string-database
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.
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Install
Works with every agent the skills CLI supports.
npx skills add https://github.com/google-deepmind/science-skills --skill string-database- 01
Install
Run the command in your project. The CLI asks which agents to install for.
- 02
Describe the task
Ask your agent for something this skill covers. It loads string-database automatically when relevant.
- 03
Review the result
The agent follows the SKILL.md steps, scripts and references bundled with the skill.
SKILL.md
The instructions your agent reads when the skill is triggered.
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 .licenses/string_database_LICENSE.txt does not already exist in the workspace root 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.
FAQ
What does the string-database skill do?
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.
How do I install string-database?
Run npx skills add https://github.com/google-deepmind/science-skills --skill string-database in your project. The skills CLI detects the agents you use and copies the skill into the right folder. For Claude Code you can also place the skill folder at ~/.claude/skills/string-database/ (personal) or .claude/skills/string-database/ (project).
Which AI agents can use string-database?
Any agent that supports the open Agent Skills format (a folder with a SKILL.md file), including Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, Windsurf, Cline, OpenCode and more.
Is string-database safe to install?
No partner security audit is available yet. Skills can run commands and scripts, so read the SKILL.md and any bundled files before installing.
Who maintains string-database?
It is published by google-deepmind in google-deepmind/science-skills. It has 2,153 recorded installs.
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