Added genetic diversity fields - Fixes #1610

docs/jsonBrowser/module.md

@@ -432,6 +432,12 @@ 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_of_parents | Ethnicity(-ies) of the donor's parents. | array | no | [See module  ethnicity_ontology](module.md#ethnicity-ontology) | Parents ethnicity |  | 
+primary_language | Primary language(s), spoken by donor. Can include dialects (for example, Hokkien). | array | no |  | Donor primary language |  | Mandarin Chinese; Hokkien; Bahasa Melayu
+language_of_family | Ancestral language(s), spoken by parents (“mother tongue” and / or “father tongue”) and / or grandparents or any other person in the donor family. Can include dialects (for example, Hokkien). | array | no |  | Language of family |  | Mandarin Chinese; Hokkien; Bahasa Melayu
+current_residence | Donor's current residence at time of sample collection. | object | no | [See module  residence](module.md#residence) | Current residence |  | 
+place_of_birth | Donor's place of birth residence. | object | no | [See module  residence](module.md#residence) | Place of birth |  | 
 
 ## Growth conditions<a name='Growth conditions'></a>
 _Information relating to how a biomaterial was grown and/or maintained in a laboratory setting._
@@ -507,6 +513,18 @@ copd_gold_abe_assessment | Indicate the Global Initiative for Chronic Obstructiv
 copd_phenotype | Indicate the COPD disease phenotype(s) of donor. Please indicate all applicable phenotypes of donor. | array | no |  | COPD phenotype | COPD not otherwise specified, COPD with emphysema, COPD with bronchitis, COPD with history of asthma, COPD with >300 eos in blood, COPD with allergy, COPD with Chronic Mucus Hypersecretion, COPD with frequent exacerbations | COPD with bronchitis; COPD with history of asthma; COPD with emphysema
 copd_emphysema_percentage | Indicate the percentage of the lung that is affected by emphysema as judged based on non-invasive imaging, such as from a CT scan. | number | no |  | Percentage of emphysema |  | 
 
+## Reproductive history<a name='Reproductive history'></a>
+_Reproductive history of the donor._
+
+Location: module/biomaterial/reproductive_history.json
+
+Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
+--- | --- | --- | --- | --- | --- | --- | --- 
+menarche_age | Age at menarche, rounded to nearest whole number. | integer | no |  | Menarche age |  | 13; 12; 16
+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 |  | Full term pregnancy - parity |  | 0; 2; 3
+gravidity | Number of pregnancies the donor has had at time of sample collection. | integer | no |  | Pregnancy - gravidity |  | 2; 3; 5
+
 ## Preservation and storage<a name='Preservation and storage'></a>
 _Information relating to how a biomaterial was preserved and/or stored over a period of time._
 
@@ -558,9 +576,24 @@ 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.
+reproductive_history | Reproductive history of the donor at the time of collection. | object | no | [See module  reproductive_history](module.md#reproductive-history) | Reproductive history |  | 
 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
 
+## Residence<a name='Residence'></a>
+_Donor's residence location information._
+
+Location: module/biomaterial/residence.json
+
+Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
+--- | --- | --- | --- | --- | --- | --- | --- 
+country_territory | Country or territory of donor's residence. |  | no |  | Country | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Eswatini, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Line Islands, Lithuania, Luxembourg, Macau, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Federated States of, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Macedonia, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, USA, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | Singapore; United Kingdom; Brazil; Australia; Nigeria
+region | Region of donor's residence. | string | no |  | Region |  | Massachusetts; Catalonia; Ondo; Ontario
+locality | Nearest city, town, or village to location of donor's residence. | string | no |  | Locality |  | Singapore; Cambridge; Boston; Kingston
+duration | Duration of residence, in years, rounded up to the nearest whole number. | string | no |  | Duration of residence |  | 20; 37; 45-65
+area_type | Urban, suburban, or rural descriptor of residence. | string | no |  | Area type of residence | urban, suburban, rural | urban; suburban; rural
+
 ## Cell morphology<a name='Cell morphology'></a>
 _Information relating to pathological and morphological features of cells._
 

docs/jsonBrowser/required_fields.md

@@ -366,6 +366,8 @@ Property name | Description | Type | Object reference? | User friendly name | Al
 name | Name of the institute where the biomaterial was collected on. | string |  | Collection institute name |  | institute_1; Addenbrooke's Hospital; University of California, San Francisco
 ### Disease profile<a name='Disease profile'></a>
 _There are no required properties in schema Disease profile_
+### Reproductive history<a name='Reproductive history'></a>
+_There are no required properties in schema Reproductive history_
 ### Preservation and storage<a name='Preservation and storage'></a>
 _There are no required properties in schema Preservation and storage_
 ### Death<a name='Death'></a>
@@ -376,6 +378,8 @@ cause_of_death | Conditions resulting in death. | string |  | Cause of death |
 _There are no required properties in schema Familial relationship_
 ### Medical history<a name='Medical history'></a>
 _There are no required properties in schema Medical history_
+### Residence<a name='Residence'></a>
+_There are no required properties in schema Residence_
 ### Cell morphology<a name='Cell morphology'></a>
 _There are no required properties in schema Cell morphology_
 ### State of specimen<a name='State of specimen'></a>

json_schema/module/biomaterial/human_specific.json

@@ -2,11 +2,16 @@
     "$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"
+        ]
+      },
     "title": "Human-specific",
     "name": "human_specific",
     "type": "object",
     "properties": {
-        "describedBy":  {
+        "describedBy": {
             "description": "The URL reference to the schema.",
             "type": "string",
             "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/human_specific"
@@ -33,6 +38,57 @@
             },
             "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_of_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"]
+        },
+        "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"]
+        },
+        "language_of_family": {
+            "description": "Ancestral language(s), spoken by parents (“mother tongue” and / or “father tongue”) and / or grandparents or any other person in the donor family. Can include dialects (for example, Hokkien).",
+            "type": "array",
+            "items": {
+                "type": "string"
+            },
+            "user_friendly": "Language of family",
+            "example": "Mandarin Chinese; Hokkien; Bahasa Melayu",
+            "bionetworks": ["genetic diversity"]
+        },
+        "current_residence": {
+            "description": "Donor's current residence at time of sample collection.",
+            "type": "object",
+            "$ref": "module/biomaterial/residence.json",
+            "user_friendly": "Current residence",
+            "bionetworks": ["genetic diversity"]
+        },
+        "place_of_birth": {
+            "description": "Donor's place of birth residence.",
+            "type": "object",
+            "$ref": "module/biomaterial/residence.json",
+            "user_friendly": "Place of birth",
+            "bionetworks": ["genetic diversity"]
         }
     }
 }

json_schema/module/biomaterial/medical_history.json

@@ -68,6 +68,20 @@
             "user_friendly": "Nutritional state",
             "example": "Should be one of: normal, fasting, or feeding tube removed."
         },
+        "diet_meat_consumption": {
+            "description": "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.",
+            "type": "boolean",
+            "user_friendly": "Meat consumption",
+            "example": "Should be one of: yes; no.",
+            "bionetworks": ["genetic diversity"]
+        },
+        "reproductive_history": {
+            "description": "Reproductive history of the donor at the time of collection.",
+            "type": "object",
+            "user_friendly": "Reproductive history",
+            "$ref": "module/biomaterial/reproductive_history.json",
+            "bionetworks": ["genetic diversity"]
+        },
         "test_results": {
             "description": "Results from medical tests performed on the individual.",
             "type": "string",
@@ -81,39 +95,39 @@
             "example": "Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer"
         }
     },
-    "allOf": 
+    "allOf":
         [
             {
                 "if": {
-                    "properties": { 
+                    "properties": {
                         "smoking_status": {
-                            "const": "active" 
-                        } 
+                            "const": "active"
+                        }
                     }
                 },
                 "then": {
                     "properties": {
-                        "years_since_smoking_cessation": { 
-                            "maximum": 0 
+                        "years_since_smoking_cessation": {
+                            "maximum": 0
                         }
                     }
                 }
             },
             {
                 "if": {
-                    "properties": { 
-                        "smoking_status": { 
-                            "const": "never" 
-                        } 
+                    "properties": {
+                        "smoking_status": {
+                            "const": "never"
+                        }
                     }
                 },
                 "then": {
                     "properties": {
-                        "years_since_smoking_cessation": { 
-                            "type": "null" 
+                        "years_since_smoking_cessation": {
+                            "type": "null"
                         },
-                        "smoking_pack_years": { 
-                            "maximum": 0 
+                        "smoking_pack_years": {
+                            "maximum": 0
                         }
                     }
                 }