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

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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)

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Phase 1: Query Disambiguation

1.1 Gene Name Resolution

If searching by gene, first resolve official identifiers:

from tooluniverse import ToolUniverse
tu = ToolUniverse()
tu.load_tools()

# For gene-focused searches, resolve official symbol first
# This helps construct better search queries
# Example: "p53" → "TP53" (official HGNC symbol)

Gene Disambiguation Checklist:

• Official gene symbol identified (HGNC for human, MGI for mouse)
• Common aliases noted for search expansion
• Species confirmed

1.2 Construct Search Strategy