scientific-skills

Scientific Skills for Claude

Natural language scientific literature search skills with semantic search over PubMed, arXiv, ChEMBL, DrugBank, bioRxiv, medRxiv, clinical trials, and more with zero API complexity.

Why These Skills Are Powerful

• No API Parameter Parsing: Just pass natural language queries - no complex search syntax or parameters needed
• Semantic Search: Understands meaning and context, not just keyword matching
• Full-Text Access: Returns complete article content, not just abstracts
• Image Links: Includes figures and images from papers
• Comprehensive Coverage: Access to ALL scientific literature across multiple databases

Example

Available Skills

Individual Data Sources (9 skills)

Skill	Data Source	Coverage
pubmed-search	PubMed	Biomedical and life sciences literature
arxiv-search	arXiv	Physics, mathematics, computer science, quantitative biology preprints
biorxiv-search	bioRxiv	Biology preprints
medrxiv-search	medRxiv	Medical and health sciences preprints
chembl-search	ChEMBL	Bioactive molecules with drug-like properties
drugbank-search	DrugBank	Comprehensive drug and drug target database
clinical-trials-search	ClinicalTrials.gov	Clinical trials registry
drug-labels-search	FDA Drug Labels	Official FDA drug information
open-targets-search	Open Targets	Drug targets and disease associations
patents-search	Patent Databases	Global patent filings

Aggregated Skills (3 skills)

Skill	Combined Sources	Best For
literature-search	PubMed + arXiv + bioRxiv + medRxiv	General scientific literature review
biomedical-search	PubMed + bioRxiv + medRxiv + ClinicalTrials + Drug Labels	Medical and clinical research
drug-discovery-search	ChEMBL + DrugBank + Drug Labels + Open Targets	Drug discovery and development

Installation

Via skills.sh (Recommended)

npx skills i yorkeccak/scientific-skills

Or browse individual skills at skills.sh - search for "yorkeccak"

Example: skills.sh/yorkeccak/scientific-skills/biomedical-search

Supports installation to multiple agents:

• Antigravity
• Claude Code
• Clawdbot
• Codex
• Cursor
• Droid
• Gemini CLI
• GitHub Copilot
• Goose
• Kilo Code
• Kiro CLI
• OpenCode
• Roo Code
• Trae
• Windsurf

Via Claude Plugin

/plugin install yorkeccak/scientific-skills

Manual Installation

# Clone the repository
cd ~/dev
git clone https://github.com/yorkeccak/scientific-skills.git

# Add as a local plugin
/plugin add ~/dev/scientific-skills

Quick Start

1. Get an API Key for the Valyu search

There is $10 free credits: platform.valyu.ai

2. First Use (Automatic Setup)

Just start using any skill! Claude will automatically:

1. Detect that no API key is configured
2. Ask you to paste your API key
3. Save it to ~/.valyu/config.json
4. Run your search

You: Search PubMed for CRISPR advances in 2024
Claude: "To search PubMed, I need your Valyu API key from https://platform.valyu.ai"
You: val_abc123...
Claude: [saves key and runs search automatically]

3. Manual Setup (Optional)

If you prefer to set up manually:

Environment Variable (recommended):

# For Zsh (macOS default)
echo 'export VALYU_API_KEY="your-api-key-here"' >> ~/.zshrc
source ~/.zshrc

# For Bash
echo 'export VALYU_API_KEY="your-api-key-here"' >> ~/.bashrc
source ~/.bashrc

Config File:

mkdir -p ~/.valyu
echo '{"apiKey": "your-api-key-here"}' > ~/.valyu/config.json

Output Format

All skills return consistent JSON output:

{
  "success": true,
  "type": "pubmed_search",
  "query": "your query",
  "result_count": 10,
  "results": [
    {
      "title": "Article Title",
      "url": "https://...",
      "content": "Full article text with figures...",
      "source": "pubmed",
      "relevance_score": 0.95,
      "images": ["https://example.com/figure1.jpg"]
    }
  ],
  "cost": 0.025
}

Processing Results with jq

# Get article titles
scripts/search "query" 10 | jq -r '.results[].title'

# Get URLs
scripts/search "query" 10 | jq -r '.results[].url'

# Extract content
scripts/search "query" 10 | jq -r '.results[].content'

# Filter by relevance score
scripts/search "query" 20 | jq '.results[] | select(.relevance_score > 0.9)'

Common Use Cases

Literature Review

Search across all scientific literature:

cd ~/dev/scientific-skills/skills/literature-search
scripts/search "epigenetic modifications in cancer" 50

Drug Discovery

Find compounds and targets: