Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-reactomegit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-reactome)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-reactome"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-reactome/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-reactome"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-reactome.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00072 | $0.02432 |
| Opus 5.5 | $0.00029 | $0.00973 |
| Sonnet 5.5 | $0.00014 | $0.00486 |
| Haiku 4.5 | $0.00007 | $0.00243 |
Grade B, and why
alterlab-reactome scanned grade B with 2 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Sends data to an external URLmediumData exfiltration
A POST to an outside endpoint may be telemetry or may be exfiltration; either way the mod talks to somewhere, and you should know where.
response = requests.post( "https://reactome.org/AnalysisService/identifiers/", Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
allowed-tools: Read WebFetch Bash(curl:*) Bash(python:*) This is a copy
86% identical to reactome-database — 88 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 330 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Reactome Database
Overview
Reactome is a free, open-source, curated pathway database (thousands of human pathways). Query biological pathways, perform overrepresentation and expression analysis, map genes to pathways, explore molecular interactions via REST API and Python client for systems biology research.
When to Use This Skill
This skill should be used when:
- Performing pathway enrichment analysis on gene or protein lists
- Analyzing gene expression data to identify relevant biological pathways
- Querying specific pathway information, reactions, or molecular interactions
- Mapping genes or proteins to biological pathways and processes
- Exploring disease-related pathways and mechanisms
- Visualizing analysis results in the Reactome Pathway Browser
- Conducting comparative pathway analysis across species
Does NOT Trigger
| Scenario | Use Instead |
|---|---|
| KEGG pathway maps, KO orthology, KEGG compound/drug IDs | alterlab-kegg |
| Protein-protein interaction networks and STRING functional enrichment | alterlab-string-db |
| Genome-scale metabolic models and flux balance analysis | alterlab-cobrapy |
| Differential expression statistics from RNA-seq counts | alterlab-pydeseq2 |
| Target-disease evidence scoring for drug discovery | alterlab-opentargets |
Core Capabilities
Reactome provides two main API services and a Python client library:
1. Content Service - Data Retrieval
Query and retrieve biological pathway data, molecular interactions, and entity information.
Common operations:
- Retrieve pathway information and hierarchies
- Query specific entities (proteins, reactions, complexes)
- Get participating molecules in pathways
- Access database version and metadata
- Explore pathway compartments and locations
API Base URL: https://reactome.org/ContentService
2. Analysis Service - Pathway Analysis
Perform computational analysis on gene lists and expression data.
Analysis types:
- Overrepresentation Analysis: Identify statistically significant pathways from gene/protein lists
- Expression Data Analysis: Analyze gene expression datasets to find relevant pathways
- Species Comparison: Compare pathway data across different organisms
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago Changed · +11 lines 3073373f8dbb
- 1mo ago First seen · 319 lines · 72 tokens per session scan B 2ff0f710960b
alterlab-reactome is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (78 stars, last pushed 2d ago), licensed MIT. It adds 72 tokens to every session and 2,432 once invoked, about $0.0003 per session on Opus 5.5. A static security scan graded it B with 2 findings (sends data to an external url, makes network calls). It is 86% identical to reactome-database, differing in 88 lines, and is treated as a copy.
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