Update nb

Run-KG-COVID-19-pipeline.ipynb → example-KG-COVID-19-usage.ipynb

@@ -419,9 +419,36 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'nodes_number': '377577',\n",
+       " 'is_directed': 'false',\n",
+       " 'density': '0.00021710748243868716',\n",
+       " 'degrees_min': '0',\n",
+       " 'traps_rate': '0.022019349695558788',\n",
+       " 'bidirectional_rate': '1',\n",
+       " 'degrees_mean': '81.97479189675218',\n",
+       " 'selfloops_rate': '0.00001554029368764255',\n",
+       " 'connected_components_number': '9068',\n",
+       " 'degrees_mode': '1',\n",
+       " 'singleton_nodes': '8314',\n",
+       " 'degrees_max': '90378',\n",
+       " 'edges_number': '30951796',\n",
+       " 'unique_node_types_number': '37',\n",
+       " 'unique_edge_types_number': '33',\n",
+       " 'strongly_connected_components_number': '9068',\n",
+       " 'degrees_median': '6'}"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "graph = EnsmallenGraph.from_csv(\n",
     "    edge_path=\"merged-kg_edges.tsv\",\n",
@@ -466,18 +493,55 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/home/reeseju/kg-covid-19/kg_covid_19/query.py:17: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.\r\n",
+      "  return yaml.load(open(yaml_file))\r\n"
+     ]
+    }
+   ],
    "source": [
     "!python run.py query -y queries/sparql/query-01-bl-cat-counts.yaml # or make a new YAML file and write your own query"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['v1', 'v0']\n",
+      "['199', 'organism taxon']\n",
+      "['19131', 'https://w3id.org/biolink/vocab/Gene']\n",
+      "['3908', 'https://w3id.org/biolink/vocab/NamedThing']\n",
+      "['20167', 'https://w3id.org/biolink/vocab/Protein']\n",
+      "['30534', 'https://w3id.org/biolink/vocab/BiologicalProcess']\n",
+      "['4468', 'https://w3id.org/biolink/vocab/CellularComponent']\n",
+      "['30018', 'https://w3id.org/biolink/vocab/ChemicalSubstance']\n",
+      "['32228', 'https://w3id.org/biolink/vocab/Drug']\n",
+      "['12241', 'https://w3id.org/biolink/vocab/MolecularActivity']\n",
+      "['62446', 'https://w3id.org/biolink/vocab/OntologyClass']\n",
+      "['6', 'https://w3id.org/biolink/vocab/OrganismalEntity']\n",
+      "['15530', 'https://w3id.org/biolink/vocab/PhenotypicFeature']\n",
+      "['129930', 'https://w3id.org/biolink/vocab/Publication']\n",
+      "['4687', 'https://w3id.org/biolink/vocab/AnatomicalEntity']\n",
+      "['48', 'https://w3id.org/biolink/vocab/Assay']\n",
+      "['703', 'https://w3id.org/biolink/vocab/Cell']\n",
+      "['24229', 'https://w3id.org/biolink/vocab/Disease']\n",
+      "['1', 'https://w3id.org/biolink/vocab/MolecularEntity']\n",
+      "['17', 'https://w3id.org/biolink/vocab/RNA']\n",
+      "['47', 'https://w3id.org/biolink/vocab/SequenceFeature']\n"
+     ]
+    }
+   ],
    "source": [
     "# have a look at biolink category counts currently in KG-COVID-19 loaded on Blazegraph endpoint\n",
     "import csv\n",