setup Miappe Showcase with Datamap and script

.gitattributes

+assays/PlantHeightMeasurement/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text
+assays/PlantHeightMeasurement/dataset/Measurement.txt filter=lfs diff=lfs merge=lfs -text

.gitignore

+# ----- macos rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/macOS.gitignore
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+# Icon must end with two \r
+Icon
+# Thumbnails
+._*
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+# ----- windows rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/Windows.gitignore
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+# Dump file
+*.stackdump
+# Folder config file
+[Dd]esktop.ini
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+# Windows shortcuts
+*.lnk
+# ----- linux rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/Linux.gitignore
+*~
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+# KDE directory preferences
+.directory
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*

ro-crate-metadata.json

+{
+  "@context": [
+    "https://w3id.org/ro/crate/1.1/context",
+    {
+      "Sample": "https://bioschemas.org/Sample",
+      "additionalProperty": "http://schema.org/additionalProperty",
+      "intendedUse": "https://bioschemas.org/intendedUse",
+      "computationalTool": "https://bioschemas.org/computationalTool",
+      "labEquipment": "https://bioschemas.org/labEquipment",
+      "reagent": "https://bioschemas.org/reagent",
+      "LabProtocol": "https://bioschemas.org/LabProtocol",
+      "executesLabProtocol": "https://bioschemas.org/executesLabProtocol",
+      "parameterValue": "https://bioschemas.org/parameterValue",
+      "LabProcess": "https://bioschemas.org/LabProcess",
+      "measurementMethod": "http://schema.org/measurementMethod"
+    }
+  ],
+  "@graph": [
+    {
+      "@id": "#CharacteristicValue_organism_Talinum_fruticosum",
+      "@type": "PropertyValue",
+      "additionalType": "CharacteristicValue",
+      "name": "organism",
+      "value": "Talinum fruticosum",
+      "propertyID": "https://bioregistry.io/OBI:0100026",
+      "valueReference": "http://purl.obolibrary.org/obo/NCBITAXON_110664",
+      "columnIndex": "0"
+    },
+    {
+      "@id": "#Source_SourceMaterial",
+      "@type": "Sample",
+      "additionalType": "Source",
+      "name": "SourceMaterial",
+      "additionalProperty": {
+        "@id": "#CharacteristicValue_organism_Talinum_fruticosum"
+      }
+    },
+    {
+      "@id": "#Sample_Plant1",
+      "@type": "Sample",
+      "additionalType": "Sample",
+      "name": "Plant1"
+    },
+    {
+      "@id": "#Protocol_Planting",
+      "@type": "LabProtocol"
+    },
+    {
+      "@id": "#Process_Planting_0",
+      "@type": "LabProcess",
+      "name": "Planting_0",
+      "object": {
+        "@id": "#Source_SourceMaterial"
+      },
+      "result": {
+        "@id": "#Sample_Plant1"
+      },
+      "executesLabProtocol": {
+        "@id": "#Protocol_Planting"
+      }
+    },
+    {
+      "@id": "#Sample_Plant2",
+      "@type": "Sample",
+      "additionalType": "Sample",
+      "name": "Plant2"
+    },
+    {
+      "@id": "#Process_Planting_1",
+      "@type": "LabProcess",
+      "name": "Planting_1",
+      "object": {
+        "@id": "#Source_SourceMaterial"
+      },
+      "result": {
+        "@id": "#Sample_Plant2"
+      },
+      "executesLabProtocol": {
+        "@id": "#Protocol_Planting"
+      }
+    },
+    {
+      "@id": "studies/PlantSetup/",
+      "@type": "Dataset",
+      "additionalType": "Study",
+      "identifier": "PlantSetup",
+      "dateModified": "2025-05-12T11:47:49.0907347",
+      "hasPart": [],
+      "name": "PlantSetup",
+      "about": [
+        {
+          "@id": "#Process_Planting_0"
+        },
+        {
+          "@id": "#Process_Planting_1"
+        }
+      ]
+    },
+    {
+      "@id": "https://bioregistry.io/NCIT:C45253",
+      "@type": "DefinedTerm",
+      "name": "String",
+      "termCode": "https://bioregistry.io/NCIT:C45253"
+    },
+    {
+      "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=1",
+      "@type": "File",
+      "name": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=1",
+      "encodingFormat": "text/plain",
+      "usageInfo": "https://datatracker.ietf.org/doc/html/rfc7111",
+      "about": {
+        "@id": "#Descriptor_assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=1"
+      },
+      "pattern": {
+        "@id": "https://bioregistry.io/NCIT:C45253"
+      }
+    },
+    {
+      "@id": "https://bioregistry.io/NCIT:C45255",
+      "@type": "DefinedTerm",
+      "name": "Integer",
+      "termCode": "https://bioregistry.io/NCIT:C45255"
+    },
+    {
+      "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=2",
+      "@type": "File",
+      "name": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=2",
+      "encodingFormat": "text/plain",
+      "usageInfo": "https://datatracker.ietf.org/doc/html/rfc7111",
+      "about": {
+        "@id": "#Descriptor_assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=2"
+      },
+      "pattern": {
+        "@id": "https://bioregistry.io/NCIT:C45255"
+      }
+    },
+    {
+      "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#row=2",
+      "@type": "File",
+      "name": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#row=2",
+      "encodingFormat": "text/plain",
+      "usageInfo": "https://datatracker.ietf.org/doc/html/rfc7111"
+    },
+    {
+      "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#row=3",
+      "@type": "File",
+      "name": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#row=3",
+      "encodingFormat": "text/plain",
+      "usageInfo": "https://datatracker.ietf.org/doc/html/rfc7111"
+    },
+    {
+      "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt",
+      "@type": "File",
+      "name": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt",
+      "encodingFormat": "text/plain",
+      "hasPart": [
+        {
+          "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=1"
+        },
+        {
+          "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=2"
+        },
+        {
+          "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#row=2"
+        },
+        {
+          "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#row=3"
+        }
+      ]
+    },
+    {
+      "@id": "#Protocol_NewTable0",
+      "@type": "LabProtocol"
+    },
+    {
+      "@id": "#Process_NewTable0_0",
+      "@type": "LabProcess",
+      "name": "NewTable0_0",
+      "object": {
+        "@id": "#Sample_Plant1"
+      },
+      "result": {
+        "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#row=2"
+      },
+      "executesLabProtocol": {
+        "@id": "#Protocol_NewTable0"
+      }
+    },
+    {
+      "@id": "#Process_NewTable0_1",
+      "@type": "LabProcess",
+      "name": "NewTable0_1",
+      "object": {
+        "@id": "#Sample_Plant2"
+      },
+      "result": {
+        "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#row=3"
+      },
+      "executesLabProtocol": {
+        "@id": "#Protocol_NewTable0"
+      }
+    },
+    {
+      "@id": "#Descriptor_assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=1",
+      "@type": "PropertyValue",
+      "name": "FragmentDescriptor",
+      "value": "identifier",
+      "propertyID": "https://github.com/nfdi4plants/ARC-specification/blob/dev/ISA-XLSX.md#datamap-table-sheets",
+      "valueReference": "http://purl.obolibrary.org/obo/ARC_00000120",
+      "subjectOf": {
+        "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=1"
+      }
+    },
+    {
+      "@id": "#Descriptor_assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=2",
+      "@type": "PropertyValue",
+      "name": "FragmentDescriptor",
+      "value": "plant height",
+      "propertyID": "https://github.com/nfdi4plants/ARC-specification/blob/dev/ISA-XLSX.md#datamap-table-sheets",
+      "unitCode": "https://bioregistry.io/UO:0000015",
+      "unitText": "centimeter",
+      "valueReference": "http://purl.obolibrary.org/obo/C_61F3CAE5",
+      "subjectOf": {
+        "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=2"
+      }
+    },
+    {
+      "@id": "assays/PlantHeightMeasurement/",
+      "@type": "Dataset",
+      "additionalType": "Assay",
+      "identifier": "PlantHeightMeasurement",
+      "hasPart": {
+        "@id": "assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt"
+      },
+      "about": [
+        {
+          "@id": "#Process_NewTable0_0"
+        },
+        {
+          "@id": "#Process_NewTable0_1"
+        }
+      ],
+      "variableMeasured": [
+        {
+          "@id": "#Descriptor_assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=1"
+        },
+        {
+          "@id": "#Descriptor_assays/PlantHeightMeasurement/dataset/./assays/PlantHeightMeasurement/dataset/Measurement.txt#col=2"
+        }
+      ]
+    },
+    {
+      "@id": "./",
+      "@type": "Dataset",
+      "additionalType": "Investigation",
+      "identifier": "Miappe_Showcase_ARC",
+      "datePublished": "2025-05-12T11:47:49.0927930",
+      "hasPart": [
+        {
+          "@id": "studies/PlantSetup/"
+        },
+        {
+          "@id": "assays/PlantHeightMeasurement/"
+        }
+      ],
+      "name": "Test ARC",
+      "license": "ALL RIGHTS RESERVED BY THE AUTHORS"
+    },
+    {
+      "@id": "ro-crate-metadata.json",
+      "@type": "CreativeWork",
+      "conformsTo": {
+        "@id": "https://w3id.org/ro/crate/1.1"
+      },
+      "about": {
+        "@id": "./"
+      }
+    }
+  ]
+}
\ No newline at end of file

to_RO-Crate.fsx

+#r "nuget: ARCtrl"
+
+open ARCtrl
+
+let arc = ARC.load(".")
+
+let roCrateMetadata = arc.ToROCrateJsonString(2)
+
+System.IO.File.WriteAllText("ro-crate-metadata.json", roCrateMetadata)
\ No newline at end of file