add example roc metadata

Add a draft for example roc metadata for the fixed script example

.arc/roc-metadata-fixed-script.json

+{ "@context": "https://w3id.org/ro/crate/1.1/context",
+  "@graph": [
+    {
+      "@type": "CreativeWork",
+      "@id": "ro-crate-metadata.json",
+      "conformsTo": { "@id": "https://w3id.org/ro/crate/1.1" },
+      "about": { "@id": "./" }
+    },
+    {
+      "@id": "./workflows",
+      "@type": "Dataset",
+      "hasPart": [
+        { "@id": "workflows/workflow.cwl" }
+      ]
+    },
+    {
+      "@id": "workflows/workflow.cwl",
+      "@type": [ "File", "SoftwareSourceCode", "ComputationalWorkflow" ],
+      "conformsTo": { "@id": "https://bioschemas.org/profiles/ComputationalWorkflow/0.5-DRAFT-2020_07_21/" },
+      "name": "Column Addition",
+      "programmingLanguage": [
+        { "@id": "#FSharp" },
+        { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl" }
+      ],
+      "creator": { "@id": "#timo" },
+      "dateCreated": "2024-02-05",
+      "input": [
+        { "@id": "#1" },
+        { "@id": "#2" }
+      ],
+      "output": [
+        { "@id": "#3" }
+      ]
+    },
+    {
+      "@id": "#1",
+      "@type": "FormalParameter",
+      "conformsTo": { "@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/" },
+      "name": "intensity_table",
+      "valueRequired": true,
+      "additionalType": { "@id": "http://edamontology.org/data_2976" },
+      "format": { "@id": "http://edamontology.org/format_3752" }
+    },
+    {
+      "@id": "#2",
+      "@type": "FormalParameter",
+      "conformsTo": { "@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/" },
+      "name": "file_name"
+    },
+    {
+      "@id": "#3",
+      "@type": "FormalParameter",
+      "conformsTo": { "@id": "https://bioschemas.org/profiles/FormalParameter/0.1-DRAFT-2020_07_21/" },
+      "name": "summed_intensities",
+      "additionalType": { "@id": "http://edamontology.org/data_2976" },
+      "encodingFormat": { "@id": "http://edamontology.org/format_3475" }
+    },
+    {
+      "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl",
+      "@type": "computerlanguage",
+      "name": "common workflow language",
+      "alternatename": "cwl",
+      "identifier": {
+        "@id": "https://w3id.org/cwl/v1.2/"
+      },
+      "url": {
+        "@id": "https://www.commonwl.org/"
+      }
+    },
+    {
+      "@id": "#FSharp",
+      "@type": "ProgrammingLanguage",
+      "name": "F Sharp",
+      "alternateName": "F#",
+      "url": "https://dotnet.microsoft.com/en-us/languages/fsharp",
+      "version": "6.0"
+    },
+    {
+      "@id": "#timo",
+      "@type": "Person",
+      "name": "Timo Mühlhaus"
+    },
+    {
+      "@id": "http://edamontology.org/format_3752",
+      "@type": "Thing",
+      "name": "Comma-separated values"
+    },
+    {
+      "@id": "http://edamontology.org/format_3475",
+      "@type": "Thing",
+      "name": "Tab-separated values"
+    },
+    {
+      "@id": "./arc/runs",
+      "@type": "Dataset",
+      "hasPart": [
+        { "@id": "runs" }
+      ]
+    },
+    {
+      "@id": "runs",
+      "@type": [ "File", "SoftwareSourceCode", "ComputationalWorkflow" ],
+      "conformsTo": { "@id": "https://bioschemas.org/profiles/ComputationalWorkflow/0.5-DRAFT-2020_07_21/" },
+      "name": "Column Addition",
+      "programmingLanguage": [
+        { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#cwl" }
+      ],
+      "creator": { "@id": "#timo" },
+      "dateCreated": "2024-02-05",
+      "about": [
+        {
+          "@id": "#Process_script.fsx",
+          "@type": [
+            "Process"
+          ],
+          "name": "script.fsx",
+          "parameterValues": [
+            {
+              "@id": "ARCtrl.Json.PropertyValue+ROCrate+genID@16[ARCtrl.Process.ProcessParameterValue]/{Name = \"Data Transformation\"}Some(Ontology\n  {Name = \"Addition\"; TSR = \"NCIT\"; TAN = \"http://purl.obolibrary.org/obo/NCIT_C64911\"})",
+              "@type": "PropertyValue",
+              "additionalType": "ProcessParameterValue",
+              "category": "Data Transformation",
+              "value": "Addition",
+              "valueCode": "http://purl.obolibrary.org/obo/NCIT_C64911",
+              "@context": {
+                "sdo": "http://schema.org/",
+                "additionalType": "sdo:additionalType",
+                "category": "sdo:name",
+                "categoryCode": "sdo:propertyID",
+                "value": "sdo:value",
+                "valueCode": "sdo:valueReference",
+                "unit": "sdo:unitText",
+                "unitCode": "sdo:unitCode",
+                "comments": "sdo:disambiguatingDescription"
+              }
+            }
+          ],
+          "inputs": [
+            {
+              "@id": "./arc/assays/measurement1/dataset/table.csv",
+              "@type": [
+                "Data"
+              ],
+              "name": "./arc/assays/measurement1/dataset/table.csv",
+              "type": "Raw Data File",
+              "@context": {
+                "sdo": "http://schema.org/",
+                "Data": "sdo:MediaObject",
+                "type": "sdo:disambiguatingDescription",
+                "name": "sdo:name",
+                "comments": "sdo:comment"
+              }
+            }
+          ],
+          "outputs": [
+            {
+              "@id": "./arc/runs/fsResult1/result.csv",
+              "@type": [
+                "Data"
+              ],
+              "name": "./arc/runs/fsResult1/result.csv",
+              "type": "Derived Data File",
+              "@context": {
+                "sdo": "http://schema.org/",
+                "Data": "sdo:MediaObject",
+                "type": "sdo:disambiguatingDescription",
+                "name": "sdo:name",
+                "comments": "sdo:comment"
+              }
+            }
+          ],
+          "@context": {
+            "sdo": "http://schema.org/",
+            "bio": "https://bioschemas.org/",
+            "Process": "bio:LabProcess",
+            "name": "sdo:name",
+            "executesProtocol": "bio:executesLabProtocol",
+            "parameterValues": "bio:parameterValue",
+            "performer": "sdo:agent",
+            "date": "sdo:endTime",
+            "inputs": "sdo:object",
+            "outputs": "sdo:result",
+            "comments": "sdo:disambiguatingDescription"
+          }
+        }
+      ]
+    }
+  ]
+}

[Caroline Ott]

I think we could reference the workflow used in that run here (hasPart), what do you think?

[Heinrich Lukas Weil]

Not sure whether hasPart would be okay here, given it being used to depict filesystem structure in RO-Crate. (Although I agree that it would make sense)

An alternative would be about. This way the relationship assay -> process would be equivalent to run -> workflow.

[Caroline Ott]

@wetzels would you also add it to the about section or do you think hasPart could be ok?

[Florian Wetzels]

I need to have a closer look into this. But first: I would disagree that assay->process is equivalent to run->workflow. Can you elaborate on this @weil?

Now some general question: what are you describing here? To me, it looks like an ro-crate for the workflow/run part of an arc only. Everything else is missing, right? Did you use any of the existing work on workflow-run profiles for ro-crate (https://www.researchobject.org/workflow-run-crate/)?

[Caroline Ott]

Whats currently described here is the general workflow in the arc, and the specific inputs used to create the result in the runs folder of the arc. The profile describing the workflow can be found here (CWL), and the execution part is based on that profile.

[Heinrich Lukas Weil]

Is this runs or a specific run, aka something like runs/ColumnAddition?

[Caroline Ott]

Yes, in this basic example it was just "runs" so far. But naming it makes more sense

[Heinrich Lukas Weil]

Also F#?

[Caroline Ott]

F# is already referenced in the workflow. We could reference it in both, or just the part where it is specified that it is F#