diff --git a/Run-KG-COVID-19-pipeline.ipynb b/example-KG-COVID-19-usage.ipynb similarity index 90% rename from Run-KG-COVID-19-pipeline.ipynb rename to example-KG-COVID-19-usage.ipynb index f08a3b50..8a887775 100644 --- a/Run-KG-COVID-19-pipeline.ipynb +++ b/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",