tooluniverse-expression-data-retrieval

Retrieve gene expression experiments and multi-omics datasets with disambiguation and quality assessment.

mims-harvard/tooluniverse|Updated Apr 8, 2026

Works with

Claude CodeCursorClineWindsurfCodexGoose

Installation Guide

Select your AI agent

How to use tooluniverse-expression-data-retrieval on Cursor

AI-first code editor with Composer

Prerequisites

Before installing skills in Cursor, ensure your development environment meets these requirements:

›Cursor installed and configured on your machine
›Node.js 16+ with npm — verify with node --version
›Active project directory where you want to add tooluniverse-expression-data-retrieval

Run the install command

Execute the skills CLI command in your project's root directory to begin installation:

$npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-expression-data-retrieval

Fetches tooluniverse-expression-data-retrieval from mims-harvard/tooluniverse and configures it for Cursor.

Select Cursor when prompted

The CLI shows a list of agents. Use arrow keys and space to select Cursor:

◆ Which agents do you want to install to?

│

│ ── Universal (.agents/skills) ────────────────

│ · Cline · Codex · Goose · Windsurf

│ ●Cursor(selected)

│ · Cursor · Aider · Continue

Verify installation

Confirm successful installation by checking the skill directory location:

.cursor/skills/tooluniverse-expression-data-retrieval

Restart Cursor to activate tooluniverse-expression-data-retrieval. Access via /tooluniverse-expression-data-retrieval in your agent's command palette.

⚠

Security Notice

We perform automated surface-level scans (Gen AI Scanner, Socket, Snyk) during installation. These checks detect common vulnerabilities but do not guarantee complete security. Always review skill source code and verify the publisher's reputation before production use.

Skills execute code in your environment. Always review source, verify the publisher, and test in isolation before production.

›View source on GitHub ›Skills CLI docs ›About Cursor ›What are agent skills?

Documentation

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Use Cases

User Story & Requirements Generation

Create detailed user stories, acceptance criteria, and feature specs

Example

Generate user stories for 'password reset feature' with acceptance criteria, edge cases, and test scenarios

✓

Reduce spec writing time by 50%, ensure comprehensive coverage

Competitive Analysis

Research competitors, compare features, identify gaps

Example

Analyze 5 competitor products, create feature comparison matrix, suggest differentiation opportunities

✓

Complete competitive research in 2 hours instead of 2 days

Roadmap Prioritization

Evaluate features using frameworks (RICE, ICE, Kano) and create prioritized backlogs

Example

Score 20 feature ideas using RICE framework, generate prioritized roadmap with rationale

User Query Type	Search Strategy
Specific accession	Direct retrieval
Gene + condition	"[gene] [condition]" + species filter
Disease only	"[disease]" + species filter
Technology-specific	Add platform keywords

Primary	Fallback
ArrayExpress search	BioStudies search
arrayexpress_get_experiment	biostudies_get_study
arrayexpress_get_experiment_files	Note "Files unavailable"

Tier	Symbol	Criteria
High	●●●	>=3 bio replicates, complete metadata, processed data available
Medium	●●○	2-3 replicates OR some metadata gaps
Low	●○○	No replicates, sparse metadata, or access issues
Caution	○○○	Single sample, no replication, outdated platform

Error	Response
"No experiments found"	Broaden keywords, remove species filter, try synonyms
"Accession not found"	Verify format, check if withdrawn
"Files not available"	Note: "Data files restricted by submitter"
"API timeout"	Retry once, note "(metadata retrieval incomplete)"

tooluniverse-expression-data-retrieval

Installation Guide

How to use tooluniverse-expression-data-retrieval on Cursor

Prerequisites

Run the install command

Select Cursor when prompted

Verify installation

Security Notice

Documentation

List & Monetize Your Skill

Use Cases

User Story & Requirements Generation

Competitive Analysis

Roadmap Prioritization

Install Skill

Gene Expression & Omics Data Retrieval

Domain Reasoning

Workflow

Phase 0: Clarification (When Needed)

Phase 1: Query Disambiguation

Phase 2: Data Retrieval (Internal)

Fallback Chains

Phase 3: Report Dataset Profile

Data Quality Tiers

Reasoning Framework

Synthesis Questions

Error Handling

Tool Reference

Search Parameters

Stakeholder Communication

Implementation Guide

Best Practices

When to Use This

Learning Path

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Reviews

Discussion