Query the Reactome database (Analysis and Content Services).
SkillScore32Maintained
Automatic
◆Research pack
Last verified 8/22/2026
What it changes
Passed 3 of 9 test cases with the skill, and 2 of 9 without it.
Without skill20%
With skill32%
Checks it passed that the model alone missed
Includes --id R-HSA-69488
Uses the report subcommand
Includes --species-filter 9606
and 6 more in the full report
6 fixed2 passed either way14 still failing3 broke
Pass-rate lift
+12 pp
Tokens
+133%
Agent turns
0%
Response time
-37%
Model gemini-3.6-flashMeasured 8/22/2026v18 of 25 cases passed with skill · 9 comparable
Tokens, turns and time describe resource use, not a dollar price.
See it in action
One of 6 test cases the skill fixed. Same model, same prompt, with and without the skill.
1 of 6
Prompt
Given analysis token 'TOK_GAMMA' which contains mixed-species hits, I want to restrict the stored result set specifically to human pathways (species ID 9606). Which token subcommand handles species filtering?
What was checked, without and with the skill
Checked
Without skill
With skill
Uses the token-filter-species subcommand
Missed
Passed
Includes --species-filter 9606
Missed
Passed
case-20 · gemini-3.6-flash · 8/22/2026 · answers are capped and redacted
What's inside
The instructions your model reads when the skill loads.
SKILL.md269 lines3 filesincludes scripts
Reactome Analysis & Content Service
Prerequisites
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.
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://reactome.org/license and https://reactome.org/cite, then (2)
create the file recording the notification text and timestamp.
Overview
Reactome is a free, open-source, curated pathway database. This skill wraps both
the Analysis Service (https://reactome.org/AnalysisService/) and the
Content Service (https://reactome.org/ContentService/) providing pathway
enrichment analysis, identifier mapping, reaction details, pathway hierarchy
navigation, diagram export, cross-reference mapping, and search.
When to Use This Skill
Performing pathway enrichment (overrepresentation) analysis on gene/protein
lists
Retrieving analysis results using a token from previous enrichment
Identifying which genes or proteins were not found in a pathway analysis
Analyzing gene expression data against pathway annotations
Mapping identifiers to Reactome entities across species