Added transplant_organ field in specimen_from_organism. Fixes #1547

changelog.md

@@ -6,11 +6,8 @@ Starting after v5.0.0 release, updates will be declared for schemas independentl
 and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). Unreleased changes may be indicated under the `Unreleased` heading.
 
 ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging)
-## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
-### [type/project/project.json - v18.0.0] - 2024-03-04
-### Added
-Added data_use_restriction field
+## [Released](https://github.com/HumanCellAtlas/metadata-schema/)
 
 ### [type/protocol/analysis/analysis_protocol.json - v10.2.0] - 2024-02-05
 ### Added

docs/jsonBrowser/required_fields.md

@@ -147,7 +147,6 @@ Property name | Description | Type | Object reference? | User friendly name | Al
 schema_type | The type of the metadata schema entity. | string |  |  | project | 
 project_core | Core project-level information. | object | [See core  project_core](core.md#project-core) | Project core |  | 
 funders | Funding source(s) supporting the project. | array | [See module  funder](module.md#funder) | Funding source(s) |  | 
-data_use_restriction | Data use restrictions that apply to the project. | string |  | Data use restriction | NRES, GRU, GRU-NCU | GRU
 ### Specimen from organism
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 

docs/jsonBrowser/type.md

@@ -327,7 +327,6 @@ insdc_study_accessions | An International Nucleotide Sequence Database Collabora
 biostudies_accessions | A BioStudies study accession. | array | no |  | BioStudies accession |  | S-EXMP1; S-HCAS33
 funders | Funding source(s) supporting the project. | array | yes | [See module  funder](module.md#funder) | Funding source(s) |  | 
 estimated_cell_count | An estimated number of cells in this project | integer | no |  | Estimated cell count |  | 10000; 2100000
-data_use_restriction | Data use restrictions that apply to the project. | string | yes |  | Data use restriction | NRES, GRU, GRU-NCU | GRU
 
 ## Specimen from organism
 _Information about the specimen that was collected from the donor organism._
@@ -342,6 +341,7 @@ 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 |  | 
+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) |  | 
 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 |  | 

json_schema/property_migrations.json

@@ -1,12 +1,5 @@
 {
     "migrations": [
-        {
-            "source_schema": "project",
-            "property": "data_use_restriction",
-            "effective_from": "18.0.0",
-            "reason": "Data access is now recorded as a mandatory field",
-            "type": "new required property"
-        },
         {
             "source_schema": "cell_line",
             "property": "timecourse",

json_schema/type/biomaterial/specimen_from_organism.json

@@ -65,6 +65,13 @@
             "guidelines": "The term organ part is very broadly defined here.",
             "user_friendly": "Organ part"
         },
+        "transplant_organ": {
+            "description": "Was the specimen collected after extraction for organ transplantation?",
+            "type": "boolean",
+            "user_friendly": "Transplant organ",
+            "guidelines": "Should be one of: yes, or no.",
+            "example": "yes; no"
+        },
         "diseases": {
             "description": "Short description of known disease(s) of the specimen.",
             "type": "array",

json_schema/type/project/project.json

@@ -6,8 +6,7 @@
         "describedBy",
         "schema_type",
         "project_core",
-        "funders",
-        "data_use_restriction"
+        "funders"
     ],
     "title": "Project",
     "name": "project",
@@ -165,18 +164,6 @@
             "type": "integer",
             "example": "10000; 2100000",
             "user_friendly": "Estimated cell count"
-        },
-        "data_use_restriction": {
-            "description": "Data use restrictions that apply to the project.",
-            "type": "string",
-            "enum": [
-                "NRES",
-                "GRU",
-                "GRU-NCU"
-            ],
-            "user_friendly": "Data use restriction",
-            "guidelines": "Must be one of: NRES, GRU, GRU-NCU. The use restriction codes are based on the DUO ontology where NRES corresponds to DUO:0000004, GRU corresponds to DUO:0000042, GRU-NCU corresponds to a combination of DUO:0000042 and DUO:0000046",
-            "example": "GRU"
         }
     }
 }

json_schema/update_log.csv

@@ -1 +1,2 @@
 Schema,Change type,Change message,Version,Date
+type/biomaterial/specimen_from_organism,minor,Added transplant_organ field in specimen_from_organism Fixes#1547",,

json_schema/versions.json

@@ -1,5 +1,5 @@
 {
-    "last_update_date": "2024-03-04T14:00:53Z",
+    "last_update_date": "2024-02-05T16:10:39Z",
     "version_numbers": {
         "core": {
             "biomaterial": {
@@ -110,7 +110,7 @@
                 "process": "9.2.0"
             },
             "project": {
-                "project": "18.0.0"
+                "project": "17.1.1"
             },
             "protocol": {
                 "analysis": {