update metadata

improve metadata to comply with FOOPS recommendations

.github/workflows/doc.yml

@@ -1,4 +1,4 @@
-name: "Sphinx: Render docs"
+name: "docs"
 
 on: 
   push:
@@ -89,9 +89,11 @@ jobs:
         git fetch --tags
         git tag | while read TAG; do
           sudo mkdir -p "docs/_build/html/versions/$TAG"
-          sudo cp "electrochemistry.ttl" "docs/_build/html/versions/$TAG/"
+          python convert_ttl.py electrochemistry.ttl electrochemistry-foops.ttl
+          python convert_ttl.py electrochemicalquantities.ttl electrochemicalquantities-foops.ttl
+          sudo cp "electrochemistry-foops.ttl" "docs/_build/html/versions/$TAG/electrochemistry.ttl"
+          sudo cp "electrochemicalquantities-foops.ttl" "docs/_build/html/versions/$TAG/electrochemicalquantities.ttl"
           sudo cp "electrochemistry-inferred.ttl" "docs/_build/html/versions/$TAG/"
-          sudo cp "electrochemicalquantities.ttl" "docs/_build/html/versions/$TAG/"
 
         if [ -d "context" ]; then
           echo "Context directory exists, copying context.json to $TAG"
@@ -106,8 +108,10 @@ jobs:
 
     - name: Copy TTL files to HTML directory
       run: |
-        sudo cp "electrochemistry.ttl" "docs/_build/html/electrochemistry.ttl"
-        sudo cp "electrochemicalquantities.ttl" "docs/_build/html/electrochemicalquantities.ttl"
+        python convert_ttl.py electrochemistry.ttl electrochemistry-foops.ttl
+        python convert_ttl.py electrochemicalquantities.ttl electrochemicalquantities-foops.ttl
+        sudo cp "electrochemistry-foops.ttl" "docs/_build/html/electrochemistry.ttl"
+        sudo cp "electrochemicalquantities-foops.ttl" "docs/_build/html/electrochemicalquantities.ttl"
         sudo cp "electrochemistry-inferred.ttl" "docs/_build/html/electrochemistry-inferred.ttl"
 
     - name: Upload artifacts

docs/assets/img/fig/src/domain-electrochemistry-logo.drawio

@@ -0,0 +1,34 @@
+<mxfile host="65bd71144e">
+    <diagram id="NrZ29duDLyXxqPhjrZT9" name="Page-1">
+        <mxGraphModel dx="799" dy="469" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="850" pageHeight="1100" math="0" shadow="0">
+            <root>
+                <mxCell id="0"/>
+                <mxCell id="1" parent="0"/>
+                <mxCell id="2" value="&lt;font style=&quot;font-size: 104px;&quot;&gt;ECHO&lt;/font&gt;" style="text;strokeColor=none;fillColor=none;html=1;fontSize=24;fontStyle=1;verticalAlign=middle;align=center;" vertex="1" parent="1">
+                    <mxGeometry x="335" y="40" width="350" height="120" as="geometry"/>
+                </mxCell>
+                <mxCell id="3" value="&lt;span style=&quot;font-weight: normal;&quot;&gt;Electrochemistry Domain Ontology&lt;/span&gt;" style="text;strokeColor=none;fillColor=none;html=1;fontSize=24;fontStyle=1;verticalAlign=middle;align=center;" vertex="1" parent="1">
+                    <mxGeometry x="320" y="160" width="380" height="40" as="geometry"/>
+                </mxCell>
+                <mxCell id="12" value="" style="group" vertex="1" connectable="0" parent="1">
+                    <mxGeometry x="140" y="40" width="181.1" height="161.88" as="geometry"/>
+                </mxCell>
+                <mxCell id="8" value="" style="ellipse;whiteSpace=wrap;html=1;fontSize=104;fillColor=none;rotation=30;shadow=1;strokeWidth=4;strokeColor=#028cae;" vertex="1" parent="12">
+                    <mxGeometry x="9.616304589462196" y="36.42974499999999" width="161.86739082107562" height="81.84383" as="geometry"/>
+                </mxCell>
+                <mxCell id="10" value="" style="ellipse;whiteSpace=wrap;html=1;fontSize=104;fillColor=none;rotation=-210;shadow=1;strokeWidth=4;strokeColor=#028cae;" vertex="1" parent="12">
+                    <mxGeometry x="9.616304589462196" y="36.42974499999999" width="161.86739082107562" height="81.84383" as="geometry"/>
+                </mxCell>
+                <mxCell id="11" value="" style="ellipse;whiteSpace=wrap;html=1;fontSize=104;fillColor=none;rotation=90;shadow=1;strokeWidth=4;strokeColor=#028cae;" vertex="1" parent="12">
+                    <mxGeometry x="9.616304589462196" y="40.018084999999985" width="161.86739082107562" height="81.84383" as="geometry"/>
+                </mxCell>
+                <mxCell id="5" value="" style="ellipse;whiteSpace=wrap;html=1;aspect=fixed;fontSize=104;fillColor=#005CA2;strokeWidth=4;strokeColor=#e4c89e;" vertex="1" parent="12">
+                    <mxGeometry x="50.0831522947311" y="36.42974499999999" width="80.93369541053781" height="80.93369541053781" as="geometry"/>
+                </mxCell>
+                <mxCell id="6" value="" style="verticalLabelPosition=bottom;verticalAlign=top;html=1;shape=mxgraph.basic.polygon;polyCoords=[[0.62,0.32],[0.57,0.43],[0.62,0.43],[0.46,0.65],[0.46,0.65],[0.51,0.48],[0.46,0.48],[0.51,0.32]];polyline=0;fontSize=104;fillColor=#E4C89E;" vertex="1" parent="12">
+                    <mxGeometry x="7.59296220419875" y="3.3792449999999934" width="155.1229162035308" height="155.135" as="geometry"/>
+                </mxCell>
+            </root>
+        </mxGraphModel>
+    </diagram>
+</mxfile>

docs/scripts/apply_foops_recommendations.py

@@ -0,0 +1,64 @@
+from rdflib import Graph, Namespace, Literal
+from rdflib.namespace import RDF, RDFS, SKOS
+import sys
+
+def add_foops_recommendations(input_file, output_file):
+    """
+    Reads an ontology from a TTL file, adds extra relationships to comply with FOOPS recommendations,
+    and writes the updated ontology to a new TTL file.
+
+    Args:
+        input_file (str): Path to the input TTL file.
+        output_file (str): Path to the output TTL file where updated ontology will be saved.
+    """
+    # Define the EMMO namespace
+    EMMO = Namespace("https://w3id.org/emmo#")
+
+    # Read the original TTL file content with UTF-8 encoding
+    with open(input_file, 'r', encoding='utf-8') as file:
+        ttl_content = file.read()
+
+    # Load the TTL content into an RDFLib graph
+    graph = Graph()
+    graph.parse(data=ttl_content, format='turtle')
+
+    # Prepare to collect new triples as a list
+    new_triples = []
+
+    # Duplicate skos:prefLabel triples as rdfs:label triples
+    for subj, pred, obj in graph.triples((None, SKOS.prefLabel, None)):
+        if isinstance(obj, Literal):
+            new_triples.append((subj, RDFS.label, obj))
+
+    # Duplicate EMMO-specific annotation triples as rdfs:comment triples
+    for subj, pred, obj in graph.triples((None, EMMO.EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9, None)):
+        if isinstance(obj, Literal):
+            new_triples.append((subj, RDFS.comment, obj))
+
+    # Add new triples to the graph
+    for triple in new_triples:
+        graph.add(triple)
+
+    # Serialize the graph to the output file with UTF-8 encoding
+    graph.serialize(destination=output_file, format='turtle')
+
+def main():
+    """
+    Main function to handle command-line arguments and invoke the FOOPS compliance update.
+    """
+    # Check for command-line arguments
+    if len(sys.argv) != 3:
+        print("Usage: python convert_ttl.py <input_file> <output_file>")
+        sys.exit(1)
+
+    # Input and output file paths from command-line arguments
+    input_file = sys.argv[1]
+    output_file = sys.argv[2]
+
+    # Update the TTL file with FOOPS recommendations
+    add_foops_recommendations(input_file, output_file)
+
+    print(f"Updated TTL file saved as {output_file}")
+
+if __name__ == "__main__":
+    main()