There is a newer version of the record available.

Published August 22, 2022 | Version v1.0.1
Dataset Open

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

Authors/Creators

  • 1. University of Pittsburgh

Contributors

Project leader:

  • 1. University of Pittsburgh
  • 2. Columbia University
  • 3. Washington State University
  • 4. University of Illinois at Urbana-Champaign
  • 5. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory

Description

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

  • PheKnowLator_machine_read_merged_instance_based_OWLNETS_v1.0.1.tsv - Merged KG with ontology-grounded KG and literature-based graph as TSV file
  • nodeLabels_v1.0.1.tsv

II. NP-KG Merged gpickle format

  • PheKnowLator_machine_read_merged_instance_based_OWLNETS_v1.0.1.gpickle - Merged KG with ontology-grounded KG and literature-based graph as NetworkX multidigraph object. 
  • nodeLabels_v1.0.1.pickle - Node labels for all nodes in the KG.

III. PheKnowLator instance-based KG (v3.0.0)

  • PheKnowLator_v3.0.0_full_instance_inverseRelations_OWLNETS_NetworkxMultiDiGraph.gpickle - PheKnowLator KG with full instance build v3.0.0 as NetworkX multidigraph object.

IV. Literature-based Graph in gpickle and ntriples format

  • machine_read_merged_with_closure_v1.0.1.pickle - Pickle file of literature-based graph
  • machine_read_merged_with_closure_v1.0.1.nt - ntriples file of literature-based graph.

Notes

Supporting Grant - National Institutes of Health National Center for Complementary and Integrative Health Grant U54 AT008909

Files

Files (5.6 GB)

Name Size
md5:bdffdc1bc069aa992d04271c35ff0709
4.4 MB Download
md5:e42ce5c7971c7bf3e9388d0b1a725d4b
4.5 MB Download
md5:4f0b213ab1d2b5ffae0deeb700f1d3e9
81.7 MB Download
md5:78f46c42b08e8a023cb648754c47c5c9
68.1 MB Download
md5:028750af543a96720a69dd569f364a97
48.9 MB Download
md5:1af7bc387eb4fe9ec23e60334ea1f167
694.2 MB Download
md5:76a60da5c36c93e1099d4e7f6a45ef32
996.8 MB Download
md5:50ae9d72b43aab7fa75945f1e175e664
3.7 GB Download