",
+            "type": "array",
+            "items": {
+                "type": "string"
+            },
+            "user_friendly": "Genetic ancestry",
+            "example": "PCA1: 0.1234; PCA2: -0.5678 or CENTRAL_SOUTH_ASIA: 0.0505; AMERICA: -0.1234",
+            "guidelines": "Separate components with double pipe character \\|\\|.",
+            "bionetworks": ["genetic diversity"]
+        },
+        "ancestry_genetic_datatype": {
+            "description": "Data type (genotyping array, whole-genome sequence, single-cell genomics data) used for inference of genetic ancestry.",
+            "type": "string",
+            "user_friendly": "Genetic ancestry datatype",
+            "example": "singlecellFASTQ; IlluminaGSAv3; WGS",
+            "bionetworks": ["genetic diversity"]
+        },
+        "ancestry_genetic_pipeline": {
+            "description": "Pipeline name used for inference of genetic ancestry.",
+            "type": "string",
+            "user_friendly": "Genetic ancestry pipeline",
+            "example": "scadmix; HCA; local",
+            "bionetworks": ["genetic diversity"]
+        },
+        "primary_language": {
+            "description": "Primary language(s), spoken by donor. Can include dialects (for example, Hokkien).",
+            "type": "array",
+            "items": {
+                "type": "string"
+            },
+            "user_friendly": "Donor primary language",
+            "example": "Mandarin Chinese; Hokkien; Bahasa Melayu",
+            "bionetworks": ["genetic diversity"]
+        },
+        "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": "array",
+            "items": {
+                "type": "string"
+            },
+            "user_friendly": "Mother/ Father Tongue",
+            "example": "Mandarin Chinese; Hokkien; Bahasa Melayu",
+            "bionetworks": ["genetic diversity"]
+        },
+        "current_residence_location_country": {
+            "description": "Country and state of donor's current residence at time of sample collection.",
+            "type": "string",
+            "user_friendly": "Country of current residence",
+            "example": "Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Nassau Bahamas",
+            "guidelines": "Enter the country and state if available.",
+            "bionetworks": ["genetic diversity"]
+        },
+        "current_residence_location_granular": {
+            "description": "Nearest city, town, or village to location of donor's current residence at time of sample collection.",
+            "type": "string",
+            "user_friendly": "Location of current residence",
+            "example": "Singapore; Cambridge; Boston; Kingston",
+            "bionetworks": ["genetic diversity"]
+        },
+        "current_residence_duration": {
+            "description": "Duration of residence, in years, rounded up to the nearest whole number, at time of sample collection.",
+            "type": "string",
+            "pattern": "^[0-9]+-?[0-9]*$",
+            "user_friendly": "Duration of current residence",
+            "example": "20; 45-65",
+            "guidelines": "Enter either a single value or a range of values. Indicate a range using a hyphen.",
+            "bionetworks": ["genetic diversity"]
+        },
+        "current_residence_urbanrural": {
+            "description": "Urban, suburban, or rural descriptor of current residence.",
+            "type": "string",
+            "enum": [
+                "urban",
+                "suburban",
+                "rural"
+            ],
+            "user_friendly": "Area type of current residence",
+            "example": "urban; suburban; rural",
+            "guidelines": "Should be one of: urban; suburban; rural",
+            "bionetworks": ["genetic diversity"]
+        },
+        "place_of_birth_location_country": {
+            "description": "Country and state of place of birth.",
+            "type": "string",
+            "user_friendly": "Country of birth",
+            "example": "Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Nassau Bahamas",
+            "guidelines": "Enter the country and state if available.",
+            "bionetworks": ["genetic diversity"]
+        },
+        "place_of_birth_location_granular": {
+            "description": "Nearest city, town, or village to location of place of birth.",
+            "type": "string",
+            "user_friendly": "Location of birth",
+            "example": "Singapore; Cambridge; Boston; Kingston",
+            "bionetworks": ["genetic diversity"]
+        },
+        "place_of_birth_duration": {
+            "description": "Duration of residence, in years, rounded up to the nearest whole number.",
+            "type": "string",
+            "pattern": "^[0-9]+-?[0-9]*$",
+            "user_friendly": "Duration in place of birth",
+            "example": "20; 45-65",
+            "guidelines": "Enter either a single value or a range of values. Indicate a range using a hyphen.",
+            "bionetworks": ["genetic diversity"]
+        },
+        "place_of_birth_urbanrural": {
+            "description": "Urban, suburban, or rural descriptor of place of birth.",
+            "type": "string",
+            "enum": [
+                "urban",
+                "suburban",
+                "rural"
+            ],
+            "user_friendly": "Area type of place of birth",
+            "example": "urban; suburban; rural",
+            "guidelines": "Should be one of: urban; suburban; rural",
+            "bionetworks": ["genetic diversity"]
         }
     }
 }