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tooluniverse-expression-data-retrieval
Maintainer FreedomIntelligence · Last updated April 1, 2026
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.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tooluniverse-expression-data-retrieval
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- 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.
- [ ] Official gene symbol identified (HGNC for human, MGI for mouse).
- [ ] Common aliases noted for search expansion.
- [ ] Species confirmed.
Source Doc
Excerpt From SKILL.md
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)
1.1 Gene Name Resolution
If searching by gene, first resolve official identifiers:
from tooluniverse import ToolUniverse
tu = ToolUniverse()
tu.load_tools()
## 1.2 Construct Search Strategy
| 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 (RNA-seq, microarray) |
---
Use cases
- Use when users need expression data, omics datasets, or mention ArrayExpress (E-MTAB, E-GEOD) or BioStudies (S-BSST) accessions.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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