Add DATS

Signed-off-by: Juan Cruz Viotti <[email protected]>

DEPENDENCIES

@@ -46,3 +46,4 @@ geojson-1-0-2 https://github.com/geojson/schema v1.0.2
 geojson-1-0-1 https://github.com/geojson/schema v1.0.1
 geojson-1-0-0 https://github.com/geojson/schema v1.0.0
 hca-metadata-5-0-0 https://github.com/HumanCellAtlas/metadata-schema 5.0.0
+dats-1-0-0 https://github.com/datatagsuite/schema 1.0.0

configuration.json

@@ -140,6 +140,12 @@
     "humancellatlas/metadata": {
       "title": "Human Cell Atlas Metadata Schema",
       "github": "humancellatlas/metadata-schema"
+    },
+    "dats": {
+      "title": "Data Tag Suite (DATS)",
+      "description": "A data model for describing datasets",
+      "github": "datatagsuite",
+      "website": "https://datatagsuite.github.io/docs/html"
     }
   },
   "schemas": {
@@ -345,6 +351,10 @@
     "humancellatlas/metadata/v5.0.0": {
       "base": "https://schema.humancellatlas.org",
       "path": "./vendor/hca-metadata-5-0-0/json_schema"
+    },
+    "dats/v1.0.0": {
+      "base": "https://w3id.org/dats/schema",
+      "path": "./vendor/dats-1-0-0"
     }
   }
 }

vendor/dats-1-0-0.mask

@@ -0,0 +1,2 @@
+README.md
+proposed_extensions_to_DATS.md

vendor/dats-1-0-0/ConsentInformationAndLicense.md

@@ -0,0 +1,23 @@
+### Proposed solution for dealing with Consent Information, Licenses and their relationship
+
+This document describes the proposed changes to the DATS schemas to deal with the
+description of consent information and how this impacts in the license information.
+
+#### Creation of a consent_info_schema.json 
+
+The proposal is to create a new entity for encapsulating the consent information associated
+with entities in a dataset, such as a subject (represented with an object compliant with the
+material_schema.json) and a study group (e.g. to indicate a dbGAP consent group).
+
+Thus, it is possible to represent the consent information for patients and for groups of patients.
+
+The consent information points to the derived license, which contains information about data use conditions.
+
+This solution is an alternative of including the consent information directly in the license, 
+following a separation of concerns between consent and data use conditions. 
+
+The relationship between material and study groups to the license comes through the consent information.
+
+#### Extension of the license_schema.json:
+
+The license schema is extended with the data use conditions. The directionality of 

vendor/dats-1-0-0/access_schema.json

@@ -0,0 +1,89 @@
+{
+  "id": "https://w3id.org/dats/schema/access_schema.json",
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "DATS access schema",
+  "description": "Information about resources that provide the means to obtain an asset (a dataset or other research object).",
+  "type": "object",
+  "properties": {
+    "@context": {
+      "description": "The JSON-LD context",
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "object"
+        },
+        {
+          "type": "array"
+        }
+      ]
+    },
+   "@id": {
+      "description": "The JSON-LD identifier",
+      "type": "string",
+      "format": "uri"
+    },
+    "@type": {
+      "description": "The JSON-LD type",
+      "type": "string",
+      "enum": [ "Access" ]
+    },
+    "identifier": {
+      "description": "The identifier of the access entity.",
+      "$ref": "identifier_info_schema.json#"
+    },
+    "alternateIdentifiers": {
+      "type": "array",
+      "items": {
+        "$ref": "alternate_identifier_info_schema.json#"
+      }
+    },
+    "relatedIdentifiers": {
+      "type": "array",
+      "items": {
+        "$ref": "related_identifier_info_schema.json#"
+      }
+    },
+    "landingPage": {
+      "description": "A web page that contains information about the associated dataset or other research object and a direct link to the object itself.",
+      "type": "string",
+      "format": "uri"
+    },
+    "accessURL": {
+      "description": "A URL from which the resource (dataset or other research object) can be retrieved, i.e. a direct link to the object itself.",
+      "type": "string",
+      "format": "uri"
+    },
+    "types": {
+      "description": "Method to obtain the resource, ideally specified from a controlled vocabulary or ontology.",
+      "type": "array",
+      "items": {
+        "$ref": "annotation_schema.json#"
+      }
+    },
+    "authorizations": {
+      "description": "Types of verification that accessing the resource is allowed. Authorization occurs before successful authentication and refers to the process of obtaining approval to use a data set. Ideally specified from a controlled vocabulary or ontology.",
+      "type": "array",
+      "items": {
+        "$ref": "annotation_schema.json#"
+      }
+    },
+    "authentications": {
+      "description": "Types of verification of the credentials for accessing the resource, it is the identification process at the time of access. ideally specified from a controlled vocabulary or ontology.",
+      "type": "array",
+      "items": {
+        "$ref": "annotation_schema.json#"
+      }
+    },
+    "extraProperties": {
+      "description": "Extra properties that do not fit in the previous specified attributes. ",
+      "type": "array",
+      "items": {
+        "$ref" : "category_values_pair_schema.json#"
+      }
+    }
+  },
+  "additionalProperties": false,
+  "required": [ "landingPage" ]
+}

vendor/dats-1-0-0/activity_schema.json

@@ -0,0 +1,125 @@
+{
+  "id": "https://w3id.org/dats/schema/activity_schema.json",
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "DATS activity (or process) schema.",
+  "description": "A type of process scheduled in a study.",
+  "type": "object",
+  "properties": {
+    "@context": {
+      "description": "The JSON-LD context",
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "object"
+        },
+        {
+          "type": "array"
+        }
+      ]
+    },
+    "@id": {
+      "description": "The JSON-LD identifier",
+      "type": "string", "format": "uri" },
+    "@type": {
+      "description": "The JSON-LD type",
+      "type": "string", "enum": [ "Activity" ]
+    },
+    "identifier": {
+      "description": "The identifier of the activity.",
+      "$ref": "identifier_info_schema.json#"
+    },
+    "alternateIdentifiers": {
+      "description": "Alternate identifiers for the activity.",
+      "type": "array",
+      "items": {
+        "$ref": "alternate_identifier_info_schema.json#"
+      }
+    },
+    "relatedIdentifiers": {
+      "description": "Related identifiers for the activity.",
+      "type": "array",
+      "items": {
+        "$ref": "related_identifier_info_schema.json#"
+      }
+    },
+    "name": {
+      "description": "The name of the activity, usually one sentece or short description of the activity.",
+      "type" :  "string"
+    },
+    "description" : {
+      "description": "A textual narrative comprised of one or more statements describing the activity.",
+      "type" : "string"
+    },
+    "startDate": {
+      "description": "A timestamp to record the starting point of the activity.",
+      "$ref": "date_info_schema.json#"
+    },
+    "endDate": {
+      "description": "A timestamp to record the end point of the activity.",
+      "$ref": "date_info_schema.json#"
+    },
+    "dates" : {
+      "description": "Relevant dates for the datasets, a date must be added, e.g. creation date or last modification date should be added.",
+      "type" : "array",
+      "items" : {
+        "$ref" : "date_info_schema.json#"
+      }
+    },
+    "duration": {
+      "description": "The time during which the activity takes place.",
+      "type" :  "string"
+    },
+    "location" : {
+      "description": "The location where the activity takes place.",
+      "$ref" : "place_schema.json#"
+    },
+    "performedBy" : {
+      "description": "The person(s) or organisation(s) responsible for executing the process.",
+      "type" : "array",
+      "items" : {
+        "anyOf": [
+          {"$ref" : "person_schema.json#"},
+          {"$ref" : "organization_schema.json#"}
+        ]
+      }
+    },
+    "keywords": {
+      "description": "Tags associated with the activity, which will help in its discovery.",
+      "type": "array",
+      "items": {
+        "$ref" : "annotation_schema.json#"
+      }
+    },
+    "input" : {
+      "description": "The entities used as input.",
+      "type": "array",
+      "items":{
+        "anyOf": [
+          {"$ref" : "dataset_schema.json#"},
+          {"$ref" : "material_schema.json#"}
+        ]
+      }
+    },
+    "output" : {
+      "description": "The entities resulting from applying the activity.",
+      "type": "array",
+      "items":{
+        "anyOf": [
+          {"$ref" : "dataset_schema.json#"},
+          {"$ref" : "material_schema.json#"}
+        ]
+      }
+    },
+    "extraProperties": {
+      "description": "Extra properties that do not fit in the previous specified attributes. ",
+      "type": "array",
+      "items": {
+        "$ref" : "category_values_pair_schema.json#"
+      }
+    }
+  },
+  "additionalProperties": false,
+  "required": [ "name" ]
+}

vendor/dats-1-0-0/alternate_identifier_info_schema.json

@@ -0,0 +1,39 @@
+{
+  "id": "https://w3id.org/dats/schema/alternate_identifier_info_schema.json",
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "DATS alternate identifier information schema",
+  "description": "Information about an alternate identifier (other than the primary).",
+  "type": "object",
+  "properties": {
+    "@context": {
+      "description": "The JSON-LD context",
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "object"
+        },
+        {
+          "type": "array"
+        }
+      ]
+    },
+    "@id": {
+      "description": "The JSON-LD identifier",
+      "type": "string", "format": "uri"
+    },
+    "@type": {
+      "description": "The JSON-LD type",
+      "type": "string", "enum": [ "AlternateIdentifier" ]},
+    "identifier": {
+      "description": "An identifier or identifiers other than the primary Identifier applied to the resource being registered. (definition from DataCite)",
+      "type" : "string"
+    },
+    "identifierSource": {
+      "description": "The identifier source represents information about the organisation/namespace responsible for minting the identifiers. It must be provided if the identifier is provided.",
+      "type" : "string"
+    }
+  },
+  "additionalProperties": false
+}

vendor/dats-1-0-0/anatomical_part_schema.json

@@ -0,0 +1,60 @@
+{
+  "id": "https://w3id.org/dats/schema/anatomical_part_schema.json",
+  "$schema": "http://json-schema.org/draft-04/schema",
+  "title": "DATS anatomical part schema",
+  "description": "A structure that is part of a multicellular organism.",
+  "type": "object",
+  "properties": {
+    "@context": {
+      "description": "The JSON-LD context",
+      "anyOf": [
+        {
+          "type": "string"
+        },
+        {
+          "type": "object"
+        },
+        {
+          "type": "array"
+        }
+      ]
+    },
+    "@id": {
+      "description": "The JSON-LD identifier",
+      "type": "string", "format": "uri" },
+    "@type": {
+      "description": "The JSON-LD type",
+      "type": "string", "enum": [ "AnatomicalPart" ]},
+    "identifier": {
+      "description": "The identifier of the anatomical part.",
+      "$ref": "identifier_info_schema.json#"
+    },
+    "alternateIdentifiers": {
+      "description": "Alternate identifiers for the anatomical part.",
+      "type": "array",
+      "items": {
+        "$ref": "alternate_identifier_info_schema.json#"
+      }
+    },
+    "relatedIdentifiers": {
+      "description": "Related identifiers for the anatomical part.",
+      "type": "array",
+      "items": {
+        "$ref": "related_identifier_info_schema.json#"
+      }
+    },
+    "name": {
+      "description": "The name of the anatomical entity or anatomical part.",
+      "type" :  "string"
+    },
+    "extraProperties": {
+      "description": "Extra properties that do not fit in the previous specified attributes. ",
+      "type": "array",
+      "items": {
+        "$ref" : "category_values_pair_schema.json#"
+      }
+    }
+  },
+  "additionalProperties": false,
+  "required" : [ "name" ]
+}