tooluniverse-metabolomics

# Metabolomics Research

Comprehensive metabolomics research skill that identifies metabolites, analyzes studies, and searches metabolomics databases. Generates structured research reports with annotated metabolite information, study details, and database statistics.

## Use Case

**Use this skill when asked to:**
- Identify or annotate metabolites (HMDB IDs, chemical properties, pathways)
- Retrieve metabolomics study information from MetaboLights or Metabolomics Workbench
- Search for metabolomics studies by keywords or disease
- Analyze metabolite profiles or datasets
- Generate comprehensive metabolomics research reports

**Example queries:**
- "What is the HMDB ID and pathway information for glucose?"
- "Get study details for MTBLS1"
- "Find metabolomics studies related to diabetes"
- "Analyze these metabolites: glucose, lactate, pyruvate"

## Databases Covered

**Primary metabolite databases:**
- **HMDB** (Human Metabolome Database): 220,000+ metabolites with structures, pathways, and biological roles
- **MetaboLights**: Public metabolomics repository with thousands of studies
- **Metabolomics Workbench**: NIH Common Fund metabolomics data repository
- **FooDB**: Food chemical-constituent database — use `FooDB_get_compound` (param `fdb_id`, e.g. `"FDB000004"`) for a food compound's structure plus HMDB/KEGG/PubChem/ChEBI cross-references; ideal for food-metabolomics annotation
- **PubChem**: Chemical properties and bioactivity data (fallback)

## Research Workflow

The skill executes a 4-phase analysis pipeline:

### Phase 1: Metabolite Identification & Annotation
For each metabolite in the input list:
1. Search HMDB by metabolite name
2. Retrieve HMDB ID, chemical formula, molecular weight
3. Get detailed metabolite information (description, pathways)
4. Fallback to PubChem for CID and chemical properties if HMDB unavailable

### Phase 2: Study Details Retrieval
For provided study IDs:
1. Detect database type (MTBLS = MetaboLights, ST = Metabolomics Workbench)
2. Retrieve study metadata (title, description, organism, status)
3. Extract experimental design and data availability

### Phase 3: Study Search
For keyword searches:
1. Search MetaboLights studies by query term
2. Return matching study IDs with preview information
3. Report total number of results

### Phase 4: Database Overview
Always included in reports:
1. Sample recent studies from MetaboLights
2. Database statistics and availability
3. Integration information for all databases

## Usage Patterns

### Pattern 1: Metabolite Identification
**Input:**
- Metabolite list: ["glucose", "lactate", "pyruvate"]

**Output report includes:**
- HMDB IDs for each metabolite
- Chemical formulas and molecular weights
- Biological pathways
- PubChem CIDs
- SMILES representations

### Pattern 2: Study Retrieval
**Input:**
- Study ID: "MTBLS1" or "ST000001"

**Output report includes:**
- Study title and description
- Organism information
- Study status and release date
- Data availability

### Pattern 3: Study Search
**Input:**
- Search query: "diabetes"
- Optional organism filter

**Output report includes:**
- Matching study IDs
- Study titles and previews
- Total result count

### Pattern 4: Comprehensive Analysis
**Input:**
- Metabolite list: ["glucose", "pyruvate"]
- Study ID: "MTBLS1"
- Search query: "diabetes"

**Output report includes:**
- All phases combined (identification, study details, search results, overview)
- Cross-referenced information
- Complete metabolomics research summary

## Input Parameters

### metabolite_list (optional)
List of metabolite names to identify and annotate.
- **Format**: List of strings
- **Examples**: `["glucose"]`, `["lactate", "pyruvate", "acetate"]`
- **Note**: Common names accepted; HMDB will find standard identifiers

### study_id (optional)
MetaboLights or Metabolomics Workbench study identifier.
- **Format**: String starting with "MTBLS" or "ST"
- **Examples**: `"MTBLS1"`, `"ST000001"`
- **Note**: Database auto-detected from prefix

### search_query (optional)
Keyword to search metabolomics studies.
- **Format**: String (disease, compound, organism, method)
- **Examples**: `"diabetes"`, `"glucose metabolism"`, `"LC-MS"`

### organism (optional)
Target organism for study filtering.
- **Format**: String (scientific name)
- **Default**: `"Homo sapiens"`
- **Examples**: `"Mus musculus"`, `"Saccharomyces cerevisiae"`

### output_file (optional)
Path for the generated markdown report.
- **Format**: String (filename with .md extension)
- **Default**: Auto-generated timestamp-based filename
- **Examples**: `"my_analysis.md"`, `"metabolomics_report.md"`

## Output Format

All analyses generate a structured markdown report with:

**Header section:**
- Report title and generation timestamp
- Input parameters summary (metabolites, study ID, search query, organism)

**Phase sections:**
- Clear section headers (## 1. Metabolite Identification, ## 2. Study Details, etc.)
- Subsections for each metabolite or result
- Consistent formatting (bold labels, tables for results)

**Database overview:**
- Available databases and statistics
- Recent studies sample
- Integration information

**Error handling:**
- Graceful error messages for unavailable data
- Fallback strategies documented in output
- "N/A" for missing fields (not blank)

## Implementation Notes

### SOAP Tool Handling
**HMDB tools are SOAP-based** and require special parameter handling:
- `HMDB_search`: Requires `operation="search"` parameter
- `HMDB_get_metabolite`: Requires `operation="get_metabolite"` parameter
- Do not use `endpoint` or `method` parameters (not applicable to SOAP)

### Response Format Variations
Tools return different response formats - handle all three:
1. **Standard format**: `{status: "success", data: [...], metadata: {...}}`
2. **Direct list**: `[...]` (e.g., metabolights_list_studies)
3. **Direct dict**: `{field1: ..., field2: ...}` (e.g., some detail endpoints)

Always check response type with `isinstance()` before accessi