Query PrimeKG for genes, drugs, diseases, and phenotypes via Python.
npx skills add https://github.com/youyinnn/skills-collection --skill primekg
Please help me install this Agent Skill. Skill: primekg Source: https://github.com/youyinnn/skills-collection/tree/main/plugins/model-development-and-experiments/skills/primekg Command: npx skills add https://github.com/youyinnn/skills-collection --skill primekg
This Skill addresses the challenge of navigating and extracting complex biological and medical data by providing programmatic access to the Precision Medicine Knowledge Graph (PrimeKG).
Use the primekg skill to find all genes associated with 'Alzheimer's disease'.
High-intent search queries and answers about installing and using this skill.
To query a precision medicine knowledge graph for disease-associated genes, you can use programmatic Python scripts to search for the disease node and retrieve its direct gene neighbors. This allows you to extract multiscale biological data for target discovery.
Finding drug repurposing opportunities with a bioinformatics knowledge graph involves using pathfinding scripts to identify paths between drugs and diseases. You can also retrieve drugs that interact with genes associated with the target disease.
Yes, you can retrieve direct drug and phenotype associations for a disease programmatically. By querying the knowledge graph for disease context analysis, you can summarize key associated genes, drugs, and phenotypes automatically without manual database searches.
Yes, the PrimeKG skill supports programmatic access via Python scripts for node searching and neighbor retrieval. It allows you to find nodes for genes, drugs, diseases, and phenotypes, and retrieve their direct associations.
This precision medicine knowledge graph integrates multiscale biological data from over 20 primary databases and scientific literature. It consolidates data on genes, drugs, diseases, and phenotypes to facilitate knowledge-based drug discovery.
Limitations of using this knowledge graph for phenotype analysis include relying on pre-integrated data from primary databases and scientific literature, which may restrict real-time updates or novel, unindexed gene-disease associations not yet present in the graph.
felixboehmQuery PrimeKG for genes, drugs, diseases, and phenotypes via Python scripts.
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shushuznSearch biomedical entities and extract neighbor associations from the PrimeKG knowledge graph.
