Added data_access module for managed access data. Fixes #1535

docs/jsonBrowser/module.md

@@ -104,6 +104,17 @@ text | The primary role of the contributor in the project. | string | yes |  | C
 ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Contributor role ontology ID |  | EFO:0009736; EFO:0009741
 ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Contributor role ontology label |  | principal investigator; experimental scientist
 
+## Data access<a name='Data access'></a>
+_A term that may be associated with a data use restriction ontology term._
+
+Location: module/ontology/data_access_ontology.json
+
+Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example 
+--- | --- | --- | --- | --- | --- | --- | --- 
+text | Type of data access permissions associated with the project. | string | yes |  | Data access type |  | No restriction 
+ontology | An ontology term identifier in the form prefix:accession. | string | no |  | Data access ontology ID | DUO:0000004, DUO:0000046, DUO:0000042 | DUO:0000004
+ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no |  | Data access ontology label |  | no restriction
+
 ## Ethnicity ontology<a name='Ethnicity ontology'></a>
 _A term that may be associated with a ethnicity-related ontology term._
 

docs/jsonBrowser/required_fields.md

@@ -147,6 +147,7 @@ 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_access | Information about the data access type for the project. | object | [See module  data_access_ontology](module.md#data-access-ontology) | Data access |  | 
 ### Specimen from organism
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
@@ -239,6 +240,10 @@ text | The name of a library amplification approach being used. | string |  | Li
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
 text | The primary role of the contributor in the project. | string |  | Contributor role |  | principal investigator; experimental scientist
+### Data access<a name='Data access'></a>
+Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
+--- | --- | --- | --- | --- | --- | --- 
+text | Type of data access permissions associated with the project. | string |  | Data access type |  | No restriction 
 ### Ethnicity ontology<a name='Ethnicity ontology'></a>
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 

docs/jsonBrowser/type.md

@@ -326,6 +326,7 @@ 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_access | Information about the data access type for the project. | object | yes | [See module  data_access_ontology](module.md#data-access-ontology) | Data access |  | 
 
 ## Specimen from organism
 _Information about the specimen that was collected from the donor organism._

json_schema/module/ontology/data_access_ontology.json

@@ -0,0 +1,48 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "description": "A term that may be associated with a data use restriction ontology term.",
+    "additionalProperties": false,
+    "required": [
+        "text"
+    ],
+    "title": "Data access",
+    "name": "data_access_ontology",
+    "type": "object",
+    "properties": {
+        "describedBy":  {
+            "description": "The URL reference to the schema.",
+            "type": "string",
+            "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/ontology/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/data_access_ontology"
+        },
+        "schema_version": {
+            "description": "The version number of the schema in major.minor.patch format.",
+            "type": "string",
+            "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
+            "example": "4.6.1"
+        },
+        "text": {
+            "description": "Type of data access permissions associated with the project.",
+            "type": "string",
+            "user_friendly": "Data access type",
+            "example": "No restriction "
+        },
+        "ontology": {
+            "description": "An ontology term identifier in the form prefix:accession.",
+            "type": "string",
+                 "enum": [
+                     "DUO:0000004",
+                     "DUO:0000046",
+                     "DUO:0000042"
+                 ],
+            "user_friendly": "Data access ontology ID",
+            "guidelines": "Must be one of: DUO:0000004, DUO:0000046, DUO:0000042",
+            "example": "DUO:0000004"
+        },
+        "ontology_label": {
+            "description": "The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field.",
+            "type": "string",
+            "user_friendly": "Data access ontology label",
+            "example": "no restriction"
+        }
+    }
+}

json_schema/property_migrations.json

@@ -1,5 +1,12 @@
 {
     "migrations": [
+        {
+            "source_schema": "project",
+            "property": "data_access",
+            "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/project/project.json

@@ -6,7 +6,8 @@
         "describedBy",
         "schema_type",
         "project_core",
-        "funders"
+        "funders",
+        "data_access"
     ],
     "title": "Project",
     "name": "project",
@@ -164,6 +165,12 @@
             "type": "integer",
             "example": "10000; 2100000",
             "user_friendly": "Estimated cell count"
+        },
+        "data_access": {
+            "description": "Information about the data access type for the project.",
+            "type": "object",
+            "$ref": "module/ontology/data_access_ontology.json",
+            "user_friendly": "Data access"
         }
     }
 }

json_schema/update_log.csv

@@ -1 +1,3 @@
 Schema,Change type,Change message,Version,Date
+type/project/project,major,"Added data_access field",,
+module/ontology/data_access_ontology,major,"Added data access type ontology module",,

json_schema/versions.json

@@ -37,6 +37,7 @@
                 "cell_type_ontology": "5.3.6",
                 "cellular_component_ontology": "1.0.5",
                 "contributor_role_ontology": "2.0.0",
+                "data_access_ontology": "0.0.0",
                 "development_stage_ontology": "5.3.6",
                 "disease_ontology": "5.4.0",
                 "enrichment_ontology": "1.2.6",
@@ -137,4 +138,4 @@
             }
         }
     }
-}
+}