tooluniverse-expression-data-retrieval
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports. Creates comprehensive dataset profiles with metadata, sample information, and download links. Use when users need expression data, omics datasets, or mention ArrayExpress (E-MTAB, E-GEOD) or BioStudies (S-BSST) accessions.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-expression-data-retrieval --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Gene Expression & Omics Data Retrieval Retrieve gene expression experiments and multi-omics datasets with proper disambiguation and quality assessment. **IMPORTANT**: Always use English terms in tool calls (gene names, tissue names, condition descriptions), even if the user writes in another language. Only try original-language terms as a fallback if English returns no results. Respond in the user's language. ## Workflow Overview ``` Phase 0: Clarify Query (if ambiguous) ↓ Phase 1: Disambiguate Gene/Condition ↓ Phase 2: Search & Retrieve (Internal) ↓ Phase 3: Report Dataset Profile ``` --- ## Phase 0: Clarification (When Needed) Ask the user ONLY if: - Gene name is ambiguous (e.g., "p53" → TP53 or MDM2 studies?) - Tissue/condition unclear for comparative studies - Organism not specified for non-human research Skip clarification for: - Specific accession numbers (E-MTAB-*, E-GEOD-*, S-BSST*) - Clear disease/tissue + organism combinations - Explicit platform requests (RNA-seq, microarray) --- ## Phase 1: Query Disambiguation ### 1.1 Gene Name Resolution If searching by gene, first resolve official identifiers: ```python from tooluniverse import ToolUniverse tu = ToolUniverse() tu.l
- Workflow Overview
- Phase 0: Clarification (When Needed)
- Phase 1: Query Disambiguation
- 1.1 Gene Name Resolution
- 1.2 Construct Search Strategy
- Phase 2: Data Retrieval (Internal)
- 2.1 Search Experiments
- 2.2 Get Experiment Details
- 2.3 BioStudies Retrieval
- Fallback Chains
- Phase 3: Report Dataset Profile
- Output Structure
- Data Quality Tiers
- Completeness Checklist
What does the tooluniverse-expression-data-retrieval skill do?
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports. Creates comprehensive dataset profiles with metadata, sample information, and download links. Use when users need expression data, omics datasets, or mention ArrayExpress (E-MTAB, E-GEOD) or BioStudies (S-BSST) accessions.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-expression-data-retrieval --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.