Release from staging to master 2025-12-15

changelog.md

@@ -9,6 +9,30 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://
 
 ## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
+### [module/biomaterial/medical_history.json - v9.0.0] - 2025-12-15
+### Deprecated
+Deprecated alcohol_history
+
+### [type/biomaterial/specimen_from_organism.json - v11.1.0] - 2025-12-15
+### Added
+Added adjacent_disease_location, indication_for_sampling and radial_tissue_term
+
+### [module/biomaterial/disease_profile.json - v1.1.0] - 2025-12-15
+### Added
+Added PUCAI_score, PCDAI_score and wPCDAI_score
+
+### [module/biomaterial/medical_history.json - v8.3.0] - 2025-12-15
+### Added
+Added alcohol_type, alcohol_usage_duration, alcohol_units, defined_diet, diet_specific and previous_surgeries
+
+### [type/protocol/biomaterial_collection/collection_protocol.json - v9.3.0] - 2025-12-15
+### Added
+Added procedure
+
+### [type/biomaterial/donor_organism.json - v18.2.0] - 2025-12-15
+### Added
+Added PUCAI_score, PCDAI_score and wPCDAI_score
+
 ### [system/file_descriptor.json - v2.2.0] - 2025-11-04
 ### Added
 Added support for compact identifier-based DRS URIs in file descriptors

docs/jsonBrowser/module.md

@@ -512,6 +512,9 @@ copd_cat_score | Indicate the COPD Assessment Test (CAT) score. | integer | no |
 copd_gold_abe_assessment | Indicate the Global Initiative for Chronic Obstructive Lung Disease (GOLD) A, B, C, D assessment group if available. | string | no |  | GOLD ABE assessment | A, B, E | A; B; E
 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 |  | 
+PUCAI_score | Indicate the Pediatric Ulcerative Colitis Activity Index (PUCAI) score if available. | number | no |  | PUCAI score |  | 
+PCDAI_score | Indicate the Pediatric Crohn’s Disease Activity Index (PCDAI) score if available. | number | no |  | PCDAI score |  | 
+wPCDAI_score | Indicate the weighted Pediatric Crohn’s Disease Activity Index (wPCDAI) score if available. | number | no |  | wPCDAI score |  | 
 
 ## Reproductive history<a name='Reproductive history'></a>
 _Reproductive history of the donor._
@@ -570,7 +573,10 @@ Location: module/biomaterial/medical_history.json
 
 Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- | --- 
-alcohol_history | Estimated amount of alcohol consumed per day. | string | no |  | Alcohol history |  | 3-6 alcohol units/day; 1 drink per day
+alcohol_status | Whether the individual is actively consuming, has formerly consumed or has never consumed alcohol beverages | string | no |  | Alcohol status | active, former, never | Should be one of: active, former, never.
+alcohol_type | Types of alcoholic beverages the donor consumed. | array | no |  | Alcohol type |  | beer; liquor; wine
+alcohol_units | Alcohol consumption of donor in alcohol units per week (strength (ABV) x volume (ml) ÷ 1,000). | number | no |  | Alcohol units |  | 2.5; 15.2; 23
+alcohol_usage_duration | Number of years in which the donor consumed alcohol. | integer | no |  | Alcohol usage duration |  | 5
 medication | Medication(s) the individual was taking at time of biomaterial collection. | array | no | [See module  medication_ontology](module.md#medication-ontology) | Medication |  | 
 smoking_status | Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc. | string | no |  | Smoking status | active, former, never | Should be one of: active, former, never.
 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
@@ -580,6 +586,9 @@ diet_meat_consumption | Dietary patterns of donor - meat (chicken, seafood, fish
 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
+previous_surgeries | Previous surgeries the individual has undergone prior to biomaterial collection. | string | no |  | Previous surgeries |  | Appendectomy; Coleostomy; Vaginoplasty; LASIK; Abdominal surgery
+defined_diet | Whether the individual was following a defined diet at the time of biomaterial collection. | boolean | no |  | Defined diet |  | yes; no
+diet_specific | Defined diet the donor was on at the time of biomaterial collection. | array | no |  | Diet Specific | vegan, vegetarian, omnivore, gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo | gluten_free; fodmap; baby_formula; breastfeeding; elimination; keto; paleo
 
 ## Residence<a name='Residence'></a>
 _Donor's residence location information._
@@ -588,7 +597,7 @@ Location: module/biomaterial/residence.json
 
 Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- | --- 
-country_territory | Country or territory of donor's residence. |  | no |  | Country | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, 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, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Line Islands, Lithuania, Luxembourg, Macau, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Federated States of, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Macedonia, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, USA, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | Singapore; United Kingdom; Brazil; Australia; Nigeria
+country_territory | Country or territory of donor's residence. |  | no |  | Country | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Eswatini, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Line Islands, Lithuania, Luxembourg, Macau, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Federated States of, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Macedonia, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, USA, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | Singapore; United Kingdom; Brazil; Australia; Nigeria
 region | Region of donor's residence. | string | no |  | Region |  | Massachusetts; Catalonia; Ondo; Ontario
 locality | Nearest city, town, or village to location of donor's residence. | string | no |  | Locality |  | Singapore; Cambridge; Boston; Kingston
 duration | Duration of residence, in years, rounded up to the nearest whole number. | string | no |  | Duration of residence |  | 20; 37; 45-65

docs/jsonBrowser/type.md

@@ -225,6 +225,7 @@ schema_type | The type of the metadata schema entity. | string | yes |  |  | pro
 provenance | Provenance information provided by the system. | object | no | [See   provenance](.md#provenance) |  |  | 
 protocol_core | Core protocol-level information. | object | yes | [See core  protocol_core](core.md#protocol-core) | Protocol core |  | 
 method | Method used to collect the biomaterial. | object | yes | [See module  process_type_ontology](module.md#process-type-ontology) | Collection method |  | 
+procedure | Procedure used to collect the specimen from the organism. | string | no |  | Procedure |  | colonoscopy; venipuncture; laparoscopic surgery
 reagents | A list of purchased reagents used in this protocol. | array | no | [See module  purchased_reagents](module.md#purchased-reagents) | Protocol reagents |  | 
 
 ## Differentiation protocol
@@ -349,13 +350,16 @@ biomaterial_core | Core biomaterial-level information. | object | yes | [See cor
 genus_species | The scientific binomial name for the species of the specimen. | array | no | [See module  species_ontology](module.md#species-ontology) | Genus species |  | 
 organ | The organ that the biomaterial came from. | object | yes | [See module  organ_ontology](module.md#organ-ontology) | Organ |  | 
 organ_parts | A term for a specific part of the organ that the biomaterial came from. | array | no | [See module  organ_part_ontology](module.md#organ-part-ontology) | Organ part |  | 
+radial_tissue_term | Layer(s) of the gut that was/were sampled. | array | no |  | Radial tissue term | EPI, LP, MLN, MUSC, SUB | EPI; LP; MUSC; SUB; MLN
 transplant_organ | Was the specimen collected after extraction for organ transplantation? | boolean | no |  | Transplant organ |  | yes; no
 diseases | Short description of known disease(s) of the specimen. | array | no | [See module  disease_ontology](module.md#disease-ontology) | Known disease(s) |  | 
 adjacent_diseases | Short description of the disease(s) adjacent to the specimen's collection site (e.g. breast cancer). | array | no | [See module  disease_ontology](module.md#disease-ontology) | Adjacent disease(s) |  | 
+adjacent_disease_location | A term for the specific location of the adjacent disease. | object | no | [See module  organ_ontology](module.md#organ-ontology) | Adjacent disease location |  | 
 state_of_specimen | State of the specimen at the time of collection. | object | no | [See module  state_of_specimen](module.md#state-of-specimen) | State of specimen |  | 
 preservation_storage | Information about how a specimen was preserved and/or stored over a period of time. | object | no | [See module  preservation_storage](module.md#preservation-storage) | Preservation/Storage |  | 
 collection_time | When the biomaterial was collected. | string | no |  | Time of collection |  | 2016-01-21T00:00:00Z; 2016-03
 collection_institute | Institute where the biomaterial was collected on. | object | no | [See module  collection_institute](module.md#collection-institute) | Collection institute |  | 
+indication_for_sampling | The medical reason why a specimen was taken from the donor | string | no |  | Indication For Sampling |  | Suspected cancer; Rejected transplant because of metastasized colon cancer
 purchased_specimen | Information about a purchased specimen. | object | no | [See module  purchased_reagents](module.md#purchased-reagents) | Purchased specimen |  | 
 
 ## Cell suspension

json_schema/module/biomaterial/disease_profile.json

@@ -77,6 +77,27 @@
             "maximum": 150,
             "minimum": 0,
             "bionetworks": ["lung"]
+        },
+        "PUCAI_score": {
+            "user_friendly": "PUCAI score",
+            "description": "Indicate the Pediatric Ulcerative Colitis Activity Index (PUCAI) score if available.",
+            "type": "number",
+            "minimum": 0,
+            "bionetworks": ["gut"]
+        },
+        "PCDAI_score": {
+            "user_friendly": "PCDAI score",
+            "description": "Indicate the Pediatric Crohn’s Disease Activity Index (PCDAI) score if available.",
+            "type": "number",
+            "minimum": 0,
+            "bionetworks": ["gut"]
+        },
+        "wPCDAI_score": {
+            "user_friendly": "wPCDAI score",
+            "description": "Indicate the weighted Pediatric Crohn’s Disease Activity Index (wPCDAI) score if available.",
+            "type": "number",
+            "minimum": 0,
+            "bionetworks": ["gut"]
         }
     }
 }