# Analyze Protein Networks with STRING

Protein interaction analysis requires specialized databases and careful identifier handling. This skill queries STRING to map proteins, retrieve networks, and assess enrichment.

## Install

```bash
npx skillstore add davila7/string-database
```

## Metadata

- Status: approved
- Slug: davila7-string-database
- Skillstore revision: r2
- Version status: missing
- Tree hash: 5b9a0cd32e8cdd351bb4fa1134f591d82fed432305bcaba6c0413b4d05aeb8a6
- Author: davila7
- GitHub username: davila7
- License: MIT
- Repository: https://github.com/davila7/claude-code-templates/tree/main/cli-tool/components/skills/scientific/string-database
- Ref: c43861a65bb95efcae259cd161c9d6f4dc7eec6f
- Supported tools: Claude, Codex, Claude Code
- Audit status: complete
- Agent install advisory: allowed
- Manual install advisory: allowed
- Artifact signature: available
- Audit attestation: unavailable
- Human verification: not\_verified
- Risk factors: network, env\_access, filesystem, scripts, external\_commands
- Quality score: 79
- Quality tier: bronze
- Public page: https://skillstore.pages.dev/skills/davila7-string-database
- Manifest: https://skillstore.pages.dev/api/skills/davila7-string-database/manifest

## Capabilities

- Maps gene names and protein identifiers to STRING identifiers.
- Retrieves functional or physical protein interaction networks with confidence thresholds.
- Finds interaction partners and expands networks with additional proteins.
- Runs GO, KEGG, Pfam, and related functional enrichment queries.
- Tests PPI enrichment and retrieves homology scores.
- Downloads STRING network visualizations as PNG image data.

## Use Cases

- Interpret proteomics results: Map an experimental protein list, retrieve its interaction network, and identify enriched biological processes.
- Develop pathway hypotheses: Expand seed proteins with high-confidence partners and compare functional versus physical associations.
- Prepare reproducible interaction reports: Record STRING version, species, thresholds, network statistics, and enrichment results for a defined protein set.

## Prompt Templates

### Map a protein name

```
Map TP53 to a human STRING identifier and explain the returned fields.
```

### Retrieve an interaction network

```
Retrieve a human interaction network for TP53, MDM2, ATM, and CHEK2 using a high-confidence threshold. Summarize the strongest associations.
```

### Assess functional enrichment

```
Analyze this protein list for GO, KEGG, and Pfam enrichment. Report significant terms, false discovery rates, and interpretation limits: [protein list].
```

### Design a cross-species comparison

```
Compare interaction evidence for [protein] in human and mouse. Map identifiers, use matching thresholds, retrieve homology, and document STRING versions and caveats.
```

## Limitations

- Requires internet access and availability of the STRING service.
- Sends identifiers, species values, and caller identity to STRING over HTTPS.
- Returns raw text or image bytes without validating response schemas.
- Requests omit explicit timeouts and only handle HTTP status errors.

## Best Practices

- Confirm permission before sending protein identifiers to STRING.
- Map identifiers and specify the NCBI taxon before network analysis.
- Record STRING version, thresholds, species, and query date for reproducible work.

## Anti Patterns

- Do not treat STRING associations as proof of direct physical binding.
- Do not submit confidential or unpublished identifiers without approval.
- Do not use low-confidence results for confirmatory conclusions.

## Security Audit

- Audited at: 2026-07-23T16:30:27.045\+00:00
- Summary: Nine low-severity indicators confirm the documented outbound STRING API behavior: eight executable HTTPS calls and their fixed service base URL. The other alerts are Markdown, documentation, import, or non-executed example false positives; no credential access, shell execution, prompt injection, or malicious intent was found.

## Stats

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- Downloads: 10
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