Profile updates for RO-Crate 1.2

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/).
-

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`.

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).

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/",

docs/profiles/0.6-DRAFT/process_run_crate/example1/ro-crate-preview.html

@@ -6,13 +6,15 @@
 
 <script type="application/ld+json"> 
   {
-  "@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"
+        "@id": "https://w3id.org/ro/crate/1.2"
       },
       "about": {
         "@id": "./"
@@ -22,7 +24,7 @@
       "@id": "./",
       "@type": "Dataset",
       "conformsTo": {
-        "@id": "https://w3id.org/ro/wfrun/process/0.4"
+        "@id": "https://w3id.org/ro/wfrun/process/0.6-DRAFT"
       },
       "hasPart": [
         {
@@ -44,10 +46,10 @@
       "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": "pics/2017-06-11%2012.56.14.jpg",
@@ -135,8 +137,8 @@
   </nav>
 <div class="container">
 <div class="jumbotron">
-<h4 class="citation"></h3>
-<h3 class="item_name">My Pictures</h4>
+<h4 class="citation"></h4>
+<h3 class="item_name">My Pictures</h3>
 
 
 <a href="./ro-crate-metadata.json">⬇️🏷️ Download all the metadata for <span class='name'>My Pictures</span> in JSON-LD format</a>
@@ -151,12 +153,12 @@ <h3 class="item_name">My Pictures</h4>
 
 <div id="summary">
 <div class='all-meta'>
-           <div>
-            <h3> My Pictures</h3>
-
-
-
-
+            <div>
+                <h3> My Pictures</h3>
+                
+                
+                
+                
         <div id="./">
 
             <table class="table metadata table-striped" >
@@ -171,7 +173,7 @@ <h3> My Pictures</h3>
             <td style='text-align:left'><span>Dataset</span></td>
             </tr><tr>
             <th style="text-align:left;" class="prop">conformsTo<span>&nbsp;</span><a href="http://purl.org/dc/terms/conformsTo">[?]</a></th>
-            <td style='text-align:left'><a href="#https%3A//w3id.org/ro/wfrun/process/0.4">Process Run Crate</a></td>
+            <td style='text-align:left'><a href="#https%3A//w3id.org/ro/wfrun/process/0.6-DRAFT">Process Run Crate</a></td>
             </tr><tr>
             <th style="text-align:left;" class="prop">hasPart<span>&nbsp;</span><a href="http://schema.org/hasPart">[?]</a></th>
             <td style='text-align:left'><ul>
@@ -194,21 +196,20 @@ <h3> My Pictures</h3>
             </tr></tbody>
             </table>
         </div>
-
-        </div>
+            </div>
         <hr/><br/><br/>
-           <div>
-            <h3><a href="https://w3id.org/ro/wfrun/process/0.4">Go to: </a> Process Run Crate</h3>
-
-
-
-
-        <div id="https://w3id.org/ro/wfrun/process/0.4">
+            <div>
+                <h3><a href="https://w3id.org/ro/wfrun/process/0.6-DRAFT">Go to: </a> Process Run Crate</h3>
+                
+                
+                
+                
+        <div id="https://w3id.org/ro/wfrun/process/0.6-DRAFT">
 
             <table class="table metadata table-striped" >
                 <tbody><tr>
             <th style="text-align:left;" class="prop">@id</th>
-            <td style='text-align:left'><a href="https://w3id.org/ro/wfrun/process/0.4">https://w3id.org/ro/wfrun/process/0.4</a></td>
+            <td style='text-align:left'><a href="https://w3id.org/ro/wfrun/process/0.6-DRAFT">https://w3id.org/ro/wfrun/process/0.6-DRAFT</a></td>
             </tr><tr>
             <th style="text-align:left;" class="prop">name<span>&nbsp;</span><a href="http://schema.org/name">[?]</a></th>
             <td style='text-align:left'><span>Process Run Crate</span></td>
@@ -217,22 +218,21 @@ <h3><a href="https://w3id.org/ro/wfrun/process/0.4">Go to: </a> Process Run Crat
             <td style='text-align:left'><span>CreativeWork</span></td>
             </tr><tr>
             <th style="text-align:left;" class="prop">version<span>&nbsp;</span><a href="http://schema.org/version">[?]</a></th>
-            <td style='text-align:left'><span>0.5</span></td>
+            <td style='text-align:left'><span>0.6-DRAFT</span></td>
             </tr><tr><th colspan="2" style="text-align:center">Items that reference this one</th><tr><tr>
             <th style="text-align:left;" class="prop">conformsTo<span>&nbsp;</span><a href="http://purl.org/dc/terms/conformsTo">[?]</a></th>
             <td style='text-align:left'><a href="#./">My Pictures</a></td>
             </tr></tbody>
             </table>
         </div>
-
-        </div>
+            </div>
         <hr/><br/><br/>
-           <div>
-            <h3><a href="pics/2017-06-11%2012.56.14.jpg">⬇️ Download: </a> 2017-06-11 12.56.14.jpg (input)</h3>
-
-            <img width='100%' style='object-fit: contain' src='pics/2017-06-11%2012.56.14.jpg'/>
-
-
+            <div>
+                <h3><a href="pics/2017-06-11%2012.56.14.jpg">⬇️ Download: </a> 2017-06-11 12.56.14.jpg (input)</h3>
+                
+                <img width='100%' style='object-fit: contain' src='pics/2017-06-11%2012.56.14.jpg'/>
+                
+                
         <div id="pics/2017-06-11%2012.56.14.jpg">
 
             <table class="table metadata table-striped" >
@@ -263,15 +263,14 @@ <h3><a href="pics/2017-06-11%2012.56.14.jpg">⬇️ Download: </a> 2017-06-11 12
             </tr></tbody>
             </table>
         </div>
-
-        </div>
+            </div>
         <hr/><br/><br/>
-           <div>
-            <h3><a href="pics/sepia_fence.jpg">⬇️ Download: </a> sepia_fence (output)</h3>
-
-            <img width='100%' style='object-fit: contain' src='pics/sepia_fence.jpg'/>
-
-
+            <div>
+                <h3><a href="pics/sepia_fence.jpg">⬇️ Download: </a> sepia_fence (output)</h3>
+                
+                <img width='100%' style='object-fit: contain' src='pics/sepia_fence.jpg'/>
+                
+                
         <div id="pics/sepia_fence.jpg">
 
             <table class="table metadata table-striped" >
@@ -299,15 +298,14 @@ <h3><a href="pics/sepia_fence.jpg">⬇️ Download: </a> sepia_fence (output)</h
             </tr></tbody>
             </table>
         </div>
-
-        </div>
+            </div>
         <hr/><br/><br/><hr/><br/><br/><hr/><br/><br/>
-           <div>
-            <h3> Convert dog image to sepia</h3>
-
-
-
-
+            <div>
+                <h3> Convert dog image to sepia</h3>
+                
+                
+                
+                
         <div id="#SepiaConversion_1">
 
             <table class="table metadata table-striped" >
@@ -344,8 +342,7 @@ <h3> Convert dog image to sepia</h3>
             </tr></tbody>
             </table>
         </div>
-
-        </div>
+            </div>
         <hr/><br/><br/></div>
 </div>