string-database▌
google-deepmind/science-skills · updated Jun 4, 2026
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### String Database
- ›name: "string-database"
- ›description: "Query the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology. Use when the user asks about interactions between specific proteins, interaction evidence, confi..."
| name | string-database |
| description | > Query the STRING database for protein-protein interactions (PPIs), functional enrichment, and homology. Use when the user asks about interactions between specific proteins, interaction evidence, confidence scores, protein interaction partners, or pathway enrichments. |
STRING Database Skill
This skill allows you to query the STRING database programmatically using a bundled Python CLI wrapper.
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://string-db.org/cgi/access, then (2) create the file recording the notification text and timestamp.
Core Rules
- MANDATORY: Ask for Species First: The STRING API requires NCBI Taxon IDs. You MUST NOT guess or assume a species. If the user does not explicitly state a species or Taxon ID, you MUST stop and ask: "Which species are you interested in? I need the NCBI Taxon ID to proceed." Even for well-known proteins like TP53, BRCA1, or MDM2 that are commonly associated with human studies, you MUST still ask — do not default to Human.
- Never print output to stdout: The
--output <file.tsv>is required. Never read large outputs into context. Instead use jq, python or file operations (grep,head) to process large output. - Map Identifiers first: If you only have common gene names (e.g.,
'TP53'), map them to STRING IDs first as this guarantees much faster server
responses. Use the
mapcommand for this. - Notification: If this skill is used, ensure this is mentioned in the output.
Tool Execution
The CLI is at scripts/string_cli.py and should be run using uv run:
uv run scripts/string_cli.py <command> [options] --output /tmp/out.tsv
Feature Domains (Progressive Disclosure)
Read the following reference files based on the user's request:
- Mapping Identifiers - Map common protein names to STRING IDs.
- Interactions & Network - Find interacting proteins, network topologies, mediators, homology, and visual network images.
- Enrichment & Functional Annotations - Analyze pathway enrichment (GO, KEGG, Pfam), PPI significance, or find all proteins associated with a specific term (e.g. Melanoma).
- Values/Ranks Enrichment - Submit full experimental datasets (e.g., logFC, p-values) for rank-based enrichment analysis using the async background API.
To begin, read the reference file most appropriate to the current task to discover the correct CLI command.
How to use string-database on Cursor
AI-first code editor with Composer
Prerequisites
Before installing skills in Cursor, ensure your development environment meets these requirements:
- ›Cursor installed and configured on your development machine
- ›Node.js version 16.0+ with npm package manager (verify with
node --version) - ›Active project directory or workspace where you want to add string-database
Execute installation command
Execute the skills CLI command in your project's root directory to begin installation:
The skills CLI fetches string-database from GitHub repository google-deepmind/science-skills and configures it for Cursor.
Select Cursor when prompted
The CLI will show a list of available agents. Use arrow keys to navigate and space to select Cursor:
Verify installation
Confirm successful installation by checking the skill directory location:
Reload or restart Cursor to activate string-database. Access the skill through slash commands (e.g., /string-database) or your agent's skill management interface.
Security & Verification Notice
We perform automated surface-level scans (Gen AI Scanner, Socket, Snyk) during installation. These checks detect common vulnerabilities but do not guarantee complete security. Always review skill source code and verify the publisher's reputation before production use.
Skills execute code in your development environment. Always verify the publisher's identity, review recent commits, and test in isolated environments before production deployment.
List & Monetize Your Skill
Submit your Claude Code skill and start earning
Use Cases▌
Task Automation & Efficiency
Automate repetitive workflows and reduce manual effort
Example
Generate reports, summarize documents, draft communications
Save 3-5 hours per week on routine tasks
Knowledge Enhancement
Learn new skills, understand complex topics, get expert guidance
Example
Explain concepts, provide examples, suggest learning resources
Accelerate learning and skill development by 2x
Quality Improvement
Enhance output quality through reviews, suggestions, and refinements
Example
Review drafts, suggest improvements, catch errors
Improve work quality by 30-40% with less effort
Implementation Guide▌
Prerequisites
- ›Claude Desktop or compatible AI client with skill support
- ›Clear understanding of task or problem to solve
- ›Willingness to iterate and refine outputs
Time Estimate
15-45 minutes depending on use case complexity
Installation Steps
- 1.Install skill using provided installation command
- 2.Test with simple use case relevant to your work
- 3.Evaluate output quality and relevance
- 4.Iterate on prompts to improve results
- 5.Integrate into regular workflow if valuable
Common Pitfalls
- ⚠Expecting perfect results without iteration
- ⚠Not providing enough context in prompts
- ⚠Using skill for tasks outside its intended scope
- ⚠Accepting outputs without review and validation
Best Practices▌
✓ Do
- +Start with clear, specific prompts
- +Provide relevant context and constraints
- +Review and refine all outputs before using
- +Iterate to improve output quality
- +Document successful prompt patterns
✗ Don't
- −Don't use without understanding skill limitations
- −Don't skip validation of outputs
- −Don't share sensitive information in prompts
- −Don't expect skill to replace human judgment
💡 Pro Tips
- ★Be specific about desired format and style
- ★Ask for multiple options to choose from
- ★Request explanations to understand reasoning
- ★Combine AI efficiency with human expertise
When to Use This▌
✓ Use When
Use when skill capabilities match your task, clear ROI on time saved, and you can validate outputs. Best for repetitive tasks, learning, and quality improvement.
✗ Avoid When
Avoid when task requires deep expertise you can't validate, involves sensitive decisions, or when learning process is more valuable than speed of completion.
Learning Path▌
- 1Familiarize yourself with skill capabilities and limitations
- 2Start with low-risk, non-critical tasks
- 3Progress to more complex and valuable use cases
- 4Build expertise through regular use and experimentation
Discussion
Product Hunt–style comments (not star reviews)- No comments yet — start the thread.
Ratings
4.7★★★★★31 reviews- ★★★★★Pratham Ware· Dec 28, 2024
We added string-database from the explainx registry; install was straightforward and the SKILL.md answered most questions upfront.
- ★★★★★Sofia Sethi· Dec 24, 2024
string-database has been reliable in day-to-day use. Documentation quality is above average for community skills.
- ★★★★★Kiara Okafor· Dec 16, 2024
Keeps context tight: string-database is the kind of skill you can hand to a new teammate without a long onboarding doc.
- ★★★★★Jin Wang· Dec 8, 2024
string-database fits our agent workflows well — practical, well scoped, and easy to wire into existing repos.
- ★★★★★Mateo Menon· Nov 15, 2024
Useful defaults in string-database — fewer surprises than typical one-off scripts, and it plays nicely with `npx skills` flows.
- ★★★★★Sofia Malhotra· Nov 11, 2024
Solid pick for teams standardizing on skills: string-database is focused, and the summary matches what you get after install.
- ★★★★★Hana Taylor· Nov 7, 2024
string-database is among the better-maintained entries we tried; worth keeping pinned for repeat workflows.
- ★★★★★Diego Li· Oct 26, 2024
Useful defaults in string-database — fewer surprises than typical one-off scripts, and it plays nicely with `npx skills` flows.
- ★★★★★Henry Taylor· Oct 6, 2024
string-database is among the better-maintained entries we tried; worth keeping pinned for repeat workflows.
- ★★★★★Jin Thompson· Oct 2, 2024
We added string-database from the explainx registry; install was straightforward and the SKILL.md answered most questions upfront.
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