diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index f5c9748c..eb15c557 100644 --- a/docs/jsonBrowser/module.md +++ b/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_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 +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 | 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 _Information relating to how a biomaterial was grown and/or maintained in a laboratory setting._ @@ -558,9 +564,23 @@ 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. +reproduction_history | Reproduction history of the donor at the time of collection. | object | no | [See module reproduction_history](module.md#reproduction-history) | Reproduction 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 +_Donor's residence location information._ + +Location: module/biomaterial/residence.json + +Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example +--- | --- | --- | --- | --- | --- | --- | --- +country | Country and state of donor's residence. | string | no | | Country | | Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Bauchi State; Nigeria +granular_location | Nearest city, town, or village to location of donor's residence. | string | no | | Location | | 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 _Information relating to pathological and morphological features of cells._ @@ -603,6 +623,18 @@ value | The numerical value in Timecourse unit associated with a time interval u unit | The unit in which the Timecourse value is expressed. | object | yes | [See module time_unit_ontology](module.md#time-unit-ontology) | Timecourse unit | | relevance | Relevance of the Timecourse value/unit to the experiment. | string | no | | Timecourse relevance | | Collection after tumor cells injected into the mammary gland; Time tissue underwent liberase digestion +## Reproduction history +_Reproduction history of the donor._ + +Location: module/biomaterial/reproduction_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 + ## Mouse-specific _Information specific to an organism that is a mouse (Mus musculus)._ diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 6f09a358..dd580a7c 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -376,6 +376,8 @@ cause_of_death | Conditions resulting in death. | string | | Cause of death | _There are no required properties in schema Familial relationship_ ### Medical history _There are no required properties in schema Medical history_ +### Residence +_There are no required properties in schema Residence_ ### Cell morphology _There are no required properties in schema Cell morphology_ ### State of specimen @@ -385,6 +387,8 @@ Property name | Description | Type | Object reference? | User friendly name | Al --- | --- | --- | --- | --- | --- | --- value | The numerical value in Timecourse unit associated with a time interval used in the experiment. | string | | Timecourse value | | 2; 5.5-10.5 unit | The unit in which the Timecourse value is expressed. | object | [See module time_unit_ontology](module.md#time-unit-ontology) | Timecourse unit | | +### Reproduction history +_There are no required properties in schema Reproduction history_ ### Mouse-specific _There are no required properties in schema Mouse-specific_ ### Purchased reagents diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index 8a26c686..c9e141fc 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/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_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"] + }, + "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": { + "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"] } } } diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 112e5587..eb19c1cb 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/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"] + }, + "reproduction_history": { + "description": "Reproduction history of the donor at the time of collection.", + "type": "object", + "user_friendly": "Reproduction history", + "$ref": "module/biomaterial/reproduction_history.json", + "bionetworks": ["genetic diversity"] + }, "test_results": { "description": "Results from medical tests performed on the individual.", "type": "string", @@ -81,39 +95,39 @@ "example": "Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer" } }, - "allOf": + "allOf": [ { "if": { - "properties": { + "properties": { "smoking_status": { - "const": "active" - } + "const": "active" + } } }, "then": { "properties": { - "years_since_smoking_cessation": { - "maximum": 0 + "years_since_smoking_cessation": { + "maximum": 0 } } } }, { "if": { - "properties": { - "smoking_status": { - "const": "never" - } + "properties": { + "smoking_status": { + "const": "never" + } } }, "then": { "properties": { - "years_since_smoking_cessation": { - "type": "null" + "years_since_smoking_cessation": { + "type": "null" }, - "smoking_pack_years": { - "maximum": 0 + "smoking_pack_years": { + "maximum": 0 } } } diff --git a/json_schema/module/biomaterial/reproduction_history.json b/json_schema/module/biomaterial/reproduction_history.json new file mode 100644 index 00000000..1a5d29aa --- /dev/null +++ b/json_schema/module/biomaterial/reproduction_history.json @@ -0,0 +1,57 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "description": "Reproduction history of the donor.", + "additionalProperties": false, + "minProperties": 1, + "title": "Reproduction history", + "name": "reproduction_history", + "type": "object", + "properties": { + "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" + }, + "schema_version": { + "description": "The version number of the schema in major.minor.patch format.", + "type": "string", + "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$", + "example": "4.6.1" + }, + "menarche_age": { + "description": "Age at menarche, rounded to nearest whole number.", + "type": "integer", + "user_friendly": "Menarche age", + "example": "13; 12; 16", + "bionetworks": ["genetic diversity"] + }, + "menopause_status": { + "description": "Menopausal status of donor at time of sample collection.", + "type": "string", + "enum": [ + "pre-menopausal", + "peri-menopausal", + "post-menopausal", + "post-menopausal (induced)" + ], + "user_friendly": "Menopause status", + "example": "pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced)", + "guidelines": "Should be one of: pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced)", + "bionetworks": ["genetic diversity"] + }, + "parity": { + "description": "Number of children (full-term pregnancies) the donor has given birth to at time of sample collection.", + "type": "integer", + "user_friendly": "Full term pregnancy - parity", + "example": "0; 2; 3", + "bionetworks": ["genetic diversity"] + }, + "gravidity": { + "description": "Number of pregnancies the donor has had at time of sample collection.", + "type": "integer", + "user_friendly": "Pregnancy - gravidity", + "example": "2; 3; 5", + "bionetworks": ["genetic diversity"] + } + } +} diff --git a/json_schema/module/biomaterial/residence.json b/json_schema/module/biomaterial/residence.json new file mode 100644 index 00000000..7e946253 --- /dev/null +++ b/json_schema/module/biomaterial/residence.json @@ -0,0 +1,64 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "description": "Donor's residence location information.", + "additionalProperties": false, + "minProperties": 1, + "dependencies": { + "granular_location": [ + "country" + ] + }, + "title": "Residence", + "name": "residence", + "type": "object", + "properties": { + "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" + }, + "schema_version": { + "description": "The version number of the schema in major.minor.patch format.", + "type": "string", + "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$", + "example": "4.6.1" + }, + "country": { + "description": "Country and state of donor's residence.", + "type": "string", + "user_friendly": "Country", + "example": "Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Bauchi State; Nigeria", + "guidelines": "Enter the country or state and country if available.", + "bionetworks": ["genetic diversity"] + }, + "granular_location": { + "description": "Nearest city, town, or village to location of donor's residence.", + "type": "string", + "user_friendly": "Location", + "example": "Singapore; Cambridge; Boston; Kingston", + "bionetworks": ["genetic diversity"] + }, + "duration": { + "description": "Duration of residence, in years, rounded up to the nearest whole number.", + "type": "string", + "pattern": "^[0-9]+-?[0-9]*$", + "user_friendly": "Duration of residence", + "example": "20; 37; 45-65", + "guidelines": "Enter either a single value or a range of values. Indicate a range using a hyphen.", + "bionetworks": ["genetic diversity"] + }, + "area_type": { + "description": "Urban, suburban, or rural descriptor of residence.", + "type": "string", + "enum": [ + "urban", + "suburban", + "rural" + ], + "user_friendly": "Area type of residence", + "example": "urban; suburban; rural", + "guidelines": "Should be one of: urban; suburban; rural", + "bionetworks": ["genetic diversity"] + } + } +} diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff19..ac695adf 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,11 @@ Schema,Change type,Change message,Version,Date +module/biomaterial/human_specific,minor,Added optional ethnicity_question,, +module/biomaterial/human_specific,minor,Added optional ethnicity_parents,, +module/biomaterial/human_specific,minor,Added optional primary_language,, +module/biomaterial/human_specific,minor,Added optional mother_father_language,, +module/biomaterial/residence,major,Added new module for residence information,, +module/biomaterial/human_specific,minor,Added optional current_residence,, +module/biomaterial/human_specific,minor,Added optional place_of_birth,, +module/biomaterial/medical_history,minor,Added optional diet_meat_consumption,, +module/biomaterial/reproduction_history,major,Added new reproduction_history module,, +module/biomaterial/medical_history,minor,Added optional reproduction_history,, diff --git a/json_schema/versions.json b/json_schema/versions.json index 63c60e54..b25402d0 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -31,6 +31,8 @@ "medical_tests": "1.0.0", "mouse_specific": "1.0.8", "preservation_storage": "6.1.1", + "reproduction_history": "0.0.0", + "residence": "0.0.0", "state_of_specimen": "6.0.0", "timecourse": "2.0.2" },