python script for owl file generation from schema

Example/convert_schema_to_owl.py

+import yaml
+from linkml_runtime.linkml_model.meta import SchemaDefinition, ClassDefinition, SlotDefinition, EnumDefinition
+from linkml_runtime.utils.schemaview import SchemaView
+from rdflib import Graph, Literal, RDF, RDFS, OWL, URIRef, Namespace
+
+def load_schema(schema_file: str) -> SchemaDefinition:
+    with open(schema_file, 'r') as f:
+        schema_dict = yaml.safe_load(f)
+    return SchemaDefinition(**schema_dict)
+
+def convert_to_owl(schema: SchemaDefinition, output_file: str):
+    g = Graph()
+    base_uri = URIRef(schema.id)
+    ns = Namespace(base_uri)
+    g.bind('owl', OWL)
+    g.bind('rdfs', RDFS)
+    g.bind('ex', ns)
+
+    # Convert classes
+    for cls_name, cls in schema.classes.items():
+        class_uri = URIRef(base_uri + cls_name)
+        g.add((class_uri, RDF.type, OWL.Class))
+        g.add((class_uri, RDFS.label, Literal(cls_name)))
+        if cls.description:
+            g.add((class_uri, RDFS.comment, Literal(cls.description)))
+        if cls.is_a:
+            parent_class_uri = URIRef(base_uri + cls.is_a)
+            g.add((class_uri, RDFS.subClassOf, parent_class_uri))
+
+    # Convert slots (properties)
+    for slot_name, slot in schema.slots.items():
+        slot_uri = URIRef(base_uri + slot_name)
+        g.add((slot_uri, RDF.type, OWL.ObjectProperty if slot.range == 'uriorcurie' else OWL.DatatypeProperty))
+        g.add((slot_uri, RDFS.label, Literal(slot_name)))
+        if slot.description:
+            g.add((slot_uri, RDFS.comment, Literal(slot.description)))
+        if slot.domain:
+            domain_class_uri = URIRef(base_uri + slot.domain)
+            g.add((slot_uri, RDFS.domain, domain_class_uri))
+        if slot.range:
+            range_class_uri = URIRef(base_uri + slot.range)
+            g.add((slot_uri, RDFS.range, range_class_uri))
+
+    # Convert enums
+    for enum_name, enum in schema.enums.items():
+        enum_uri = URIRef(base_uri + enum_name)
+        g.add((enum_uri, RDF.type, OWL.Class))
+        g.add((enum_uri, RDFS.label, Literal(enum_name)))
+        for pv_name, pv in enum.permissible_values.items():
+            pv_uri = URIRef(base_uri + pv_name)
+            g.add((pv_uri, RDF.type, OWL.NamedIndividual))
+            g.add((pv_uri, RDF.type, enum_uri))
+            g.add((pv_uri, RDFS.label, Literal(pv_name)))
+            if pv.description:
+                g.add((pv_uri, RDFS.comment, Literal(pv.description)))
+
+    # Save the graph to a file
+    g.serialize(destination=output_file, format='xml')
+
+# Main function
+def main():
+    schema_file = 'pizza.yaml'
+    output_file = 'pizza_schema.owl'
+    schema = load_schema(schema_file)
+    convert_to_owl(schema, output_file)
+    print(f'Converted {schema_file} to {output_file}')
+
+if __name__ == '__main__':
+    main()

Example/pizza_schema.owl

+<?xml version="1.0" encoding="utf-8"?>
+<rdf:RDF
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+>
+  <rdf:Description rdf:about="http://example.org/pizzaSpicinessLevel">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
+    <rdfs:label>SpicinessLevel</rdfs:label>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaHot">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+    <rdf:type rdf:resource="http://example.org/pizzaSpicinessLevel"/>
+    <rdfs:label>Hot</rdfs:label>
+    <rdfs:comment>Hot level of spiciness</rdfs:comment>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaStuffedCrustBase">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+    <rdf:type rdf:resource="http://example.org/pizzaPizzaBase"/>
+    <rdfs:label>StuffedCrustBase</rdfs:label>
+    <rdfs:comment>Thick Base</rdfs:comment>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaWholeWheatBase">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+    <rdf:type rdf:resource="http://example.org/pizzaPizzaBase"/>
+    <rdfs:label>WholeWheatBase</rdfs:label>
+    <rdfs:comment>Thick Base</rdfs:comment>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaMild">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+    <rdf:type rdf:resource="http://example.org/pizzaSpicinessLevel"/>
+    <rdfs:label>Mild</rdfs:label>
+    <rdfs:comment>Mild level of spiciness</rdfs:comment>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaDeepPanBase">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+    <rdf:type rdf:resource="http://example.org/pizzaPizzaBase"/>
+    <rdfs:label>DeepPanBase</rdfs:label>
+    <rdfs:comment>Thick Base</rdfs:comment>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaThinAndCrispyBase">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+    <rdf:type rdf:resource="http://example.org/pizzaPizzaBase"/>
+    <rdfs:label>ThinAndCrispyBase</rdfs:label>
+    <rdfs:comment>Thin Base</rdfs:comment>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaMedium">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+    <rdf:type rdf:resource="http://example.org/pizzaSpicinessLevel"/>
+    <rdfs:label>Medium</rdfs:label>
+    <rdfs:comment>Medium level of spiciness</rdfs:comment>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaPizza">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
+    <rdfs:label>Pizza</rdfs:label>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaNone">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#NamedIndividual"/>
+    <rdf:type rdf:resource="http://example.org/pizzaSpicinessLevel"/>
+    <rdfs:label>None</rdfs:label>
+    <rdfs:comment>No spiciness</rdfs:comment>
+  </rdf:Description>
+  <rdf:Description rdf:about="http://example.org/pizzaPizzaBase">
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
+    <rdfs:label>PizzaBase</rdfs:label>
+  </rdf:Description>
+</rdf:RDF>

Example/visualise_owl.py

+
+import rdflib
+import networkx as nx
+import matplotlib.pyplot as plt
+from networkx.drawing.nx_pydot import graphviz_layout
+
+# Load the OWL file into an rdflib graph
+def load_owl(file_path):
+    g = rdflib.Graph()
+    g.parse(file_path, format='xml')
+    return g
+
+# Convert rdflib graph to NetworkX graph with safe node names
+def rdflib_to_networkx(graph):
+    nx_graph = nx.DiGraph()
+    for s, p, o in graph:
+        safe_s = str(s).replace(':', '_')
+        safe_o = str(o).replace(':', '_')
+        safe_p = str(p).replace(':', '_')
+        nx_graph.add_edge(safe_s, safe_o, label=safe_p)
+    return nx_graph
+
+# Visualize the graph using Matplotlib and Graphviz, and save as PNG
+def visualize_graph(nx_graph, output_file):
+    pos = graphviz_layout(nx_graph, prog='dot')
+    plt.figure(figsize=(12, 12))
+    labels = nx.get_edge_attributes(nx_graph, 'label')
+    nx.draw(nx_graph, pos, with_labels=True, node_size=3000, node_color='skyblue', font_size=10, font_weight='bold', arrows=True)
+    nx.draw_networkx_edge_labels(nx_graph, pos, edge_labels=labels, font_size=8)
+    plt.savefig(output_file, format='png')
+    plt.show()
+
+def main():
+    owl_file = 'pizza_schema.owl'
+    output_file = 'pizza_schema.png'
+    rdf_graph = load_owl(owl_file)
+    nx_graph = rdflib_to_networkx(rdf_graph)
+    visualize_graph(nx_graph, output_file)
+    print(f'Graph saved as {output_file}')
+
+if __name__ == '__main__':
+    main()
+

Example/visualise_yaml.py

+import yaml
+import networkx as nx
+import matplotlib.pyplot as plt
+from networkx.drawing.nx_pydot import graphviz_layout
+
+# Load the YAML schema
+def load_yaml(file_path):
+    with open(file_path, 'r') as f:
+        return yaml.safe_load(f)
+
+# Convert YAML schema to NetworkX graph
+def yaml_to_networkx(schema):
+    nx_graph = nx.DiGraph()
+    classes = schema.get('classes', {})
+    enums = schema.get('enums', {})
+
+    # Add classes and attributes
+    for class_name, class_info in classes.items():
+        nx_graph.add_node(class_name, type='class')
+        attributes = class_info.get('attributes', {})
+        for attr_name, attr_info in attributes.items():
+            attr_range = attr_info.get('range', 'unknown')
+            nx_graph.add_node(attr_name, type='attribute', range=attr_range)
+            nx_graph.add_edge(class_name, attr_name, label='has attribute')
+            nx_graph.add_edge(attr_name, attr_range, label='range')
+
+    # Add enums and their values
+    for enum_name, enum_info in enums.items():
+        nx_graph.add_node(enum_name, type='enum')
+        permissible_values = enum_info.get('permissible_values', {})
+        for value_name, value_info in permissible_values.items():
+            nx_graph.add_node(value_name, type='enum_value', description=value_info.get('description', ''))
+            nx_graph.add_edge(enum_name, value_name, label='has value')
+
+    return nx_graph
+
+# Visualize the graph using Matplotlib and Graphviz, and save as PNG
+def visualize_graph(nx_graph, output_file):
+    pos = graphviz_layout(nx_graph, prog='dot')
+    plt.figure(figsize=(12, 12))
+    node_labels = {node: f"{node}\n({data['type']})" for node, data in nx_graph.nodes(data=True)}
+    edge_labels = nx.get_edge_attributes(nx_graph, 'label')
+    
+    nx.draw(nx_graph, pos, labels=node_labels, with_labels=True, node_size=3000, node_color='skyblue', font_size=10, font_weight='bold', arrows=True)
+    nx.draw_networkx_edge_labels(nx_graph, pos, edge_labels=edge_labels, font_size=8)
+    
+    plt.savefig(output_file, format='png')
+    plt.show()
+
+def main():
+    yaml_file = 'pizza_schema.yaml'
+    output_file = 'pizza_schema.png'
+    schema = load_yaml(yaml_file)
+    nx_graph = yaml_to_networkx(schema)
+    visualize_graph(nx_graph, output_file)
+    print(f'Graph saved as {output_file}')
+
+if __name__ == '__main__':
+    main()