# String Database

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- **Type:** Skill
- **Install:** `agentstack add skill-google-deepmind-science-skills-string-database`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [google-deepmind](https://agentstack.voostack.com/s/google-deepmind)
- **Installs:** 0
- **Category:** [Databases](https://agentstack.voostack.com/c/databases)
- **Latest version:** 0.1.0
- **License:** Apache-2.0
- **Upstream author:** [google-deepmind](https://github.com/google-deepmind)
- **Source:** https://github.com/google-deepmind/science-skills/tree/main/skills/string_database
- **Website:** https://antigravity.google/use-cases/science

## Install

```sh
agentstack add skill-google-deepmind-science-skills-string-database
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# STRING Database Skill

This skill allows you to query the STRING database programmatically using a
bundled Python CLI wrapper.

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **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

1.  **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.
2.  **Never print output to stdout:** The `--output ` is required.
    Never read large outputs into context. Instead use jq, python or file
    operations (`grep`, `head`) to process large output.
3.  **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 `map` command for this.
4.  **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`:

```bash
uv run scripts/string_cli.py  [options] --output /tmp/out.tsv
```

## Feature Domains (Progressive Disclosure)

Read the following reference files based on the user's request:

*   **[Mapping Identifiers](references/mapping.md)** - Map common protein names
    to STRING IDs.
*   **[Interactions & Network](references/interactions.md)** - Find interacting
    proteins, network topologies, mediators, homology, and visual network
    images.
*   **[Enrichment & Functional Annotations](references/enrichment.md)** -
    Analyze pathway enrichment (GO, KEGG, Pfam), PPI significance, or find all
    proteins associated with a specific term (e.g. Melanoma).
*   **[Values/Ranks Enrichment](references/valuesranks.md)** - 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.

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [google-deepmind](https://github.com/google-deepmind)
- **Source:** [google-deepmind/science-skills](https://github.com/google-deepmind/science-skills)
- **License:** Apache-2.0
- **Homepage:** https://antigravity.google/use-cases/science

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-google-deepmind-science-skills-string-database
- Seller: https://agentstack.voostack.com/s/google-deepmind
- Browse the marketplace: https://agentstack.voostack.com/browse

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