diff --git a/docs/index.md b/docs/index.md index 145d980..4f05fd2 100644 --- a/docs/index.md +++ b/docs/index.md @@ -92,7 +92,7 @@ Several workflow engines have implemented the [WRROC profiles](https://www.resea [WfExS](https://wfexs-backend.readthedocs.io/) | Workflow | [WfExS 0.10.1](https://github.com/inab/WfExS-backend/releases/tag/0.10.1) or later | [10.5281/zenodo.10091550](https://doi.org/10.5281/zenodo.10091550) | [Sapporo](https://github.com/sapporo-wes/sapporo) | Workflow | [sapporo-service 1.5.1](https://github.com/sapporo-wes/sapporo-service/releases/tag/1.5.1) or later | [10.5281/zenodo.10134581](https://doi.org/10.5281/zenodo.10134581) | [Autosubmit](https://autosubmit.readthedocs.io/) | Workflow | [Autosubmit v4.0.100](https://pypi.org/project/autosubmit/4.0.100/) or later | [10.5281/zenodo.8144612](https://doi.org/10.5281/zenodo.8144612) | -[Nextflow](https://nextflow.io/) | Provenance | ([nf-prov](https://github.com/nextflow-io/nf-prov/blob/main/docs/WRROC.md) 1.4.0 or later | [example](https://github.com/nextflow-io/nf-prov/files/13070992/ro-crate-metadata.json) | +[Nextflow](https://nextflow.io/) | Provenance | [nf-prov](https://github.com/nextflow-io/nf-prov/blob/main/docs/WRROC.md) 1.4.0 or later | [example](https://github.com/nextflow-io/nf-prov/files/13070992/ro-crate-metadata.json) | The Process Crate profile can also be implemented outside workflow systems, see for example [BY-COVID WP5 T5.2 Baseline Use Case](https://w3id.org/ro/doi/10.5281/zenodo.6913045) and [combination with Common Provenance Model](https://doi.org/10.5281/zenodo.7676923). Editors like [Crate-O](https://language-research-technology.github.io/crate-o/) can be used for making such crates by hand. @@ -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 1.1](https://www.researchobject.org/ro-crate/1.1/) -- [RO-Crate profiles](https://www.researchobject.org/ro-crate/1.2-DRAFT/profiles) (from 1.2-DRAFT -- feedback welcome) +- [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) - [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) @@ -158,4 +158,3 @@ Unless required by applicable law or agreed to in writing, software distributed Profile Crates and JSON-LD examples within this specification are distributed under [CC0 1.0 Universal (CC0 1.0) Public Domain Dedication](https://creativecommons.org/publicdomain/zero/1.0/). - diff --git a/docs/profiles/0.6-DRAFT/changelog.md b/docs/profiles/0.6-DRAFT/changelog.md new file mode 100644 index 0000000..a8f51de --- /dev/null +++ b/docs/profiles/0.6-DRAFT/changelog.md @@ -0,0 +1,8 @@ +# Changelog + +## 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`. diff --git a/docs/profiles/0.6-DRAFT/index.md b/docs/profiles/0.6-DRAFT/index.md index 6316a5a..fa2fde1 100644 --- a/docs/profiles/0.6-DRAFT/index.md +++ b/docs/profiles/0.6-DRAFT/index.md @@ -10,3 +10,7 @@ This section defines three [RO-Crate profiles](https://www.researchobject.org/ro * [Process Run Crate](process_run_crate) can be used to describe the execution of one or more tools that contribute to the same computation; * [Workflow Run Crate](workflow_run_crate) is similar to Process Run Crate, but assumes that the coordinated execution of the tools is driven by a [computational workflow](https://bioschemas.org/types/ComputationalWorkflow/1.0-RELEASE) * [Provenance Run Crate](provenance_run_crate) extends Workflow Run Crate with guidelines for describing the internal details of each step of the workflow. + +## Latest changes + +See the [changelog](changelog). diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-metadata.json b/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-metadata.json index 05cd8d6..32314b6 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-metadata.json +++ b/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-metadata.json @@ -1,15 +1,15 @@ -{ "@context": "https://w3id.org/ro/crate/1.1/context", +{ "@context": "https://w3id.org/ro/crate/1.2/context", "@graph": [ { "@id": "ro-crate-metadata.json", "@type": "CreativeWork", - "conformsTo": {"@id": "https://w3id.org/ro/crate/1.1"}, + "conformsTo": {"@id": "https://w3id.org/ro/crate/1.2"}, "about": {"@id": "./"} }, { "@id": "./", "@type": "Dataset", - "conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.4"}, + "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"} @@ -21,10 +21,10 @@ "mentions": {"@id": "#SepiaConversion_1"}, "name": "My Pictures" }, - { "@id": "https://w3id.org/ro/wfrun/process/0.4", + { "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT", "@type": "CreativeWork", "name": "Process Run Crate", - "version": "0.5" + "version": "0.6-DRAFT" }, { "@id": "https://www.imagemagick.org/", diff --git a/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html b/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html index 7877d6b..e0eae5a 100644 --- a/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html +++ b/docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html @@ -6,13 +6,15 @@