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Merged
simleo merged 5 commits into from
Jul 2, 2026
Merged

Profile updates for RO-Crate 1.3 #104

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bec91d6
update 1.2 references -> 1.3
elichad Jun 26, 2026
7d72a47
rename index.hml -> index.html
elichad Jun 26, 2026
a090548
update bioschemas IRIs
elichad Jun 26, 2026
8945ea6
add notes on updated IRIs
elichad Jun 26, 2026
d4ef53e
update links to ro-crate spec and profiles in the main page
simleo Jul 2, 2026
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4 changes: 2 additions & 2 deletions docs/index.md
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Expand Up @@ -121,8 +121,8 @@ In addition, some computational workflow approaches have RO-Crate support which
### RO-Crate links

- [RO-Crate homepage](https://w3id.org/ro/crate)
- [RO-Crate specification 1.2](https://www.researchobject.org/ro-crate/1.2/)
- [RO-Crate profiles](https://www.researchobject.org/ro-crate/1.2/profiles) (within the specification above)
- [RO-Crate specification 1.3](https://w3id.org/ro/crate/1.3)
- [RO-Crate profiles](https://www.researchobject.org/ro-crate/specification/1.3/profiles.html) (within the specification above)
- [Workflow Crate](https://w3id.org/workflowhub/workflow-ro-crate/) (profile for a workflow _definition_)
- [Workflow Testing Crate](https://lifemonitor.eu/workflow_testing_ro_crate) (profile for defining workflow tests)
- [Adding a ComputationalWorkflow in RO-Crate](https://www.researchobject.org/ro-crate/1.1/workflows.html)
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26 changes: 22 additions & 4 deletions docs/profiles/0.6-DRAFT/changelog.md
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## 0.6-DRAFT

* Updated all three profiles and their examples to align with RO-Crate 1.2 and Workflow RO-Crate 1.1.
* The IRI mappings for the properties `input` and `output` have been updated in the [RO-Crate 1.2 JSON-LD context](https://www.researchobject.org/ro-crate/specification/1.2/context.jsonld). This means that from this version onward, Workflow Run Crate and Provenance Run Crate are not backward compatible with RO-Crate 1.1/Workflow RO-Crate 1.0.
* `input` has changed from `https://bioschemas.org/ComputationalWorkflow#input` to `https://bioschemas.org/properties/input` .
* `output` has changed from `https://bioschemas.org/ComputationalWorkflow#output` to `https://bioschemas.org/properties/output`.
* Updated all three profiles and their examples to align with RO-Crate 1.3 and Workflow RO-Crate 1.1.
* The IRI mappings for `ComputationalWorkflow`, `FormalParameter`, `input`, and `output` were updated in the [RO-Crate 1.3 JSON-LD context](https://www.researchobject.org/ro-crate/specification/1.3/context.jsonld). This means that from this version onward, Workflow Run Crate and Provenance Run Crate are not backward compatible with RO-Crate 1.1/Workflow RO-Crate 1.0. The changes are shown in the table below:

| Term | RO-Crate 1.3 context (latest) | RO-Crate 1.2 context | RO-Crate 1.1 context |
| --- | --- | --- | --- |
| ComputationalWorkflow | <https://bioschemas.org/terms/ComputationalWorkflow> | https://bioschemas.org/ComputationalWorkflow | https://bioschemas.org/ComputationalWorkflow |
| FormalParameter | <https://bioschemas.org/terms/FormalParameter> | https://bioschemas.org/FormalParameter | https://bioschemas.org/FormalParameter |
| input | <https://bioschemas.org/terms/input> | https://bioschemas.org/properties/input | https://bioschemas.org/ComputationalWorkflow#input |
| output | <https://bioschemas.org/terms/output> | https://bioschemas.org/properties/output | https://bioschemas.org/ComputationalWorkflow#output |

Note that `ComputationalWorkflow` and `FormalParameter` did not have IRI changes between 1.1 and 1.2, whereas `input` and `output` had IRI changes between all three versions.

* Implementers should further note: while RO-Crate 1.2 was never formally supported by the Process Run Crate, Workflow Run Crate, or Provenance Run Crate profiles, there may nonetheless be crates which declare conformance to both RO-Crate 1.2 and one or more of these profiles, and therefore use the RO-Crate 1.2 context mappings.

## Compatibility table

| RO-Crate version | Workflow RO-Crate version | Compatible Workflow Run RO-Crate version(s) |
| --- | --- | --- |
| 1.1 | 1.0 | 0.1 - 0.5 |
| 1.2 | None | None |
| 1.3 | 1.1 | 0.6-DRAFT |
| later minor versions | 1.1, unless context changes are made that affect terms used in the profile | 0.6-DRAFT, unless context changes are made that affect terms used in the profiles |
170 changes: 97 additions & 73 deletions docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-metadata.json
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@@ -1,75 +1,99 @@
{ "@context": "https://w3id.org/ro/crate/1.2/context",
"@graph": [
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"conformsTo": {"@id": "https://w3id.org/ro/crate/1.2"},
"about": {"@id": "./"}
},
{
"@id": "./",
"@type": "Dataset",
"conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT"},
"hasPart": [
{"@id": "pics/2017-06-11%2012.56.14.jpg"},
{"@id": "pics/sepia_fence.jpg"}
],
"isBasedOn": {
"@id": "https://doi.org/10.5281/zenodo.1009240"
{
"@context": "https://w3id.org/ro/crate/1.3/context",
"@graph": [
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"conformsTo": {
"@id": "https://w3id.org/ro/crate/1.3"
},
"about": {
"@id": "./"
}
},
"license": {"@id": "http://spdx.org/licenses/CC0-1.0"},
"mentions": {"@id": "#SepiaConversion_1"},
"name": "My Pictures"
},
{ "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT",
"@type": "CreativeWork",
"name": "Process Run Crate",
"version": "0.6-DRAFT"
},
{
"@id": "https://www.imagemagick.org/",
"@type": "SoftwareApplication",
"url": "https://www.imagemagick.org/",
"name": "ImageMagick",
"softwareVersion": "6.9.7-4"
},
{
"@id": "#SepiaConversion_1",
"@type": "CreateAction",
"name": "Convert dog image to sepia",
"description": "convert -sepia-tone 80% pics/2017-06-11\\ 12.56.14.jpg pics/sepia_fence.jpg",
"endTime": "2024-05-17T01:04:52+01:00",
"instrument": {"@id": "https://www.imagemagick.org/"},
"object": {"@id": "pics/2017-06-11%2012.56.14.jpg"},
"result": {"@id": "pics/sepia_fence.jpg"},
"agent": {"@id": "https://orcid.org/0000-0001-9842-9718"}
},
{
"@id": "pics/2017-06-11%2012.56.14.jpg",
"@type": "File",
"description": "Original image",
"encodingFormat": "image/jpeg",
"name": "2017-06-11 12.56.14.jpg (input)",
"author": {
"@id": "https://orcid.org/0000-0002-3545-944X"
{
"@id": "./",
"@type": "Dataset",
"conformsTo": {
"@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT"
},
"hasPart": [
{
"@id": "pics/2017-06-11%2012.56.14.jpg"
},
{
"@id": "pics/sepia_fence.jpg"
}
],
"isBasedOn": {
"@id": "https://doi.org/10.5281/zenodo.1009240"
},
"license": {
"@id": "http://spdx.org/licenses/CC0-1.0"
},
"mentions": {
"@id": "#SepiaConversion_1"
},
"name": "My Pictures"
},
{
"@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT",
"@type": "CreativeWork",
"name": "Process Run Crate",
"version": "0.6-DRAFT"
},
{
"@id": "https://www.imagemagick.org/",
"@type": "SoftwareApplication",
"url": "https://www.imagemagick.org/",
"name": "ImageMagick",
"softwareVersion": "6.9.7-4"
},
{
"@id": "#SepiaConversion_1",
"@type": "CreateAction",
"name": "Convert dog image to sepia",
"description": "convert -sepia-tone 80% pics/2017-06-11\\ 12.56.14.jpg pics/sepia_fence.jpg",
"endTime": "2024-05-17T01:04:52+01:00",
"instrument": {
"@id": "https://www.imagemagick.org/"
},
"object": {
"@id": "pics/2017-06-11%2012.56.14.jpg"
},
"result": {
"@id": "pics/sepia_fence.jpg"
},
"agent": {
"@id": "https://orcid.org/0000-0001-9842-9718"
}
},
{
"@id": "pics/2017-06-11%2012.56.14.jpg",
"@type": "File",
"description": "Original image",
"encodingFormat": "image/jpeg",
"name": "2017-06-11 12.56.14.jpg (input)",
"author": {
"@id": "https://orcid.org/0000-0002-3545-944X"
}
},
{
"@id": "pics/sepia_fence.jpg",
"@type": "File",
"description": "The converted picture, now sepia-colored",
"encodingFormat": "image/jpeg",
"name": "sepia_fence (output)"
},
{
"@id": "https://orcid.org/0000-0001-9842-9718",
"@type": "Person",
"name": "Stian Soiland-Reyes"
},
{
"@id": "https://orcid.org/0000-0002-3545-944X",
"@type": "Person",
"name": "Peter Sefton"
}
},
{
"@id": "pics/sepia_fence.jpg",
"@type": "File",
"description": "The converted picture, now sepia-colored",
"encodingFormat": "image/jpeg",
"name": "sepia_fence (output)"
},
{
"@id": "https://orcid.org/0000-0001-9842-9718",
"@type": "Person",
"name": "Stian Soiland-Reyes"
},
{
"@id": "https://orcid.org/0000-0002-3545-944X",
"@type": "Person",
"name": "Peter Sefton"
}
]
}
]
}
4 changes: 2 additions & 2 deletions docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html
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Expand Up @@ -7,14 +7,14 @@
<script type="application/ld+json">
{
"@context": [
"https://w3id.org/ro/crate/1.2/context"
"https://w3id.org/ro/crate/1.3/context"
],
"@graph": [
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"conformsTo": {
"@id": "https://w3id.org/ro/crate/1.2"
"@id": "https://w3id.org/ro/crate/1.3"
},
"about": {
"@id": "./"
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