From 66407010ce84c83ee0f02b4b0ac67bfe9c1aa1fc Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 20 Feb 2025 22:03:42 +0000 Subject: [PATCH 01/27] Added ethnicity genetic diversity fields --- docs/jsonBrowser/module.md | 2 ++ .../module/biomaterial/human_specific.json | 17 +++++++++++++++++ json_schema/update_log.csv | 2 ++ 3 files changed, 21 insertions(+) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 430e1b72c..20c6c7354 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -432,6 +432,8 @@ 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. 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.)* Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.)* Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.)* Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.)* Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.)* Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.)* White (for example, English, European, French, German, Irish, Italian, Polish, etc.)* None of these fully describe me (optional free text answer) 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 | | ## Growth conditions _Information relating to how a biomaterial was grown and/or maintained in a laboratory setting._ diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index 8a26c686b..ec8dc8a4e 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -33,6 +33,23 @@ }, "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. 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.)* Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.)* Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.)* Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.)* Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.)* Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.)* White (for example, English, European, French, German, Irish, Italian, Polish, etc.)* None of these fully describe me (optional free text answer) 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"] } } } diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..f6873fe24 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,3 @@ 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,, From 1615c7287c9bcfaae59f0ac99cce4157388587cc Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 20 Feb 2025 22:06:16 +0000 Subject: [PATCH 02/27] Added language genetic diversity fields --- .../module/biomaterial/human_specific.json | 20 +++++++++++++++++++ json_schema/update_log.csv | 2 ++ 2 files changed, 22 insertions(+) diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index ec8dc8a4e..7b6718a41 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -50,6 +50,26 @@ "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"] } } } diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index f6873fe24..6728ac821 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1,5 @@ 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,, From 7dd118b04df023bd4e0a9a430fc78a54e47f1554 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 20 Feb 2025 22:07:13 +0000 Subject: [PATCH 03/27] Added residence and place of birth genetic diversity fields --- .../module/biomaterial/human_specific.json | 74 +++++++++++++++++++ json_schema/update_log.csv | 8 ++ 2 files changed, 82 insertions(+) diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index 7b6718a41..f3f6c9b11 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -70,6 +70,80 @@ "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"] } } } diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 6728ac821..fdcdd729b 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -3,3 +3,11 @@ Schema,Change type,Change message,Version,Date /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/human_specific,minor,Added optional current_residence_location_country,, +/module/biomaterial/human_specific,minor,Added optional current_residence_location_granular,, +/module/biomaterial/human_specific,minor,Added optional current_residence_duration,, +/module/biomaterial/human_specific,minor,Added optional current_residence_urbanrural,, +/module/biomaterial/human_specific,minor,Added optional place_of_birth_location_country,, +/module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, +/module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, +/module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, From f75abbd746073df38611b91003596cb728d6cd60 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 20 Feb 2025 22:08:33 +0000 Subject: [PATCH 04/27] Added dietary state fields --- .../module/biomaterial/medical_history.json | 19 +++++++++++++++++++ json_schema/update_log.csv | 1 + 2 files changed, 20 insertions(+) diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 112e5587d..f8eb4bcfd 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -68,6 +68,25 @@ "user_friendly": "Nutritional state", "example": "Should be one of: normal, fasting, or feeding tube removed." }, + "dietary_state": { + "description": "Dietary state of donor at the time of collection.", + "type": "string", + "enum": [ + "gluten_free", + "fodmap", + "baby_formula", + "breastfeeding", + "elimination", + "keto", + "paleo", + "vegan", + "vegetarian", + "omnivore" + ], + "user_friendly": "Dietary state", + "example": "Should be one of: gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore.", + "bionetworks": ["genetic diversity"] + }, "test_results": { "description": "Results from medical tests performed on the individual.", "type": "string", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index fdcdd729b..ba6491ea0 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -11,3 +11,4 @@ Schema,Change type,Change message,Version,Date /module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, /module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, /module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, +/module/biomaterial/medical_history,minor,Added optional dietary_state,, From d56461e21a0d39c31f1f088223f42a6822ebf93f Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 20 Feb 2025 22:10:10 +0000 Subject: [PATCH 05/27] Added reproduction genetic diversity fields --- .../module/biomaterial/medical_history.json | 35 +++++++++++++++++++ json_schema/update_log.csv | 4 +++ 2 files changed, 39 insertions(+) diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index f8eb4bcfd..f0a3ee23c 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -87,6 +87,41 @@ "example": "Should be one of: gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore.", "bionetworks": ["genetic diversity"] }, + "menarche_age": { + "description": "Age at menarche, rounded to nearest whole number.", + "type": "integer", + "user_friendly": "Menarche age", + "example": "10; 11;, 15", + "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": "Pregnancy - parity", + "example": "0; 3, 7", + "bionetworks": ["genetic diversity"] + }, + "gravidity": { + "description": "Number of pregnancies the donor has had at time of sample collection.", + "type": "integer", + "user_friendly": "Pregnancy - gravidity", + "example": "0; 3, 7", + "bionetworks": ["genetic diversity"] + }, "test_results": { "description": "Results from medical tests performed on the individual.", "type": "string", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index ba6491ea0..8a2d1b595 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -12,3 +12,7 @@ Schema,Change type,Change message,Version,Date /module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, /module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, /module/biomaterial/medical_history,minor,Added optional dietary_state,, +/module/biomaterial/medical_history,minor,Added optional menarche_age,, +/module/biomaterial/medical_history,minor,Added optional menopause_status,, +/module/biomaterial/medical_history,minor,Added optional parity,, +/module/biomaterial/medical_history,minor,Added optional gravidity,, From 3b37ae4d7f7d4c2e6aa0af6b145535b7f553d130 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 20 Feb 2025 22:11:55 +0000 Subject: [PATCH 06/27] Removed trailing whitespaces --- .../module/biomaterial/medical_history.json | 32 +++++++++---------- json_schema/update_log.csv | 24 +++++++------- 2 files changed, 28 insertions(+), 28 deletions(-) diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index f0a3ee23c..bf60570a6 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -73,7 +73,7 @@ "type": "string", "enum": [ "gluten_free", - "fodmap", + "fodmap", "baby_formula", "breastfeeding", "elimination", @@ -100,7 +100,7 @@ "enum": [ "pre-menopausal", "peri-menopausal", - "post-menopausal", + "post-menopausal", "post-menopausal (induced)" ], "user_friendly": "Menopause status", @@ -135,39 +135,39 @@ "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/update_log.csv b/json_schema/update_log.csv index 8a2d1b595..a1ec12bae 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,16 +1,16 @@ 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/human_specific,minor,Added optional current_residence_location_country,, -/module/biomaterial/human_specific,minor,Added optional current_residence_location_granular,, -/module/biomaterial/human_specific,minor,Added optional current_residence_duration,, -/module/biomaterial/human_specific,minor,Added optional current_residence_urbanrural,, -/module/biomaterial/human_specific,minor,Added optional place_of_birth_location_country,, -/module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, -/module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, -/module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, +/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/human_specific,minor,Added optional current_residence_location_country,, +/module/biomaterial/human_specific,minor,Added optional current_residence_location_granular,, +/module/biomaterial/human_specific,minor,Added optional current_residence_duration,, +/module/biomaterial/human_specific,minor,Added optional current_residence_urbanrural,, +/module/biomaterial/human_specific,minor,Added optional place_of_birth_location_country,, +/module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, +/module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, +/module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, /module/biomaterial/medical_history,minor,Added optional dietary_state,, /module/biomaterial/medical_history,minor,Added optional menarche_age,, /module/biomaterial/medical_history,minor,Added optional menopause_status,, From 7049d184bb9f0cb8aa5430a405e10279224b7e5d Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 20 Feb 2025 22:13:14 +0000 Subject: [PATCH 07/27] Ran human_readable_json.py script --- docs/jsonBrowser/module.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 20c6c7354..0df27071e 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -434,6 +434,16 @@ body_mass_index | The body mass index of the donor. | number | no | | Body mass 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. 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.)* Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.)* Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.)* Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.)* Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.)* Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.)* White (for example, English, European, French, German, Irish, Italian, Polish, etc.)* None of these fully describe me (optional free text answer) 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_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 _Information relating to how a biomaterial was grown and/or maintained in a laboratory setting._ @@ -549,6 +559,11 @@ 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. +dietary_state | Dietary state of donor at the time of collection. | string | no | | Dietary state | gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore | Should be one of: gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore. +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 From 836c7954ea1da0603c61f8115c6a8a68815fe007 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 20 Feb 2025 22:25:40 +0000 Subject: [PATCH 08/27] Updated update_log.csv --- json_schema/update_log.csv | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index a1ec12bae..6ecc6a405 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,18 +1,18 @@ 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/human_specific,minor,Added optional current_residence_location_country,, -/module/biomaterial/human_specific,minor,Added optional current_residence_location_granular,, -/module/biomaterial/human_specific,minor,Added optional current_residence_duration,, -/module/biomaterial/human_specific,minor,Added optional current_residence_urbanrural,, -/module/biomaterial/human_specific,minor,Added optional place_of_birth_location_country,, -/module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, -/module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, -/module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, -/module/biomaterial/medical_history,minor,Added optional dietary_state,, -/module/biomaterial/medical_history,minor,Added optional menarche_age,, -/module/biomaterial/medical_history,minor,Added optional menopause_status,, -/module/biomaterial/medical_history,minor,Added optional parity,, -/module/biomaterial/medical_history,minor,Added optional gravidity,, +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/human_specific,minor,Added optional current_residence_location_country,, +module/biomaterial/human_specific,minor,Added optional current_residence_location_granular,, +module/biomaterial/human_specific,minor,Added optional current_residence_duration,, +module/biomaterial/human_specific,minor,Added optional current_residence_urbanrural,, +module/biomaterial/human_specific,minor,Added optional place_of_birth_location_country,, +module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, +module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, +module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, +module/biomaterial/medical_history,minor,Added optional dietary_state,, +module/biomaterial/medical_history,minor,Added optional menarche_age,, +module/biomaterial/medical_history,minor,Added optional menopause_status,, +module/biomaterial/medical_history,minor,Added optional parity,, +module/biomaterial/medical_history,minor,Added optional gravidity,, From 078808ee9c673930c97272193a28a4491b890050 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 21 Feb 2025 13:34:58 +0000 Subject: [PATCH 09/27] Added diet_meat in place of dietary_state --- docs/jsonBrowser/module.md | 2 +- .../module/biomaterial/medical_history.json | 22 +++++-------------- json_schema/update_log.csv | 2 +- 3 files changed, 7 insertions(+), 19 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 0df27071e..1b0c2db37 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -559,7 +559,7 @@ 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. -dietary_state | Dietary state of donor at the time of collection. | string | no | | Dietary state | gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore | Should be one of: gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore. +diet_meat | Dietary patterns of donor - meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet - at time of sample collection. | boolean | no | | Meat consumption | | Should be one of: yes; no. yes stands for donor consumes meat, no stands for donor does not consume meat 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 diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index bf60570a6..d4388a5f8 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -68,23 +68,11 @@ "user_friendly": "Nutritional state", "example": "Should be one of: normal, fasting, or feeding tube removed." }, - "dietary_state": { - "description": "Dietary state of donor at the time of collection.", - "type": "string", - "enum": [ - "gluten_free", - "fodmap", - "baby_formula", - "breastfeeding", - "elimination", - "keto", - "paleo", - "vegan", - "vegetarian", - "omnivore" - ], - "user_friendly": "Dietary state", - "example": "Should be one of: gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo, vegan, vegetarian, omnivore.", + "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": "boolean", + "user_friendly": "Meat consumption", + "example": "Should be one of: yes; no. yes stands for donor consumes meat, no stands for donor does not consume meat", "bionetworks": ["genetic diversity"] }, "menarche_age": { diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 6ecc6a405..0612334ac 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -11,7 +11,7 @@ module/biomaterial/human_specific,minor,Added optional place_of_birth_location_c module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, -module/biomaterial/medical_history,minor,Added optional dietary_state,, +module/biomaterial/medical_history,minor,Added optional diet_meat,, module/biomaterial/medical_history,minor,Added optional menarche_age,, module/biomaterial/medical_history,minor,Added optional menopause_status,, module/biomaterial/medical_history,minor,Added optional parity,, From 697794dacdba52f0887ff5d88e4ab4ad3f1024fa Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 12 May 2025 13:03:02 +0100 Subject: [PATCH 10/27] Fixed diet_meat_consumption field name --- docs/jsonBrowser/module.md | 2 +- json_schema/module/biomaterial/medical_history.json | 6 +++--- json_schema/update_log.csv | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 1071f49d5..e16850f5a 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -570,7 +570,7 @@ 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 | Dietary patterns of donor - meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet - at time of sample collection. | boolean | no | | Meat consumption | | Should be one of: yes; no. yes stands for donor consumes meat, no stands for donor does not consume meat +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 diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index d4388a5f8..7d74667ed 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -68,11 +68,11 @@ "user_friendly": "Nutritional state", "example": "Should be one of: normal, fasting, or feeding tube removed." }, - "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.", + "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. yes stands for donor consumes meat, no stands for donor does not consume meat", + "example": "Should be one of: yes; no.", "bionetworks": ["genetic diversity"] }, "menarche_age": { diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 0612334ac..390bd6080 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -11,7 +11,7 @@ module/biomaterial/human_specific,minor,Added optional place_of_birth_location_c module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, -module/biomaterial/medical_history,minor,Added optional diet_meat,, +module/biomaterial/medical_history,minor,Added optional diet_meat_consumption,, module/biomaterial/medical_history,minor,Added optional menarche_age,, module/biomaterial/medical_history,minor,Added optional menopause_status,, module/biomaterial/medical_history,minor,Added optional parity,, From 9e47276e118eaab247823aa6797592cd31651064 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 12 May 2025 13:05:00 +0100 Subject: [PATCH 11/27] Added dependency for ethnicity_question field. --- json_schema/module/biomaterial/human_specific.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index f3f6c9b11..05d7537b4 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -2,6 +2,11 @@ "$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", From 0773d4962f660cae7ff33e078a5a71c9a728028b Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 12 May 2025 13:52:24 +0100 Subject: [PATCH 12/27] Added ancestry genetic fields. --- docs/jsonBrowser/module.md | 3 ++ .../module/biomaterial/human_specific.json | 31 +++++++++++++++++++ json_schema/update_log.csv | 3 ++ 3 files changed, 37 insertions(+) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index e16850f5a..ab26ee94e 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -434,6 +434,9 @@ body_mass_index | The body mass index of the donor. | number | no | | Body mass 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. 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.)* Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.)* Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.)* Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.)* Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.)* Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.)* White (for example, English, European, French, German, Irish, Italian, Polish, etc.)* None of these fully describe me (optional free text answer) 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 diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index 05d7537b4..333807a13 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -5,6 +5,12 @@ "dependencies": { "ethnicity_question": [ "ethnicity" + ], + "ancestry_genetic_datatype": [ + "ancestry_genetic" + ], + "ancestry_genetic_pipeline": [ + "ancestry_genetic" ] }, "title": "Human-specific", @@ -56,6 +62,31 @@ "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", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 390bd6080..ac13cb34f 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -11,6 +11,9 @@ module/biomaterial/human_specific,minor,Added optional place_of_birth_location_c module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, +module/biomaterial/human_specific,minor,Added optional ancestry_genetic,, +module/biomaterial/human_specific,minor,Added optional ancestry_genetic_datatype,, +module/biomaterial/human_specific,minor,Added optional ancestry_genetic_pipeline,, module/biomaterial/medical_history,minor,Added optional diet_meat_consumption,, module/biomaterial/medical_history,minor,Added optional menarche_age,, module/biomaterial/medical_history,minor,Added optional menopause_status,, From e6eae2d737f6b5f167a6e6a65df243033fc028b8 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 13 May 2025 13:50:12 +0100 Subject: [PATCH 13/27] Replaced special characters in ethnicity_question. --- docs/jsonBrowser/module.md | 2 +- json_schema/module/biomaterial/human_specific.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index ab26ee94e..97814af41 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -432,7 +432,7 @@ 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. 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.)* Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.)* Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.)* Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.)* Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.)* Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.)* White (for example, English, European, French, German, Irish, Italian, Polish, etc.)* None of these fully describe me (optional free text answer) Prefer not to answer +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 diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index 333807a13..af19128c2 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -49,7 +49,7 @@ "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. 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.)* Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.)* Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.)* Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.)* Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.)* Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.)* White (for example, English, European, French, German, Irish, Italian, Polish, etc.)* None of these fully describe me (optional free text answer) Prefer not to answer", + "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": { From ad34acf5aeebcbee3d2a69fd43aab3f2806aa6ba Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 13 May 2025 17:41:39 +0100 Subject: [PATCH 14/27] Removed ancestry_genetic fields to be added in Liver --- docs/jsonBrowser/module.md | 3 --- .../module/biomaterial/human_specific.json | 25 ------------------- json_schema/update_log.csv | 3 --- 3 files changed, 31 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 97814af41..5cd3f2860 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -434,9 +434,6 @@ body_mass_index | The body mass index of the donor. | number | no | | Body mass 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 diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index af19128c2..af53e6aec 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -62,31 +62,6 @@ "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", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index ac13cb34f..390bd6080 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -11,9 +11,6 @@ module/biomaterial/human_specific,minor,Added optional place_of_birth_location_c module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, -module/biomaterial/human_specific,minor,Added optional ancestry_genetic,, -module/biomaterial/human_specific,minor,Added optional ancestry_genetic_datatype,, -module/biomaterial/human_specific,minor,Added optional ancestry_genetic_pipeline,, module/biomaterial/medical_history,minor,Added optional diet_meat_consumption,, module/biomaterial/medical_history,minor,Added optional menarche_age,, module/biomaterial/medical_history,minor,Added optional menopause_status,, From 19c68b3fe66a5a518984767a8b7fb6dc02e115ab Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 14 May 2025 10:04:34 +0100 Subject: [PATCH 15/27] Updated place_of_birth_duration definition --- docs/jsonBrowser/module.md | 2 +- json_schema/module/biomaterial/human_specific.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 5cd3f2860..90748f69b 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -442,7 +442,7 @@ current_residence_duration | Duration of residence, in years, rounded up to the 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_duration | Duration of residence in the place of birth, 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 diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index af53e6aec..e762a2c60 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -135,7 +135,7 @@ "bionetworks": ["genetic diversity"] }, "place_of_birth_duration": { - "description": "Duration of residence, in years, rounded up to the nearest whole number.", + "description": "Duration of residence in the place of birth, in years, rounded up to the nearest whole number.", "type": "string", "pattern": "^[0-9]+-?[0-9]*$", "user_friendly": "Duration in place of birth", From e35998520d55976b74525b4fdcdb2b438615cb2f Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 14 May 2025 14:47:31 +0100 Subject: [PATCH 16/27] Removed ancestry_genetic dependecies. --- json_schema/module/biomaterial/human_specific.json | 6 ------ 1 file changed, 6 deletions(-) diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index e762a2c60..b8828534d 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -5,12 +5,6 @@ "dependencies": { "ethnicity_question": [ "ethnicity" - ], - "ancestry_genetic_datatype": [ - "ancestry_genetic" - ], - "ancestry_genetic_pipeline": [ - "ancestry_genetic" ] }, "title": "Human-specific", From e25686dd95f2f665ebcbcdd4f51eaea516b5cbda Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 14 May 2025 15:04:50 +0100 Subject: [PATCH 17/27] Updated examples in genetic diversity values --- json_schema/module/biomaterial/human_specific.json | 8 ++++---- json_schema/module/biomaterial/medical_history.json | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index b8828534d..80621d603 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -80,7 +80,7 @@ "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", + "example": "Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Bauchi State; Nigeria", "guidelines": "Enter the country and state if available.", "bionetworks": ["genetic diversity"] }, @@ -96,7 +96,7 @@ "type": "string", "pattern": "^[0-9]+-?[0-9]*$", "user_friendly": "Duration of current residence", - "example": "20; 45-65", + "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"] }, @@ -117,7 +117,7 @@ "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", + "example": "Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Bauchi State; Nigeria", "guidelines": "Enter the country and state if available.", "bionetworks": ["genetic diversity"] }, @@ -133,7 +133,7 @@ "type": "string", "pattern": "^[0-9]+-?[0-9]*$", "user_friendly": "Duration in place of birth", - "example": "20; 45-65", + "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"] }, diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 7d74667ed..3df6a7cb1 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -79,7 +79,7 @@ "description": "Age at menarche, rounded to nearest whole number.", "type": "integer", "user_friendly": "Menarche age", - "example": "10; 11;, 15", + "example": "13; 12; 16", "bionetworks": ["genetic diversity"] }, "menopause_status": { @@ -100,14 +100,14 @@ "description": "Number of children (full-term pregnancies) the donor has given birth to at time of sample collection.", "type": "integer", "user_friendly": "Pregnancy - parity", - "example": "0; 3, 7", + "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": "0; 3, 7", + "example": "2; 3; 5", "bionetworks": ["genetic diversity"] }, "test_results": { From a16c5e40d748263bb7cdbac409143504f26d3b16 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 2 Jun 2025 11:38:57 +0100 Subject: [PATCH 18/27] Replaced special character in diet description --- json_schema/module/biomaterial/medical_history.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 3df6a7cb1..0e2ae9ab7 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -69,7 +69,7 @@ "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.", + "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.", From 32d999af1fa7759d5f49b3bc08c85fb53f7b3ef5 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 2 Jun 2025 11:50:19 +0100 Subject: [PATCH 19/27] Added residence module in human_specific --- docs/jsonBrowser/module.md | 30 ++++--- docs/jsonBrowser/required_fields.md | 2 + .../module/biomaterial/human_specific.json | 80 +++---------------- json_schema/module/biomaterial/residence.json | 64 +++++++++++++++ json_schema/versions.json | 1 + 5 files changed, 95 insertions(+), 82 deletions(-) create mode 100644 json_schema/module/biomaterial/residence.json diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 90748f69b..924e38f91 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -436,14 +436,8 @@ ethnicity_question | Question and response options posed to donors for collectin 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_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 the place of birth, 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 +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._ @@ -570,14 +564,26 @@ 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 +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 | | 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 | | 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 +parity | Number of children (full-term pregnancies) the donor has given birth to at time of sample collection. | integer | no | | 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 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._ diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 6f09a3587..04fb27df8 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 diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index 80621d603..6dc8e8a39 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -76,78 +76,18 @@ "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; Bauchi State; Nigeria", - "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; 37; 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", + "current_residence": { + "description": "Donor's current residence at time of sample collection.", + "type": "object", + "$ref": "module/biomaterial/residence.json", + "user_friendly": "Current residence", "bionetworks": ["genetic diversity"] }, - "place_of_birth_location_country": { - "description": "Country and state of place of birth.", - "type": "string", - "user_friendly": "Country of birth", - "example": "Singapore; United Kingdom; Massachusetts USA; New South Wales Australia; Bauchi State; Nigeria", - "guidelines": "Enter the country and state if available.", - "bionetworks": ["genetic diversity"] - }, - "place_of_birth_location_granular": { - "description": "Nearest city, town, or village to location of place of birth.", - "type": "string", - "user_friendly": "Location of birth", - "example": "Singapore; Cambridge; Boston; Kingston", - "bionetworks": ["genetic diversity"] - }, - "place_of_birth_duration": { - "description": "Duration of residence in the place of birth, in years, rounded up to the nearest whole number.", - "type": "string", - "pattern": "^[0-9]+-?[0-9]*$", - "user_friendly": "Duration in place of birth", - "example": "20; 37; 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", + "place_of_birth": { + "description": "Donor's place of birth residence.", + "type": "object", + "$ref": "module/biomaterial/residence.json", + "user_friendly": "Place of birth", "bionetworks": ["genetic diversity"] } } diff --git a/json_schema/module/biomaterial/residence.json b/json_schema/module/biomaterial/residence.json new file mode 100644 index 000000000..964ad8c75 --- /dev/null +++ b/json_schema/module/biomaterial/residence.json @@ -0,0 +1,64 @@ +{ + "$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.json", + "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/versions.json b/json_schema/versions.json index 63c60e542..477a2d870 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -31,6 +31,7 @@ "medical_tests": "1.0.0", "mouse_specific": "1.0.8", "preservation_storage": "6.1.1", + "residence": "0.0.0", "state_of_specimen": "6.0.0", "timecourse": "2.0.2" }, From 6717c3c292a352b12c26a77e4a9ff413cfcfe8ce Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 3 Jun 2025 10:44:50 +0100 Subject: [PATCH 20/27] Updated update_log.csv --- json_schema/update_log.csv | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 390bd6080..b703d70dd 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -3,16 +3,7 @@ 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/human_specific,minor,Added optional current_residence_location_country,, -module/biomaterial/human_specific,minor,Added optional current_residence_location_granular,, -module/biomaterial/human_specific,minor,Added optional current_residence_duration,, -module/biomaterial/human_specific,minor,Added optional current_residence_urbanrural,, -module/biomaterial/human_specific,minor,Added optional place_of_birth_location_country,, -module/biomaterial/human_specific,minor,Added optional place_of_birth_location_granular,, -module/biomaterial/human_specific,minor,Added optional place_of_birth_duration,, -module/biomaterial/human_specific,minor,Added optional place_of_birth_urbanrural,, +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/medical_history,minor,Added optional menarche_age,, -module/biomaterial/medical_history,minor,Added optional menopause_status,, -module/biomaterial/medical_history,minor,Added optional parity,, -module/biomaterial/medical_history,minor,Added optional gravidity,, From dc1ef4eec3144e7b59417c7aaa6956cf9e7ae2c7 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Tue, 3 Jun 2025 10:51:39 +0100 Subject: [PATCH 21/27] Added reproduction_history module --- docs/jsonBrowser/module.md | 17 ++++-- docs/jsonBrowser/required_fields.md | 2 + .../module/biomaterial/medical_history.json | 37 ++---------- .../biomaterial/reproduction_history.json | 57 +++++++++++++++++++ json_schema/update_log.csv | 2 + json_schema/versions.json | 1 + 6 files changed, 79 insertions(+), 37 deletions(-) create mode 100644 json_schema/module/biomaterial/reproduction_history.json diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 924e38f91..61418adf4 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -565,10 +565,7 @@ smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day mu 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 | | 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 | | 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 +reproduction_history | Reproduction history of the donor at the time of collection. | object | no | [See module reproduction_history](module.md#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 @@ -626,6 +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 04fb27df8..dd580a7c7 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -387,6 +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/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 0e2ae9ab7..8c9257b89 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -75,39 +75,10 @@ "example": "Should be one of: yes; no.", "bionetworks": ["genetic diversity"] }, - "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": "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", + "reproduction_history": { + "description": "Reproduction history of the donor at the time of collection.", + "type": "object", + "$ref": "module/biomaterial/reproduction_history.json", "bionetworks": ["genetic diversity"] }, "test_results": { diff --git a/json_schema/module/biomaterial/reproduction_history.json b/json_schema/module/biomaterial/reproduction_history.json new file mode 100644 index 000000000..83c8ed660 --- /dev/null +++ b/json_schema/module/biomaterial/reproduction_history.json @@ -0,0 +1,57 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "description": "Reproduction history of the donor.", + "additionalProperties": false, + "minProperties": 1, + "title": "Reproduction history", + "name": "reproduction_history.json", + "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/update_log.csv b/json_schema/update_log.csv index b703d70dd..30c7d7d01 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -7,3 +7,5 @@ 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/medical_history,minor,Added optional reproduction_history,, +module/biomaterial/reproduction_history,minor,Added new reproduction_history module,, diff --git a/json_schema/versions.json b/json_schema/versions.json index 477a2d870..b25402d00 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -31,6 +31,7 @@ "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" From a9056e054d04b305b7cf36304adfe82089302ca9 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 4 Jun 2025 11:49:16 +0100 Subject: [PATCH 22/27] Removed unnecessary space --- json_schema/module/biomaterial/human_specific.json | 2 +- json_schema/module/biomaterial/reproduction_history.json | 2 +- json_schema/module/biomaterial/residence.json | 2 +- json_schema/update_log.csv | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index 6dc8e8a39..c9e141fce 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -11,7 +11,7 @@ "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" diff --git a/json_schema/module/biomaterial/reproduction_history.json b/json_schema/module/biomaterial/reproduction_history.json index 83c8ed660..24eacf593 100644 --- a/json_schema/module/biomaterial/reproduction_history.json +++ b/json_schema/module/biomaterial/reproduction_history.json @@ -7,7 +7,7 @@ "name": "reproduction_history.json", "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" diff --git a/json_schema/module/biomaterial/residence.json b/json_schema/module/biomaterial/residence.json index 964ad8c75..3450c4397 100644 --- a/json_schema/module/biomaterial/residence.json +++ b/json_schema/module/biomaterial/residence.json @@ -12,7 +12,7 @@ "name": "residence.json", "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" diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 30c7d7d01..ac695adf0 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -7,5 +7,5 @@ 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,, -module/biomaterial/reproduction_history,minor,Added new reproduction_history module,, From e8f4a70839153017724c9b13073a59d9dc0cff89 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 4 Jun 2025 12:02:46 +0100 Subject: [PATCH 23/27] Fixed names of new modules --- json_schema/module/biomaterial/reproduction_history.json | 2 +- json_schema/module/biomaterial/residence.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/json_schema/module/biomaterial/reproduction_history.json b/json_schema/module/biomaterial/reproduction_history.json index 24eacf593..1a5d29aae 100644 --- a/json_schema/module/biomaterial/reproduction_history.json +++ b/json_schema/module/biomaterial/reproduction_history.json @@ -4,7 +4,7 @@ "additionalProperties": false, "minProperties": 1, "title": "Reproduction history", - "name": "reproduction_history.json", + "name": "reproduction_history", "type": "object", "properties": { "describedBy": { diff --git a/json_schema/module/biomaterial/residence.json b/json_schema/module/biomaterial/residence.json index 3450c4397..7e946253a 100644 --- a/json_schema/module/biomaterial/residence.json +++ b/json_schema/module/biomaterial/residence.json @@ -9,7 +9,7 @@ ] }, "title": "Residence", - "name": "residence.json", + "name": "residence", "type": "object", "properties": { "describedBy": { From d9bcedc386983ae91366bc74aca3508f4e7cc215 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 18 Jun 2025 11:52:22 +0100 Subject: [PATCH 24/27] Added user friendly name for reproduction_history --- docs/jsonBrowser/module.md | 2 +- json_schema/module/biomaterial/medical_history.json | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 61418adf4..eb15c557d 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -565,7 +565,7 @@ smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day mu 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 | 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 diff --git a/json_schema/module/biomaterial/medical_history.json b/json_schema/module/biomaterial/medical_history.json index 8c9257b89..eb19c1cbe 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -78,6 +78,7 @@ "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"] }, From e60820b065d3b8cf51a268faf4d6ad98f4080796 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Wed, 9 Jul 2025 14:18:08 +0100 Subject: [PATCH 25/27] Rename reproductive_history module --- docs/jsonBrowser/module.md | 26 +++++++++---------- docs/jsonBrowser/required_fields.md | 4 +-- .../module/biomaterial/medical_history.json | 8 +++--- ...history.json => reproductive_history.json} | 6 ++--- 4 files changed, 22 insertions(+), 22 deletions(-) rename json_schema/module/biomaterial/{reproduction_history.json => reproductive_history.json} (94%) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index eb15c557d..cda011685 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -513,6 +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 +_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 _Information relating to how a biomaterial was preserved and/or stored over a period of time._ @@ -565,7 +577,7 @@ smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day mu 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 | | +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 @@ -623,18 +635,6 @@ 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 dd580a7c7..aefd876ee 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/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 _There are no required properties in schema Disease profile_ +### Reproductive history +_There are no required properties in schema Reproductive history_ ### Preservation and storage _There are no required properties in schema Preservation and storage_ ### Death @@ -387,8 +389,6 @@ 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/medical_history.json b/json_schema/module/biomaterial/medical_history.json index eb19c1cbe..92642097d 100644 --- a/json_schema/module/biomaterial/medical_history.json +++ b/json_schema/module/biomaterial/medical_history.json @@ -75,11 +75,11 @@ "example": "Should be one of: yes; no.", "bionetworks": ["genetic diversity"] }, - "reproduction_history": { - "description": "Reproduction history of the donor at the time of collection.", + "reproductive_history": { + "description": "Reproductive history of the donor at the time of collection.", "type": "object", - "user_friendly": "Reproduction history", - "$ref": "module/biomaterial/reproduction_history.json", + "user_friendly": "Reproductive history", + "$ref": "module/biomaterial/reproductive_history.json", "bionetworks": ["genetic diversity"] }, "test_results": { diff --git a/json_schema/module/biomaterial/reproduction_history.json b/json_schema/module/biomaterial/reproductive_history.json similarity index 94% rename from json_schema/module/biomaterial/reproduction_history.json rename to json_schema/module/biomaterial/reproductive_history.json index 1a5d29aae..48f47b19c 100644 --- a/json_schema/module/biomaterial/reproduction_history.json +++ b/json_schema/module/biomaterial/reproductive_history.json @@ -1,10 +1,10 @@ { "$schema": "http://json-schema.org/draft-07/schema#", - "description": "Reproduction history of the donor.", + "description": "Reproductive history of the donor.", "additionalProperties": false, "minProperties": 1, - "title": "Reproduction history", - "name": "reproduction_history", + "title": "Reproductive history", + "name": "reproductive_history", "type": "object", "properties": { "describedBy": { From 5f4b27f898f05fe70fa6aa0344b506a64822f96f Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 17 Oct 2025 20:56:17 +0100 Subject: [PATCH 26/27] Added INSDC country enum and region field --- docs/jsonBrowser/module.md | 5 +- json_schema/module/biomaterial/residence.json | 298 +++++++++++++++++- 2 files changed, 296 insertions(+), 7 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index cda011685..551127d83 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -588,8 +588,9 @@ 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 +country | Country of donor's residence. | | no | | Country | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baltic Sea, 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, Indian Ocean, 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, Mediterranean Sea, 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, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, 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, Ross Sea, 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, Southern Ocean, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, 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 +granular_location | Nearest city, town, or village to location of donor's residence. | string | no | | Granular 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 diff --git a/json_schema/module/biomaterial/residence.json b/json_schema/module/biomaterial/residence.json index 7e946253a..31e302a1c 100644 --- a/json_schema/module/biomaterial/residence.json +++ b/json_schema/module/biomaterial/residence.json @@ -24,17 +24,305 @@ "example": "4.6.1" }, "country": { - "description": "Country and state of donor's residence.", - "type": "string", + "description": "Country of donor's residence.", + "enum": [ + "Afghanistan", + "Albania", + "Algeria", + "American Samoa", + "Andorra", + "Angola", + "Anguilla", + "Antarctica", + "Antigua and Barbuda", + "Arctic Ocean", + "Argentina", + "Armenia", + "Aruba", + "Ashmore and Cartier Islands", + "Atlantic Ocean", + "Australia", + "Austria", + "Azerbaijan", + "Bahamas", + "Bahrain", + "Baltic Sea", + "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", + "Indian Ocean", + "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", + "Mediterranean Sea", + "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", + "North Sea", + "Northern Mariana Islands", + "Norway", + "Oman", + "Pacific Ocean", + "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", + "Ross Sea", + "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", + "Southern Ocean", + "Spain", + "Spratly Islands", + "Sri Lanka", + "State of Palestine", + "Sudan", + "Suriname", + "Svalbard", + "Sweden", + "Switzerland", + "Syria", + "Taiwan", + "Tajikistan", + "Tanzania", + "Tasman Sea", + "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" + ], "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.", + "example": "Singapore; United Kingdom; Brazil; Australia; Nigeria", + "bionetworks": ["genetic diversity"] + }, + "region": { + "description": "Region of donor's residence.", + "type": "string", + "user_friendly": "Region", + "example": "Massachusetts; Catalonia; Ondo; Ontario", + "guidelines": "State, province, county, or other first-level administrative division within the country.", "bionetworks": ["genetic diversity"] }, "granular_location": { "description": "Nearest city, town, or village to location of donor's residence.", "type": "string", - "user_friendly": "Location", + "user_friendly": "Granular Location", "example": "Singapore; Cambridge; Boston; Kingston", "bionetworks": ["genetic diversity"] }, From cbca40415c6a10c8abdb12815efe1468997e24d4 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Fri, 17 Oct 2025 21:00:53 +0100 Subject: [PATCH 27/27] Renamed fields to ethnicity_of_parents and to language_of_family in human_specific.json --- docs/jsonBrowser/module.md | 4 ++-- json_schema/module/biomaterial/human_specific.json | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 551127d83..2b472306f 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -433,9 +433,9 @@ 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 | | +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 -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 +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 | | diff --git a/json_schema/module/biomaterial/human_specific.json b/json_schema/module/biomaterial/human_specific.json index c9e141fce..ea95e9e3e 100644 --- a/json_schema/module/biomaterial/human_specific.json +++ b/json_schema/module/biomaterial/human_specific.json @@ -46,7 +46,7 @@ "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": { + "ethnicity_of_parents": { "description": "Ethnicity(-ies) of the donor's parents.", "type": "array", "items": { @@ -66,13 +66,13 @@ "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).", + "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": "Mother/ Father Tongue", + "user_friendly": "Language of family", "example": "Mandarin Chinese; Hokkien; Bahasa Melayu", "bionetworks": ["genetic diversity"] },