Doc + entity for raw data

Author: bclenet

provenance_manual/README.md

@@ -13,29 +13,27 @@ This example aims at showing provenance metadata for a study dataset in which se
 .
 ├── dataset_description.json
 ├── derivatives
-│   └── segmentations
+│   └── seg
 │       ├── dataset_description.json
+│       ├── descriptions.tsv
+│       ├── docs
+│       │   └── prov.jsonld
+│       ├── prov
+│       │   ├── provenance.tsv
+│       │   ├── prov-seg_desc-exp1_act.json
+│       │   ├── prov-seg_desc-exp1_soft.json
+│       │   ├── prov-seg_desc-exp2_act.json
+│       │   └── prov-seg_desc-exp2_soft.json
 │       └── sub-001
 │           └── anat
 │               ├── sub-001_space-orig_desc-exp1_dseg.json
 │               ├── sub-001_space-orig_desc-exp1_dseg.nii.gz
 │               ├── sub-001_space-orig_desc-exp2_dseg.json
-│               ├── sub-001_space-orig_desc-exp2_dseg.nii.gz
-│               ├── sub-001_space-orig_desc-exp3_dseg.json
-│               └── sub-001_space-orig_desc-exp3_dseg.nii.gz
-├── docs
-│   └── prov.jsonld
-├── prov
-│   ├── provenance.tsv
-│   ├── prov-seg1_act.json
-│   ├── prov-seg1_soft.json
-│   ├── prov-seg2_act.json
-│   ├── prov-seg2_soft.json
-│   ├── prov-seg3_act.json
-│   └── prov-seg3_soft.json
+│               └── sub-001_space-orig_desc-exp2_dseg.nii.gz
 ├── README.md
 └── sourcedata
     └── raw
+        ├── dataset_description.json
         ├── participants.tsv
         └── sub-001
             └── anat

provenance_manual/derivatives/seg/dataset_description.json

@@ -7,6 +7,9 @@
     "Boris Clénet"
   ],
   "DatasetLinks": {
-    "raw": "../../sourcedata/raw",
-  }
+    "raw": "../../sourcedata/raw"
+  },
+  "GeneratedBy": [
+    {"Name": ""}
+  ]
 }

provenance_manual/docs/prov.jsonld renamed to provenance_manual/derivatives/seg/docs/prov.jsonld

@@ -14,12 +14,6 @@
         "Label": "ITK-SNAP",
         "Version": "4.4.0",
         "AltIdentifier": "RRID:SCR_002010"
-      },
-      {
-        "Id": "bids::prov#itksnap-zz55eds6",
-        "Label": "ITK-SNAP",
-        "Version": "4.4.0",
-        "AltIdentifier": "RRID:SCR_002010"
       }
     ],
     "Activities": [
@@ -44,20 +38,27 @@
         "Used": [
           "bids:raw:sub-001/anat/sub-001_T1w.nii.gz"
         ]
+      }
+    ],
+    "ProvEntities": [
+      {
+        "Id": "bids:raw:sub-001/anat/sub-001_T1w.nii.gz",
+        "Label": "sub-001/anat/sub-001_T1w.nii.gz",
+        "AtLocation": "../../sourcedata/raw/sub-001/anat/sub-001_T1w.nii.gz"
       },
       {
-        "Id": "bids::prov#segmentation-af6s5v2d",
-        "Label": "Semi-automatic brain segmentation",
-        "Command": "itk-snap sourcedata/raw/sub-001/anat/sub-001_T1w.nii.gz",
-        "AssociatedWith": [
-          "bids::prov#itksnap-zz55eds6"
-        ],
-        "Used": [
-          "bids:raw:sub-001/anat/sub-001_T1w.nii.gz"
-        ]
+        "Id": "bids::sub-001/anat/sub-001_space-orig_desc-exp1_dseg.nii.gz",
+        "Label": "sub-001_space-orig_desc-exp1_dseg.nii.gz",
+        "AtLocation": "sub-001/anat/sub-001_space-orig_desc-exp1_dseg.nii.gz",
+        "GeneratedBy": "bids::prov#segmentation-nO5RGsrb"
+      },
+      {
+        "Id": "bids::sub-001/anat/sub-001_space-orig_desc-exp2_dseg.nii.gz",
+        "Label": "sub-001_space-orig_desc-exp2_dseg.nii.gz",
+        "AtLocation": "sub-001/anat/sub-001_space-orig_desc-exp2_dseg.nii.gz",
+        "GeneratedBy": "bids::prov#segmentation-mOOypIYB"
       }
     ],
-    "ProvEntities": [],
     "Environments": []
   }
 }

provenance_manual/derivatives/seg/docs/prov.png

@@ -0,0 +1,9 @@
+{
+  "ProvEntities": [
+  	{
+      "Id": "bids:raw:sub-001/anat/sub-001_T1w.nii.gz",
+      "Label": "sub-001/anat/sub-001_T1w.nii.gz",
+      "AtLocation": "../../sourcedata/raw/sub-001/anat/sub-001_T1w.nii.gz"
+    }
+  ]
+}

provenance_manual/derivatives/seg/prov/prov-seg_ent.json

@@ -1,3 +1,3 @@
 {
-  "GeneratedBy": "bids:study:prov#segmentation-nO5RGsrb"
+  "GeneratedBy": "bids::prov#segmentation-nO5RGsrb"
 }

provenance_manual/derivatives/seg/sub-001/anat/sub-001_space-orig_desc-exp1_dseg.json

@@ -1,3 +1,3 @@
 {
-  "GeneratedBy": "bids:study:prov#segmentation-mOOypIYB"
+  "GeneratedBy": "bids::prov#segmentation-mOOypIYB"
 }