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primekg

Maintainer K-Dense Inc. (PrimeKG original from Harvard MIMS) · Last updated April 1, 2026

PrimeKG is a precision medicine knowledge graph that integrates over 20 primary databases and high-quality scientific literature into a single resource. It contains over 100,000 nodes and 4 million edges across 29 relationship types, including drug-target, disease-gene, and phenotype-disease associations. **Key capabilities:** - Search for nodes (genes, proteins, drugs, diseases, phenotypes) - Retrieve direct neighb….

Claude CodeAnalysisReproductionprimekgchemistrypackagecheminformatics & drug discovery

Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/primekg

Maintainer
K-Dense Inc. (PrimeKG original from Harvard MIMS)
License
Unknown
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Search for nodes (genes, proteins, drugs, diseases, phenotypes).
  • Retrieve direct neighbors (associated entities and clinical evidence).
  • Analyze local disease context (related genes, drugs, phenotypes).
  • Identify drug-disease paths (potential repurposing opportunities).
  • PrimeKG is a precision medicine knowledge graph that integrates over 20 primary databases and high-quality scientific literature into a single resource. It contains over 100,000 nodes and 4 million edges across 29 relationship types, including drug-target, disease-gene, and phenotype-disease associations.

Source Doc

Excerpt From SKILL.md

When to Use This Skill

This skill should be used when:

  • Knowledge-based drug discovery: Identifying targets and mechanisms for diseases.
  • Drug repurposing: Finding existing drugs that might have evidence for new indications.
  • Phenotype analysis: Understanding how symptoms/phenotypes relate to diseases and genes.
  • Multiscale biology: Bridging the gap between molecular targets (genes) and clinical outcomes (diseases).
  • Network pharmacology: Investigating the broader network effects of drug-target interactions.

1. Search for Entities

Find identifiers for genes, drugs, or diseases.

from scripts.query_primekg import search_nodes

## 2. Get Neighbors (Direct Associations)

Retrieve all connected nodes and relationship types.

```python
from scripts.query_primekg import get_neighbors

Use cases

  • **Knowledge-based drug discovery:** Identifying targets and mechanisms for diseases.
  • **Drug repurposing:** Finding existing drugs that might have evidence for new indications.
  • **Phenotype analysis:** Understanding how symptoms/phenotypes relate to diseases and genes.
  • **Multiscale biology:** Bridging the gap between molecular targets (genes) and clinical outcomes (diseases).

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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