# Analyze Reactome Pathways

Biology teams need fast access to curated pathway data without memorizing Reactome endpoints. This skill guides Claude, Codex, and Claude Code through pathway queries, enrichment analysis, and result interpretation.

## Install

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

## Metadata

- Status: approved
- Slug: davila7-reactome-database
- Skillstore revision: r1
- Version status: missing
- Tree hash: 46966266d0de16aaba91f9476a9b56ae012783df07eb57011520ad52e319b65f
- Author: davila7
- GitHub username: davila7
- License: MIT
- Repository: https://github.com/davila7/claude-code-templates/tree/main/cli-tool/components/skills/scientific/reactome-database
- Ref: b959ebfd1043a07c0c4378ab94ca4342cb0259f5
- 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, filesystem, external\_commands
- Quality score: 79
- Quality tier: bronze
- Public page: https://skillstore.pages.dev/skills/davila7-reactome-database
- Manifest: https://skillstore.pages.dev/api/skills/davila7-reactome-database/manifest

## Capabilities

- Query Reactome Content Service endpoints for database versions, pathway records, entities, and molecular participants.
- Submit gene or protein lists to the Reactome Analysis Service for enrichment results.
- Retrieve prior pathway analysis results with Reactome analysis tokens.
- Generate Reactome Pathway Browser links for selected analysis results.
- Use the included Python helper script for version, query, search, entities, and analyze commands.
- Reference documented input formats for overrepresentation and expression analysis.

## Use Cases

- Find enriched pathways from a gene list: Submit identifiers and review significant Reactome pathways with p-values, FDR values, and matched entity counts.
- Inspect pathway participants: Retrieve proteins, complexes, and small molecules that participate in a selected Reactome pathway.
- Create reproducible pathway summaries: Use documented API calls and helper commands to create consistent pathway reports for teams.

## Prompt Templates

### Look up one pathway

```
Use the Reactome skill to summarize pathway R-HSA-69278. Include its name, species, type, and a short biological description.
```

### Analyze a gene list

```
Use the Reactome Analysis Service for these identifiers: TP53, BRCA1, EGFR, MYC. Summarize the top enriched pathways and FDR values.
```

### Compare pathway entities

```
For pathway R-HSA-69278, retrieve participating physical entities. Group the first results by entity type and explain their roles.
```

### Build a reproducible workflow

```
Design a Reactome workflow for a differential expression file. Include input validation, analysis submission, token handling, result filtering, and reporting steps.
```

## Limitations

- Requires network access to Reactome public services.
- Does not provide local copies of the Reactome database.
- Analysis tokens expire after seven days according to the skill documentation.
- The optional reactome2py package is described as functional but not actively maintained.

## Best Practices

- Confirm that gene identifiers use supported formats before submitting analysis requests.
- Tell users when identifiers or expression values will be sent to Reactome services.
- Store analysis tokens only when users need to retrieve results within seven days.

## Anti Patterns

- Do not submit private clinical or unpublished expression data without user approval.
- Do not treat Reactome enrichment results as proof of biological causality.
- Do not overwrite input files when saving helper script output.

## Security Audit

- Audited at: 2026-07-09T07:53:36.162\+00:00
- Summary: Confirmed findings are limited to expected Reactome network access and controlled result-file writes. The high device-file alerts are false positives from Reactome documentation URLs, and the command-execution alerts are Markdown formatting matches. No prompt injection or malicious intent was found in the reviewed files.

## Stats

- Views: 213
- Downloads: 10
- Favorites: 0
- Popularity score: 0