Merge pull request #98 from psychoinformatics-de/ex-dats

Example of a converted DATS metadata record

src/examples/dataset-version/DatasetVersionObject-customproperties.json

@@ -0,0 +1,14 @@
+{
+  "properties": [
+    {
+      "label": "Planned Number of Female Subjects",
+      "range": "xsd:nonNegativeInteger",
+      "type": "http://purl.obolibrary.org/obo/NCIT_C90437",
+      "value": [
+        "54"
+      ]
+    }
+  ],
+  "name": "growing-dataset",
+  "@type": "DatasetVersionObject"
+}

src/examples/dataset-version/DatasetVersionObject-customproperties.yaml

@@ -0,0 +1,6 @@
+name: growing-dataset
+properties:
+  - type: http://purl.obolibrary.org/obo/NCIT_C90437
+    label: Planned Number of Female Subjects
+    range: xsd:nonNegativeInteger
+    value: 54

src/examples/dataset-version/DatasetVersionObject-dats.json

@@ -0,0 +1,108 @@
+{
+  "properties": [
+    {
+      "label": "Total number of sessions",
+      "value": [
+        "521"
+      ]
+    },
+    {
+      "label": "logo",
+      "value": [
+        "logo.png"
+      ]
+    },
+    {
+      "label": "CONP_status",
+      "value": [
+        "CONP"
+      ]
+    },
+    {
+      "label": "files",
+      "value": [
+        "3771"
+      ]
+    },
+    {
+      "label": "subjects",
+      "type": "http://purl.obolibrary.org/obo/NCIT_C98703",
+      "value": [
+        "1"
+      ]
+    },
+    {
+      "label": "origin_consortium",
+      "value": [
+        "IBIS"
+      ]
+    },
+    {
+      "label": "origin_institution",
+      "value": [
+        "McGill Centre for Integrative Neuroscience"
+      ]
+    },
+    {
+      "label": "origin_city",
+      "value": [
+        "Montreal"
+      ]
+    },
+    {
+      "label": "origin_province",
+      "value": [
+        "Quebec"
+      ]
+    },
+    {
+      "label": "origin_country",
+      "type": "http://purl.obolibrary.org/obo/HSO_0000360",
+      "value": [
+        "Canada"
+      ]
+    }
+  ],
+  "license": "licenses:CC-BY-ND-4.0",
+  "was_attributed_to": [
+    {
+      "meta_code": "MCIN",
+      "meta_type": "dlco:OrganizationObject",
+      "name": "McGill Center for Integrative Neuroscience"
+    },
+    {
+      "meta_code": "ACEvans",
+      "meta_type": "dlco:ResearchContributorObject",
+      "name": "Alan C. Evans"
+    }
+  ],
+  "was_generated_by": [
+    {
+      "at_location": {
+        "name": "North America",
+        "description": "13 scanners in 6 sites across North America"
+      },
+      "started_at": "2008-04-25T00:00:00",
+      "ended_at": "2019-04-15T00:00:00"
+    }
+  ],
+  "qualified_attribution": [
+    {
+      "agent": "ACEvans",
+      "had_role": [
+        "marcrel:ccp",
+        "marcrel:cre",
+        "marcrel:ldr",
+        "marcrel:rth"
+      ]
+    }
+  ],
+  "description": "Longitudinal brain scans of a single human phantom acquired on multiple MRI devices across North America over a period of 11 years. In addition to the human brain images, lego phantom scans have been acquired in parallel for quality assessments over time across sites.",
+  "keyword": [
+    "phantom",
+    "MRI"
+  ],
+  "title": "Multicenter Single Subject Human MRI Phantom",
+  "version": "2.0",
+  "@type": "DatasetVersionObject"
+}

src/examples/dataset-version/DatasetVersionObject-dats.yaml

@@ -0,0 +1,149 @@
+#
+# DATS-compliant record taken from
+# https://portal.conp.ca/dataset?id=projects/multicenter-phantom
+#
+title: Multicenter Single Subject Human MRI Phantom
+description: >-
+  Longitudinal brain scans of a single human phantom acquired on multiple
+  MRI devices across North America over a period of 11 years. In addition
+  to the human brain images, lego phantom scans have been acquired in
+  parallel for quality assessments over time across sites.
+was_generated_by:
+  # data collection
+  - started_at: "2008-04-25T00:00:00"
+    ended_at: "2019-04-15T00:00:00"
+    at_location:
+      name: North America
+      description: 13 scanners in 6 sites across North America
+was_attributed_to:
+  - meta_type: dlco:OrganizationObject
+    meta_code: MCIN
+    name: McGill Center for Integrative Neuroscience
+  - meta_type: dlco:ResearchContributorObject
+    meta_code: ACEvans
+    name: Alan C. Evans
+qualified_attribution:
+  - agent: ACEvans
+    had_role:
+      # conceptor
+      - marcrel:ccp
+      # creator
+      - marcrel:cre
+      # laboratory director
+      - marcrel:ldr
+      # research team head
+      - marcrel:rth
+#"types": [
+#    {
+#        "information": {
+#            "value": "MRI",
+#            "valueIRI": ""
+#        }
+#    },
+#    {
+#        "information": {
+#            "value": "quality control subject",
+#            "valueIRI": "http://uri.interlex.org/base/ilx_0381893"
+#        }
+#    }
+#],
+version: "2.0"
+#"privacy": "open",
+#"distributions": [
+#    {
+#        "@type": "DatasetDistribution",
+#        "formats": [
+#            "MINC",
+#            "JSON"
+#        ],
+#        "size" : 40,
+#        "unit" : {
+#            "value": "GB"
+#        },
+#        "access" : {
+#            "landingPage" : "https://phantom.loris.ca",
+#                            "authorizations": [
+#                                    {
+#                                            "value": "private"
+#                                    }
+#                            ]
+#        }
+#    }
+#],
+# "isAbout": [
+#     {
+#           "identifier": {
+#                     "identifier": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606",
+#                                     "identifierSource": "NCBI Taxonomy Database"
+#           },
+#           "name":"Homo sapiens"
+#     },
+#     {
+#         "name": "adult"
+#     }
+# ],
+license: licenses:CC-BY-ND-4.0
+# "aggregation": "instance of dataset",
+# "dimensions": [
+#     {
+#         "name" : {
+#             "value": "resting BOLD"
+#         }
+#     },
+#     {
+#         "name" : {
+#             "value": "fieldmap BOLD"
+#         }
+#     },
+#     {
+#         "name" : {
+#             "value": "fieldmap DWI"
+#         }
+#     },
+#     {
+#         "name" : {
+#             "value": "DWI 65 directions"
+#         }
+#     },
+#     {
+#         "name" : {
+#             "value": "DWI 25 directions"
+#         }
+#     },
+#     {
+#         "name" : {
+#             "value": "T1W"
+#         }
+#     },
+#     {
+#         "name" : {
+#             "value": "T2W"
+#         }
+#     }
+# ],
+keyword:
+  - phantom
+  - MRI
+properties:
+  - label: Total number of sessions
+    value: 521
+  - label: logo
+    value: logo.png
+  - label: CONP_status
+    value: CONP
+  - label: files
+    value: 3771
+  - label: subjects
+    type: http://purl.obolibrary.org/obo/NCIT_C98703
+    value: 1
+  - label: origin_consortium
+    value: IBIS
+  - label: origin_institution
+    value: McGill Centre for Integrative Neuroscience
+  - label: origin_city
+    value: Montreal
+  - label: origin_province
+    value: Quebec
+  - label: origin_country
+    type: http://purl.obolibrary.org/obo/HSO_0000360
+    value: Canada

src/linkml/ontology/common.yaml

@@ -10,7 +10,7 @@ prefixes:
   linkml: https://w3id.org/linkml/
   iao: http://purl.obolibrary.org/obo/
   pav: http://purl.org/pav/
-  rdfs: http://www.w3.org/2000/01/rdf-schema#
+  RDFS: http://www.w3.org/2000/01/rdf-schema#
   schema: http://schema.org/
   sio: http://semanticscience.org/resource/
   spdx: http://spdx.org/rdf/terms#
@@ -93,7 +93,7 @@ slots:
     slot_uri: dlco:name
     description: Name of an item or entity.
     exact_mappings:
-      - rdfs:label
+      - RDFS:label
       - schema:name
       - foaf:name
     range: string

src/linkml/ontology/datalad.yaml

@@ -8,7 +8,7 @@ description: >
 prefixes:
   dlco: https://concepts.datalad.org/ontology/
   dcterms: http://purl.org/dc/terms/
-  rdfs: http://www.w3.org/2000/01/rdf-schema#
+  RDFS: http://www.w3.org/2000/01/rdf-schema#
 imports:
   - ../ontology/datasets
   - ../ontology/git

src/linkml/ontology/datasets.yaml

@@ -148,14 +148,6 @@ slots:
     todos:
       - Rename to `named_part`? See also todo for `QualifiedPart`
 
-  type:
-    slot_uri: dlco:type
-    description: >-
-      The nature of the resource.
-    range: string
-    exact_mappings:
-      - dcterms:type
-
   keyword:
     slot_uri: dlco:keyword
     description: >-
@@ -186,9 +178,9 @@ classes:
       - qualified_part
       - relation
       - title
-      - type
       - version
       - was_attributed_to
+      - was_generated_by
     slot_usage:
       has_part:
         range: Resource

src/linkml/ontology/projects.yaml

@@ -9,7 +9,7 @@ prefixes:
   dlco: https://concepts.datalad.org/ontology/
   linkml: https://w3id.org/linkml/
   iao: http://purl.obolibrary.org/obo/
-  rdfs: http://www.w3.org/2000/01/rdf-schema#
+  RDFS: http://www.w3.org/2000/01/rdf-schema#
   schema: http://schema.org/
   spdx: http://spdx.org/rdf/terms#
   reproduceme: https://w3id.org/reproduceme#

src/linkml/ontology/provenance.yaml

@@ -123,6 +123,18 @@ slots:
     notes:
       - we have our own `datetime`, because of a linkml problem with handling the actual one, see https://github.com/linkml/linkml/issues/1806
 
+  started_at:
+    slot_uri: dlco:started_at
+    description: >-
+      Start is when an activity is deemed to have been started by an entity,
+      known as trigger. The activity did not exist before its start.
+      Any usage, generation, or invalidation involving an activity follows
+      the activity's start.
+    domain: Activity
+    range: W3CISO8601
+    exact_mappings:
+      - prov:startedAtTime
+
   # Commit generated_at DateTime (committer time)
   generated_at:
     slot_uri: dlco:generated_at
@@ -218,6 +230,10 @@ classes:
       An activity is something that occurs over a period of time and acts
       upon or with entities; it may include consuming, processing,
       transforming, modifying, relocating, using, or generating entities.
+    slots:
+      - at_location
+      - started_at
+      - ended_at
     exact_mappings:
       - prov:Activity
 
@@ -369,5 +385,8 @@ classes:
       row, or column. As such, there are numerous ways in which location
       can be expressed, such as by a coordinate, address, landmark, and
       so forth.
+    slots:
+      - name
+      - description
     exact_mappings:
       - prov:Location