diff --git a/docs/profiles/0.1-DRAFT/process_run_crate.md b/docs/profiles/0.1-DRAFT/process_run_crate.md
index 66dfeea..ecfc2e1 100644
--- a/docs/profiles/0.1-DRAFT/process_run_crate.md
+++ b/docs/profiles/0.1-DRAFT/process_run_crate.md
@@ -21,13 +21,21 @@ By "implicit workflow" we mean that the composition of these tools may have been
This profile requires the indication of [Software used to create files](https://www.researchobject.org/ro-crate/1.1/provenance.html#software-used-to-create-files), namely a [SoftwareApplication](http://schema.org/SoftwareApplication) (the tool) and a [CreateAction](http://schema.org/CreateAction) (the execution of said tool).
-## Example
+## Example Metadata File (`ro-crate-metadata.json`)
```json
-[
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
+ "@graph": [
+ {
+ "@id": "ro-crate-metadata.json",
+ "@type": "CreativeWork",
+ "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"},
+ "about": {"@id": "./"}
+ },
{
"@id": "./",
"@type": "Dataset",
+ "conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.1"},
"hasPart": [
{"@id": "pics/2017-06-11%2012.56.14.jpg"},
{"@id": "pics/sepia_fence.jpg"}
@@ -35,6 +43,11 @@ This profile requires the indication of [Software used to create files](https://
"mentions": {"@id": "#SepiaConversion_1"},
"name": "My Pictures"
},
+ { "@id": "https://w3id.org/ro/wfrun/process/0.1",
+ "@type": "CreativeWork",
+ "name": "Process Run Crate",
+ "version": "0.1"
+ },
{
"@id": "https://www.imagemagick.org/",
"@type": "SoftwareApplication",
@@ -73,6 +86,7 @@ This profile requires the indication of [Software used to create files](https://
"name": "Stian Soiland-Reyes"
}
]
+}
```
Note that the command line shown in the action's `description` is not directly re-executable, as file paths are not required to match the RO-Crate locations. For a more structural and reproducible description of tool executions, see [Workflow Run Crate](workflow_run_crate).
@@ -88,6 +102,15 @@ Note that the command line shown in the action's `description` is not directly r
Description |
+
+ Dataset (the root data entity, e.g. "@id": "./" ) |
+
+
+ conformsTo |
+ MUST |
+ MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, e.g. {"@id": "https://w3id.org/ro/wfrun/process/0.1"} |
+
+
SoftwareApplication |
@@ -135,7 +158,7 @@ Note that the command line shown in the action's `description` is not directly r
@id |
MUST |
- A unique identifier for the execution, e.g. "urn:uuid:50ec5c76-1f7a-4130-8ef6-846756b228c1" , "#f99a8e6c" . MAY be an absolute URI, e.g. http://example.com/runs/846756b228c1. The use of randomly generated UUIDs (type 4) is RECOMMENDED. SHOULD be listed under mentions of the [root data entity](https://www.researchobject.org/ro-crate/1.1/root-data-entity.html). |
+ A unique identifier for the execution, e.g. "urn:uuid:50ec5c76-1f7a-4130-8ef6-846756b228c1" , "#f99a8e6c" . MAY be an absolute URI, e.g. http://example.com/runs/846756b228c1. The use of randomly generated UUIDs (type 4) is RECOMMENDED. SHOULD be listed under mentions of the root data entity. |
diff --git a/docs/profiles/0.1-DRAFT/provenance_run_crate.md b/docs/profiles/0.1-DRAFT/provenance_run_crate.md
index acebf5e..235628e 100644
--- a/docs/profiles/0.1-DRAFT/provenance_run_crate.md
+++ b/docs/profiles/0.1-DRAFT/provenance_run_crate.md
@@ -29,13 +29,29 @@ The following diagram shows the relationships between all provenance-related ent
-## Example
+## Example Metadata File (`ro-crate-metadata.json`)
```json
-[
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
+ "@graph": [
+ {
+ "@id": "ro-crate-metadata.json",
+ "@type": "CreativeWork",
+ "about": {"@id": "./"},
+ "conformsTo": [
+ {"@id": "https://w3id.org/ro/crate/1.1"},
+ {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}
+ ]
+ },
{
"@id": "./",
"@type": "Dataset",
+ "conformsTo": [
+ {"@id": "https://w3id.org/ro/wfrun/process/0.1"},
+ {"@id": "https://w3id.org/ro/wfrun/workflow/0.1"},
+ {"@id": "https://w3id.org/ro/wfrun/provenance/0.1"},
+ {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}
+ ],
"hasPart": [
{"@id": "packed.cwl"},
{"@id": "327fc7aedf4f6b69a42a7c8b808dc5a7aff61376"},
@@ -47,14 +63,25 @@ The following diagram shows the relationships between all provenance-related ent
{"@id": "#4154dad3-00cc-4e35-bb8f-a2de5cd7dc49"}
]
},
- {
- "@id": "ro-crate-metadata.json",
+ { "@id": "https://w3id.org/ro/wfrun/process/0.1",
"@type": "CreativeWork",
- "about": {"@id": "./"},
- "conformsTo": [
- {"@id": "https://w3id.org/ro/crate/1.1"},
- {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}
- ]
+ "name": "Process Run Crate",
+ "version": "0.1"
+ },
+ { "@id": "https://w3id.org/ro/wfrun/workflow/0.1",
+ "@type": "CreativeWork",
+ "name": "Workflow Run Crate",
+ "version": "0.1"
+ },
+ { "@id": "https://w3id.org/ro/wfrun/provenance/0.1",
+ "@type": "CreativeWork",
+ "name": "Provenance Run Crate",
+ "version": "0.1"
+ },
+ { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0",
+ "@type": "CreativeWork",
+ "name": "Workflow RO-Crate",
+ "version": "1.0"
},
{
"@id": "packed.cwl",
@@ -294,6 +321,7 @@ The following diagram shows the relationships between all provenance-related ent
"value": "True"
}
]
+}
```
@@ -415,6 +443,15 @@ The requirements of this profile are those of [Workflow Run Crate](workflow_run_
Description |
+
+ Dataset (the root data entity, e.g. "@id": "./" ) |
+
+
+ conformsTo |
+ MUST |
+ Array MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, and SHOULD also reference versioned permalinks for Process Run Crate, Workflow Run Crate and Workflow RO-Crate. |
+
+
ComputationalWorkflow |
diff --git a/docs/profiles/0.1-DRAFT/workflow_run_crate.md b/docs/profiles/0.1-DRAFT/workflow_run_crate.md
index 206f605..02d0635 100644
--- a/docs/profiles/0.1-DRAFT/workflow_run_crate.md
+++ b/docs/profiles/0.1-DRAFT/workflow_run_crate.md
@@ -21,13 +21,28 @@ This profile is a combination of [Process Run Crate](process_run_crate) and [Wor
Some workflows have multiple inputs/outputs that, in conformance with the [Bioschemas ComputationalWorkflow profile](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE) are defined as [FormalParameter](https://bioschemas.org/types/FormalParameter/1.0-RELEASE) entities. It is OPTIONAL to include these definitions on a `ComputationalWorkflow`. A data entity or `PropertyValue` that realizes a `FormalParameter` definition SHOULD refer to it via [exampleOfWork](https://schema.org/exampleOfWork); additionally, if the data entity or `PropertyValue` is an illustrative example of the parameter, the latter MAY refer back to the former using the reverse property [workExample](https://schema.org/workExample). This links the `input` of a `ComputationalWorkflow` to the `object` of a `CreateAction`, and the `output` of a `ComputationalWorkflow` to the `result` of a `CreateAction`. An `object` item that does not match a slot in the workflow's input interface (e.g., a [configuration file](process_run_crate#referencing-configuration-files) read from a predefined path) MUST NOT refer to a `FormalParameter` of the `ComputationalWorkflow` via `exampleOfWork`. A `FormalParameter` that maps to a `PropertyValue` SHOULD have a subclass of [DataType](https://schema.org/DataType) (e.g., [Integer](https://schema.org/Integer)) — or [PropertyValue](https://schema.org/PropertyValue), in the case of dictionary-like structured types — as its `additionalType`. See [CWL parameter mapping](/workflow-run-crate/cwl_param_mapping) for an example.
-## Example
+## Example Metadata File (`ro-crate-metadata.json`)
```json
-[
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
+ "@graph": [
+ {
+ "@id": "ro-crate-metadata.json",
+ "@type": "CreativeWork",
+ "about": {"@id": "./"},
+ "conformsTo": [
+ {"@id": "https://w3id.org/ro/crate/1.1"},
+ {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}
+ ]
+ },
{
"@id": "./",
"@type": "Dataset",
+ "conformsTo": [
+ {"@id": "https://w3id.org/ro/wfrun/process/0.1"},
+ {"@id": "https://w3id.org/ro/wfrun/workflow/0.1"},
+ {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}
+ ],
"hasPart": [
{"@id": "Galaxy-Workflow-Hello_World.ga"},
{"@id": "inputs/abcdef.txt"},
@@ -38,6 +53,21 @@ Some workflows have multiple inputs/outputs that, in conformance with the [Biosc
"mainEntity": {"@id": "Galaxy-Workflow-Hello_World.ga"},
"mentions": {"@id": "#wfrun-5a5970ab-4375-444d-9a87-a764a66e3a47"}
},
+ { "@id": "https://w3id.org/ro/wfrun/process/0.1",
+ "@type": "CreativeWork",
+ "name": "Process Run Crate",
+ "version": "0.1"
+ },
+ { "@id": "https://w3id.org/ro/wfrun/workflow/0.1",
+ "@type": "CreativeWork",
+ "name": "Workflow Run Crate",
+ "version": "0.1"
+ },
+ { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0",
+ "@type": "CreativeWork",
+ "name": "Workflow RO-Crate",
+ "version": "1.0"
+ },
{
"@id": "Galaxy-Workflow-Hello_World.ga",
"@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
@@ -171,6 +201,7 @@ Some workflows have multiple inputs/outputs that, in conformance with the [Biosc
"name": "Workflow Execution Summary of Hello World"
}
]
+}
```
@@ -186,6 +217,15 @@ This profile inherits the requirements of [Process Run Crate](process_run_crate)
Description |
+
+ Dataset (the root data entity, e.g. "@id": "./" ) |
+
+
+ conformsTo |
+ MUST |
+ Array MUST reference a CreativeWork entity with an @id URI that is consistent with the versioned Permalink of this document, and SHOULD also reference versioned permalinks for Process Run Crate and Workflow RO-Crate. |
+
+
CreateAction |