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:
pythonfrom 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
| 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) |
Phase 2: Data Retrieval (Internal)
Search silently. Do NOT narrate the process.
2.1 Search Experiments
python# ArrayExpress search result = tu.tools.arrayexpress_search_experiments( keywords="[gene/disease] [condition]", species="[species]", limit=20 ) # BioStudies for multi-omics biostudies_result = tu.tools.biostudies_search_studies( query="[keywords]", limit=10 )
2.2 Get Experiment Details
For top results, retrieve full metadata:
python# Get details for each relevant experiment details = tu.tools.arrayexpress_get_experiment_details( accession=accession ) # Get sample information samples = tu.tools.arrayexpress_get_experiment_samples( accession=accession ) # Get available files files = tu.tools.arrayexpress_get_experiment_files( accession=accession )
2.3 BioStudies Retrieval
python# Multi-omics study details study_details = tu.tools.biostudies_get_study_details( accession=study_accession ) # Study structure sections = tu.tools.biostudies_get_study_sections( accession=study_accession ) # Available files files = tu.tools.biostudies_get_study_files( accession=study_accession )
Fallback Chains
| Primary | Fallback | Notes |
|---|---|---|
| ArrayExpress search | BioStudies search | ArrayExpress empty |
| arrayexpress_get_experiment_details | biostudies_get_study_details | E-GEOD may have BioStudies mirror |
| arrayexpress_get_experiment_files | Note "Files unavailable" | Some studies restrict downloads |
Phase 3: Report Dataset Profile
Output Structure
Present as a Dataset Search Report. Hide search process.
markdown# Expression Data: [Query Topic] **Search Summary** - Query: [gene/disease] in [species] - Databases: ArrayExpress, BioStudies - Results: [N] relevant experiments found **Data Quality Overview**: [assessment based on criteria below] --- ## Top Experiments ### 1. [E-MTAB-XXXX]: [Title] | Attribute | Value | |-----------|-------| | **Accession** | [accession with link] | | **Organism** | [species] | | **Experiment Type** | RNA-seq / Microarray | | **Platform** | [specific platform] | | **Samples** | [N] samples | | **Release Date** | [date] | **Description**: [Brief description from metadata] **Experimental Design**: - Conditions: [treatment vs control, etc.] - Replicates: [N biological, M technical] - Tissue/Cell type: [if specified] **Sample Groups**: | Group | Samples | Description | |-------|---------|-------------| | Control | [N] | [description] | | Treatment | [N] | [description] | **Data Files Available**: | File | Type | Size | |------|------|------| | [filename] | Processed data | [size] | | [filename] | Raw data | [size] | | [filename] | Sample metadata | [size] | **Quality Assessment**: ●●● High / ●●○ Medium / ●○○ Low - Sample size: [adequate/limited] - Replication: [yes/no] - Metadata completeness: [complete/partial] --- ### 2. [E-GEOD-XXXXX]: [Title] [Same structure as above] --- ## Multi-Omics Studies (from BioStudies) ### [S-BSST-XXXXX]: [Title] | Attribute | Value | |-----------|-------| | **Accession** | [accession] | | **Study Type** | [proteomics/metabolomics/integrated] | | **Organism** | [species] | | **Samples** | [N] | **Data Types Included**: - [ ] Transcriptomics - [ ] Proteomics - [ ] Metabolomics - [ ] Other: [specify] --- ## Summary Table | Accession | Type | Samples | Platform | Quality | |-----------|------|---------|----------|---------| | [E-MTAB-X] | RNA-seq | [N] | Illumina | ●●● | | [E-GEOD-X] | Microarray | [N] | Affymetrix | ●●○ | --- ## Recommendations **For [specific analysis type]**: - Best experiment: [accession] - [reason] - Alternative: [accession] - [reason] **Data Integration Notes**: - Platform compatibility: [notes on combining datasets] - Batch considerations: [if applicable] --- ## Data Access ### Direct Download Links - [E-MTAB-XXXX processed data](link) - [E-MTAB-XXXX raw data](link) ### Database Links - ArrayExpress: https://www.ebi.ac.uk/arrayexpress/experiments/[accession] - BioStudies: https://www.ebi.ac.uk/biostudies/studies/[accession] Retrieved: [date]
Data Quality Tiers
Assessment criteria for expression experiments:
| Tier | Symbol | Criteria |
|---|---|---|
| High Quality | ●●● | ≥3 bio replicates, complete metadata, processed data available |
| Medium Quality | ●●○ | 2-3 replicates OR some metadata gaps, data accessible |
| Low Quality | ●○○ | No replicates, sparse metadata, or data access issues |
| Use with Caution | ○○○ | Single sample, no replication, outdated platform |
Include assessment rationale:
markdown**Quality**: ●●● High - ✓ 4 biological replicates per condition - ✓ Complete sample annotations - ✓ Processed and raw data available - ✓ Recent RNA-seq platform
Completeness Checklist
Every dataset report MUST include:
Per Experiment (Required)
- Accession number with database link
- Organism
- Experiment type (RNA-seq/microarray/etc.)
- Sample count
- Brief description
- Quality assessment
Search Summary (Required)
- Query parameters stated
- Number of results
- Databases searched
Recommendations (Required)
- Best dataset for user's purpose (or "No suitable data found")
- Data access notes
Include Even If Empty
- Multi-omics studies section (or "No multi-omics studies found")
- Data integration notes (or "Single-platform data, no integration needed")
Common Use Cases
Disease Gene Expression
User: "Find breast cancer RNA-seq data"
pythonresult = tu.tools.arrayexpress_search_experiments( keywords="breast cancer RNA-seq", species="Homo sapiens", limit=20 )
→ Report top experiments with quality assessment
Gene-Specific Studies
User: "Find TP53 expression experiments in mouse"
pythonresult = tu.tools.arrayexpress_search_experiments( keywords="TP53 p53", # Include aliases species="Mus musculus", limit=15 )
→ Report experiments studying this gene
Specific Accession Lookup
User: "Get details for E-MTAB-5214" → Single experiment profile with all details and files
Multi-Omics Integration
User: "Find proteomics and transcriptomics studies for liver disease" → Search both ArrayExpress and BioStudies, note integration potential
Error Handling
| Error | Response |
|---|---|
| "No experiments found" | Broaden keywords, remove species filter, try synonyms |
| "Accession not found" | Verify format (E-MTAB-, E-GEOD-, S-BSST*), check if withdrawn |
| "Files not available" | Note in report: "Data files restricted by submitter" |
| "API timeout" | Retry once, then note: "(metadata retrieval incomplete)" |
Tool Reference
ArrayExpress (Gene Expression)
| Tool | Purpose |
|---|---|
arrayexpress_search_experiments | Keyword/species search |
arrayexpress_get_experiment_details | Full metadata |
arrayexpress_get_experiment_files | Download links |
arrayexpress_get_experiment_samples | Sample annotations |
BioStudies (Multi-Omics)
| Tool | Purpose |
|---|---|
biostudies_search_studies | Multi-omics search |
biostudies_get_study_details | Study metadata |
biostudies_get_study_files | Data files |
biostudies_get_study_sections | Study structure |
Search Parameters Reference
ArrayExpress
| Parameter | Description | Example |
|---|---|---|
keywords | Free text search | "breast cancer RNA-seq" |
species | Scientific name | "Homo sapiens" |
array | Platform filter | "Illumina" |
limit | Max results | 20 |
BioStudies
| Parameter | Description | Example |
|---|---|---|
query | Free text | "proteomics liver" |
limit | Max results | 10 |
