NP-KG: Knowledge Graph Framework for Natural Product-Drug Interactions

NP-KG is a biomedical knowledge graph (KG) to identify and generate mechanistic hypotheses for pharmacokinetic natural product-drug interactions (NPDIs). NP-KG uses the PheKnowLator ecosystem to create an ontology-grounded KG. It then uses two relation extraction systems to extract triples from natural product-related biomedical literature to create a literature-based graph, and integrates the nodes and edges in the ontology-grounded KG. See GitHub repository for more details and instructions: https://github.com/sanyabt/np-kg. <strong>File Descriptions:</strong> <em>1. nodeLabels_v1.0.pickle - </em>Node labels for all nodes in the KG. <em>2. PheKnowLator_machine_read_merged_instance_based_OWLNETS_v1.0.gpickle - </em>Merged KG with ontology-grounded KG and literature-based graph as NetworkX multidigraph object. <em>3. PheKnowLator_machine_read_merged_instance_based_OWLNETS_v1.0.nt - </em>Triples in merged KG with ontology-grounded KG and literature-based graph in ntriples file. <em>4. machine_read_merged_with_closure_v1.0.pickle - </em>Pickle file of literature-based graph. <em>5. machine_read_merged_with_closure_v1.0.nt - </em>ntriples file of literature-based graph. <em>6. PheKnowLator_v3.0.0_full_instance_inverseRelations_OWLNETS_NetworkxMultiDiGraph.gpickle - </em>PheKnowLator KG with full instance build v3.0.0 as NetworkX multidigraph object. <em>7. PheKnowLator_v3.0.0_full_instance_inverseRelations_OWLNETS_20220616.nt - </em>PheKnowLator KG with full instance build v3.0.0 as ntriples file.