Profile updates for RO-Crate 1.2

[elichad]

Updates to 0.6-DRAFT:

• 1.1 -> 1.2 in examples and profile text
• 1.2-DRAFT -> 1.2 in profile crates and profile text
• adds datePublished, keywords, description to profile crates (keywords are used in the profile registry)
• Updates the isBasedOn for the workflow-run context to 1.2 - wasn't as sure about this one but the ro-terms repo doesn't seem to declare this at all. I just found Remove reference to RO-Crate context from the JSON(LD) files ro-terms#28 too - is this actually just obsolete and we should remove isBasedOn altogether?
• regenerates all the HTML previews

Depends on release of Workflow RO-Crate 1.1.

Fixes #99, fixes #98

[simleo]

• Updates the isBasedOn for the workflow-run context to 1.2 - wasn't as sure about this one but the ro-terms repo doesn't seem to declare this at all. I just found Remove reference to RO-Crate context from the JSON(LD) files ro-terms#28 too - is this actually just obsolete and we should remove isBasedOn altogether?

I think we should remove isBasedOn altogether. Everything else LGTM.

[elichad]

I think we should remove isBasedOn altogether. Everything else LGTM.

thanks, done

[elichad]

from community call: state what version(s) of WROC the WRROC profile is compatible with

[elichad]

I made these dates the same as the 0.5 publication date for now

[elichad]

Recent commit changes:

• updated examples to use most recent version of these profiles in conformsTo
• updated examples to use Workflow ROC 1.1 where relevant (means the conformsTo doesn't need to appear on the metadata descriptor any more)
• updated Workflow Run to state compatibility with Workflow ROC 1.0 or later
• updated Process Run to state compatibility with RO-Crate 1.1 or later (but see below)

However, I've just realised that there is a change in 1.2 that has a subtle impact on compatibility here - from the changelog:

Updated the Bioschemas namespace for properties from https://bioschemas.org/ComputationalWorkflow# to https://bioschemas.org/properties/. This change affects only the input and output properties in the JSON-LD context.

Workflow Run and Provenance Run do use those input and output terms, so a WRROC won't be exactly the same in RO-Crate 1.1 vs 1.2 if it's treated as RDF. @simleo what's your perspective on what compatibility we should declare? This will affect the SHACL validator too.

(this actually affects Workflow RO-Crate 1.1 as well thanks to workflowhub-eu/about#87)

[simleo]

Workflow Run and Provenance Run do use those input and output terms, so a WRROC won't be exactly the same in RO-Crate 1.1 vs 1.2 if it's treated as RDF. @simleo what's your perspective on what compatibility we should declare? This will affect the SHACL validator too.

We actually have several occurrences of the full IRIs for input and output here in the profiles, e.g.:

$ git grep -F 'https://bioschemas.org/ComputationalWorkflow#input' -- docs/profiles/0.6-DRAFT/
docs/profiles/0.6-DRAFT/provenance_run_crate/example3/ro-crate-preview.html:            <th style="text-align:left;" class="prop">input<span>&nbsp;</span><a href="https://bioschemas.org/ComputationalWorkflow#input">[?]</a></th>
docs/profiles/0.6-DRAFT/workflow_run_crate/example2/ro-crate-preview.html:            <th style="text-align:left;" class="prop">input<span>&nbsp;</span><a href="https://bioschemas.org/ComputationalWorkflow#input">[?]</a></th>
docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json:        "@id": "https://bioschemas.org/ComputationalWorkflow#input"
docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-metadata.json:    "@id": "https://bioschemas.org/ComputationalWorkflow#input",
docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html:          "@id": "https://bioschemas.org/ComputationalWorkflow#input"
docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html:      "@id": "https://bioschemas.org/ComputationalWorkflow#input",
docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html:            <h3><a href="https://bioschemas.org/ComputationalWorkflow#input">Go to: </a> input</h3>
docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html:        <div id="https://bioschemas.org/ComputationalWorkflow#input">
docs/profiles/0.6-DRAFT/workflow_run_crate/ro-crate-preview.html:            <td style='text-align:left'><a href="https://bioschemas.org/ComputationalWorkflow#input">https://bioschemas.org/ComputationalWorkflow#input</a></td>

Most notably in the profile crate. So for version 0.6 of the profiles I guess we should declare compatibility with RO-Crate 1.2 only and change the input and output IRIs to the new ones supported by RO-Crate 1.2. The validator will have a different set of SHACL shapes for version 0.6 of the profiles, which will be able to include the new IRIs (@kikkomep please correct me if I'm wrong).

[elichad]

We actually have several occurrences of the full IRIs for input and output here in the profiles, e.g.:

Thanks, I think I have fixed these now, though couldn't find the ones below in my local copy (they have the updated IRI for me):

docs/profiles/0.6-DRAFT/provenance_run_crate/example3/ro-crate-preview.html:            <th style="text-align:left;" class="prop">input<span>&nbsp;</span><a href="https://bioschemas.org/ComputationalWorkflow#input">[?]</a></th>
docs/profiles/0.6-DRAFT/workflow_run_crate/example2/ro-crate-preview.html:            <th style="text-align:left;" class="prop">input<span>&nbsp;</span><a href="https://bioschemas.org/ComputationalWorkflow#input">[?]</a></th>

[elichad]

So for version 0.6 of the profiles I guess we should declare compatibility with RO-Crate 1.2 only and change the input and output IRIs to the new ones supported by RO-Crate 1.2.

I agree, I'll implement this tomorrow