NP-KG: Knowledge Graph 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.
File Descriptions:
I. NP-KG Merged TSV format

NP-KG_v2.0.0.tsv - Merged KG with ontology-grounded KG and literature-based graph as TSV file
nodeLabels_v2.0.0.tsv
II. NP-KG Merged gpickle format

NP-KG_v2.0.0.gpickle - Merged KG with ontology-grounded KG and literature-based graph as NetworkX multidigraph object.
nodeLabels_v2.0.0.pickle - Node labels for all nodes in the KG in dictionary format.
III. PheKnowLator instance-based KG (v3.1.1)

PheKnowLator_v3.1.1_full_instance_inverseRelations_OWLNETS_NetworkxMultiDiGraph.gpickle - PheKnowLator KG with full instance build v3.1.1 as NetworkX multidigraph object.
IV. Literature-based Graph in gpickle and ntriples format

machine_read_merged_v2.0.0.gpickle - Literature-based graph
machine_read_merged_with_closure_v2.0.0.nt

NP-KG是一款生物医学知识图谱（Knowledge Graph, KG），用于识别药代动力学维度的天然产物-药物相互作用（natural product-drug interactions, NPDIs）并生成其机制假说。NP-KG依托PheKnowLator生态系统构建本体锚定知识图谱，随后通过两套关系抽取系统从天然产物相关生物医学文献中抽取三元组，构建基于文献的知识图谱，并将该图谱与本体锚定知识图谱中的节点和边进行整合。更多细节与使用说明请参阅GitHub仓库：https://github.com/sanyabt/np-kg。
文件说明：
I. NP-KG 合并TSV格式
NP-KG_v2.0.0.tsv —— 整合本体锚定知识图谱与基于文献知识图谱的合并版知识图谱，格式为TSV文件
nodeLabels_v2.0.0.tsv
II. NP-KG 合并gpickle格式
NP-KG_v2.0.0.gpickle —— 以NetworkX多有向图（multidigraph）对象存储的整合版知识图谱，包含本体锚定知识图谱与基于文献知识图谱
nodeLabels_v2.0.0.pickle —— 以字典格式存储的知识图谱所有节点的标签文件
III. 基于实例的PheKnowLator知识图谱（v3.1.1）
PheKnowLator_v3.1.1_full_instance_inverseRelations_OWLNETS_NetworkxMultiDiGraph.gpickle —— 以NetworkX多有向图对象存储的完整实例构建版PheKnowLator知识图谱v3.1.1
IV. 基于文献的知识图谱（gpickle与ntriples格式）
machine_read_merged_v2.0.0.gpickle —— 基于文献构建的知识图谱
machine_read_merged_with_closure_v2.0.0.nt