rdflib_for_edamfu.ipynb

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    "input_owl_string = \"\"\"<?xml version=\"1.0\"?>\n",
    "<rdf:RDF xmlns=\"http://edamontology.org/\"\n",
    "     xml:base=\"http://edamontology.org/\"\n",
    "     xmlns:dc=\"http://purl.org/dc/elements/1.1/\"\n",
    "     xmlns:dcterms=\"http://purl.org/dc/terms/\"\n",
    "     xmlns:owl=\"http://www.w3.org/2002/07/owl#\"\n",
    "     xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"\n",
    "     xmlns:skos=\"http://www.w3.org/2004/02/skos/core#\"\n",
    "     xmlns:xml=\"http://www.w3.org/XML/1998/namespace\"\n",
    "     xmlns:xsd=\"http://www.w3.org/2001/XMLSchema#\"\n",
    "     xmlns:doap=\"http://usefulinc.com/ns/doap#\"\n",
    "     xmlns:foaf=\"http://xmlns.com/foaf/0.1/\"\n",
    "     xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"\n",
    "     xmlns:oboInOwl=\"http://www.geneontology.org/formats/oboInOwl#\"\n",
    "     xmlns:oboLegacy=\"http://purl.obolibrary.org/obo/\">\n",
    "    <owl:Ontology rdf:about=\"http://edamontology.org\">\n",
    "        <next_id>4040</next_id>\n",
    "    </owl:Ontology>\n",
    "    \n",
    "\n",
    "\n",
    "    <!-- http://edamontology.org/data_0007 -->\n",
    "\n",
    "    <owl:Class rdf:about=\"http://edamontology.org/data_0007\">\n",
    "        <rdfs:subClassOf rdf:resource=\"http://www.w3.org/2002/07/owl#DeprecatedClass\"/>\n",
    "        <created_in>beta12orEarlier</created_in>\n",
    "        <obsolete_since>beta12orEarlier</obsolete_since>\n",
    "        <oldParent rdf:resource=\"http://www.w3.org/2002/07/owl#Thing\"/>\n",
    "        <oboInOwl:hasDefinition>A bioinformatics package or tool, e.g. a standalone application or web service.</oboInOwl:hasDefinition>\n",
    "        <oboInOwl:inSubset rdf:resource=\"http://edamontology.org/obsolete\"/>\n",
    "        <oboInOwl:replacedBy rdf:resource=\"http://edamontology.org/data_0958\"/>\n",
    "        <rdfs:label>Tool</rdfs:label>\n",
    "        <owl:deprecated rdf:datatype=\"http://www.w3.org/2001/XMLSchema#boolean\">true</owl:deprecated>\n",
    "    </owl:Class>\n",
    "    \n",
    "\n",
    "\n",
    "    <!-- http://edamontology.org/data_0581 -->\n",
    "\n",
    "    <owl:Class rdf:about=\"http://edamontology.org/data_0581\">\n",
    "        <rdfs:subClassOf rdf:resource=\"http://www.w3.org/2002/07/owl#DeprecatedClass\"/>\n",
    "        <created_in>beta12orEarlier</created_in>\n",
    "        <obsolete_since>beta12orEarlier</obsolete_since>\n",
    "        <oldParent rdf:resource=\"http://www.w3.org/2002/07/owl#Thing\"/>\n",
    "        <oboInOwl:hasDefinition>A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model.</oboInOwl:hasDefinition>\n",
    "        <oboInOwl:inSubset rdf:resource=\"http://edamontology.org/obsolete\"/>\n",
    "        <oboInOwl:replacedBy rdf:resource=\"http://edamontology.org/data_0957\"/>\n",
    "        <rdfs:label>Database</rdfs:label>\n",
    "        <owl:deprecated rdf:datatype=\"http://www.w3.org/2001/XMLSchema#boolean\">true</owl:deprecated>\n",
    "    </owl:Class>\n",
    "\n",
    "    <!-- http://www.w3.org/2002/07/owl#DeprecatedClass -->\n",
    "\n",
    "    <owl:Class rdf:about=\"http://www.w3.org/2002/07/owl#DeprecatedClass\"/>\n",
    "</rdf:RDF>\n",
    "\"\"\""
   ]
  },
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   "cell_type": "code",
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   "id": "b7e77467-4816-4447-8828-a88d05adfce0",
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<?xml version=\"1.0\" ?>\n",
      "<rdf:RDF xmlns=\"http://edamontology.org/\" xmlns:oboInOwl=\"http://www.geneontology.org/formats/oboInOwl#\" xmlns:owl=\"http://www.w3.org/2002/07/owl#\" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\">\n",
      "\t\n",
      "  \n",
      "\t<rdf:Description rdf:about=\"http://edamontology.org/data_0581\">\n",
      "\t\t\n",
      "    \n",
      "\t\t<rdf:type rdf:resource=\"http://www.w3.org/2002/07/owl#Class\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<rdfs:subClassOf rdf:resource=\"http://www.w3.org/2002/07/owl#DeprecatedClass\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<created_in>beta12orEarlier</created_in>\n",
      "\t\t\n",
      "    \n",
      "\t\t<obsolete_since>beta12orEarlier</obsolete_since>\n",
      "\t\t\n",
      "    \n",
      "\t\t<oldParent rdf:resource=\"http://www.w3.org/2002/07/owl#Thing\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<oboInOwl:hasDefinition>A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model.</oboInOwl:hasDefinition>\n",
      "\t\t\n",
      "    \n",
      "\t\t<oboInOwl:inSubset rdf:resource=\"http://edamontology.org/obsolete\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<oboInOwl:replacedBy rdf:resource=\"http://edamontology.org/data_0957\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<rdfs:label>Database</rdfs:label>\n",
      "\t\t\n",
      "    \n",
      "\t\t<owl:deprecated rdf:datatype=\"http://www.w3.org/2001/XMLSchema#boolean\">true</owl:deprecated>\n",
      "\t\t\n",
      "  \n",
      "\t</rdf:Description>\n",
      "\t\n",
      "  \n",
      "\t<rdf:Description rdf:about=\"http://edamontology.org/data_0007\">\n",
      "\t\t\n",
      "    \n",
      "\t\t<rdf:type rdf:resource=\"http://www.w3.org/2002/07/owl#Class\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<rdfs:subClassOf rdf:resource=\"http://www.w3.org/2002/07/owl#DeprecatedClass\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<created_in>beta12orEarlier</created_in>\n",
      "\t\t\n",
      "    \n",
      "\t\t<obsolete_since>beta12orEarlier</obsolete_since>\n",
      "\t\t\n",
      "    \n",
      "\t\t<oldParent rdf:resource=\"http://www.w3.org/2002/07/owl#Thing\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<oboInOwl:hasDefinition>A bioinformatics package or tool, e.g. a standalone application or web service.</oboInOwl:hasDefinition>\n",
      "\t\t\n",
      "    \n",
      "\t\t<oboInOwl:inSubset rdf:resource=\"http://edamontology.org/obsolete\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<oboInOwl:replacedBy rdf:resource=\"http://edamontology.org/data_0958\"/>\n",
      "\t\t\n",
      "    \n",
      "\t\t<rdfs:label>Tool</rdfs:label>\n",
      "\t\t\n",
      "    \n",
      "\t\t<owl:deprecated rdf:datatype=\"http://www.w3.org/2001/XMLSchema#boolean\">true</owl:deprecated>\n",
      "\t\t\n",
      "  \n",
      "\t</rdf:Description>\n",
      "\t\n",
      "  \n",
      "\t<rdf:Description rdf:about=\"http://www.w3.org/2002/07/owl#DeprecatedClass\">\n",
      "\t\t\n",
      "    \n",
      "\t\t<rdf:type rdf:resource=\"http://www.w3.org/2002/07/owl#Class\"/>\n",
      "\t\t\n",
      "  \n",
      "\t</rdf:Description>\n",
      "\t\n",
      "\n",
      "</rdf:RDF>\n",
      "\n"
     ]
    }
   ],
   "source": [
    "from rdflib import Graph, URIRef, RDF, OWL, Namespace\n",
    "\n",
    "from rdflib.plugins.serializers.rdfxml import XMLSerializer\n",
    "\n",
    "from io import BytesIO\n",
    "\n",
    "import xml.dom.minidom\n",
    "\n",
    "def create_owl_elements(input_owl_string):\n",
    "    try:\n",
    "         # Define custom namespace prefixes\n",
    "        edam_namespace = Namespace(\"http://edamontology.org/\")\n",
    "        dc_namespace = Namespace(\"http://purl.org/dc/elements/1.1/\")\n",
    "        dcterms_namespace = Namespace(\"http://purl.org/dc/terms/\")\n",
    "        owl_namespace = Namespace(\"http://www.w3.org/2002/07/owl#\")\n",
    "        rdf_namespace = Namespace(\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\")\n",
    "        skos_namespace = Namespace(\"http://www.w3.org/2004/02/skos/core#\")\n",
    "        xml_namespace = Namespace(\"http://www.w3.org/XML/1998/namespace\")\n",
    "        xsd_namespace = Namespace(\"http://www.w3.org/2001/XMLSchema#\")\n",
    "        doap_namespace = Namespace(\"http://usefulinc.com/ns/doap#\")\n",
    "        foaf_namespace = Namespace(\"http://xmlns.com/foaf/0.1/\")\n",
    "        rdfs_namespace = Namespace(\"http://www.w3.org/2000/01/rdf-schema#\")\n",
    "        oboInOwl_namespace = Namespace(\"http://www.geneontology.org/formats/oboInOwl#\")\n",
    "        oboLegacy_namespace = Namespace(\"http://purl.obolibrary.org/obo/\")\n",
    "\n",
    "        # Load the RDF graph from the input string with explicit namespaces\n",
    "        namespaces = {\n",
    "            \"\": edam_namespace,\n",
    "            \"dc\": dc_namespace,\n",
    "            \"dcterms\": dcterms_namespace,\n",
    "            \"owl\": owl_namespace,\n",
    "            \"rdf\": rdf_namespace,\n",
    "            \"skos\": skos_namespace,\n",
    "            \"xml\": xml_namespace,\n",
    "            \"xsd\": xsd_namespace,\n",
    "            \"doap\": doap_namespace,\n",
    "            \"foaf\": foaf_namespace,\n",
    "            \"rdfs\": rdfs_namespace,\n",
    "            \"oboInOwl\": oboInOwl_namespace,\n",
    "            \"oboLegacy\": oboLegacy_namespace,            \n",
    "        }\n",
    "        graph = Graph()\n",
    "        graph.parse(data=input_owl_string, format=\"xml\", namespaces=namespaces)\n",
    "\n",
    "\n",
    "        # Create a new graph for the result\n",
    "        result_graph = Graph()\n",
    "        # Replace namespace prefixes in the result graph to use the \"canonical\" ones\n",
    "        for prefix, namespace in namespaces.items():\n",
    "            result_graph.bind(prefix, namespace, replace=True)\n",
    "\n",
    "        # Iterate through each class in the input graph\n",
    "        for class_uri in graph.subjects(RDF.type, OWL.Class):\n",
    "            class_element = URIRef(class_uri)\n",
    "\n",
    "            # Add owl:Class triple\n",
    "            result_graph.add((class_element, RDF.type, OWL.Class))\n",
    "\n",
    "            # Add other properties to the owl:Class element\n",
    "            for triple in graph.triples((class_uri, None, None)):\n",
    "                result_graph.add((class_element, triple[1], triple[2]))\n",
    "\n",
    "        # Create an XMLSerializer instance\n",
    "        serializer = XMLSerializer(result_graph)\n",
    "\n",
    "        # Use BytesIO to create an in-memory file-like object for bytes\n",
    "        stream = BytesIO()\n",
    "\n",
    "        # Serialize the modified graph to the in-memory stream\n",
    "        serializer.serialize(stream)\n",
    "\n",
    "        # Get the resulting string from the stream\n",
    "        result_string = xml.dom.minidom.parseString(stream.getvalue()).toprettyxml()\n",
    "        \n",
    "        return result_string\n",
    "\n",
    "    except Exception as e:\n",
    "        print(f\"An error occurred: {e}\")\n",
    "        return None\n",
    "\n",
    "# Perform reformatting and get the resulting OWL string\n",
    "result_owl_string = create_owl_elements(input_owl_string)\n",
    "\n",
    "if result_owl_string is not None:\n",
    "    print(result_owl_string)\n",
    "else:\n",
    "    print(\"Error processing OWL data.\")\n",
    "\n"
   ]
  },
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