primekg
Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological relationships across genes and proteins, drugs, diseases, phenotypes, pathways, biological processes, exposures and anatomy. Use this skill to search entities by name, pull direct neighbours and their evidence types, summarise the local network around a disease, and find direct or two-hop drug-disease connections for repurposing hypotheses. Also trigger on PrimeKG, kg.csv, Harvard Dataverse knowledge graph, disease_protein, drug_protein, indication and contraindication edges, or network pharmacology over a biomedical knowledge graph.
- Version
- 1.3
- License
- MIT
- Compatibility
- Requires Python 3.10+ with pandas. Needs the PrimeKG edge list (kg.csv, roughly 4 million rows and several hundred MB) downloaded from Harvard Dataverse and pointed at with the PRIMEKG_DATA environment variable. No network access at query time; the whole graph is read into memory, so budget a few GB of RAM.
Pinned to revision f67572246d9b, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
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