Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties, pathways), retrieve metabolomics study information from MetaboLights (MTBLS*) or Metabolomics Workbench (ST*), search for studies by keywords or disease, or generate comprehensive metabolomics research reports.
Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties, pathways), retrieve metabolomics study information from MetaboLights (MTBLS*) or Metabolomics Workbench (ST*), search for studies by keywords or disease, or generate comprehensive metabolomics research reports.
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
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:
Search HMDB by metabolite name
Retrieve HMDB ID, chemical formula, molecular weight
Get detailed metabolite information (description, pathways)
Fallback to PubChem for CID and chemical properties if HMDB unavailable
Phase 2: Study Details Retrieval
For provided study IDs:
Detect database type (MTBLS = MetaboLights, ST = Metabolomics Workbench)
Retrieve study metadata (title, description, organism, status)
Extract experimental design and data availability
Phase 3: Study Search
For keyword searches:
Search MetaboLights studies by query term
Return matching study IDs with preview information
PubChem_get_compound_properties_by_CID: Get chemical properties
No manual tool configuration required - all tools loaded automatically.
Common Issues
Issue: HMDB returns "Error querying HMDB: 0"
Cause: HMDB search returned empty results or index error accessing first result
Solution: This is expected for uncommon metabolites; PubChem fallback will be attempted
Issue: Study details show "N/A" for all fields
Cause: Study ID not found or API unavailable
Solution: Verify study ID format (MTBLS* or ST*), check if study is public
Issue: Tool not found errors
Cause: Missing API keys for some databases
Solution: Check .env.template, add required API keys to .env file (most metabolomics tools work without keys)
Issue: Large metabolite lists cause slow execution
Cause: Pipeline queries each metabolite individually
Solution: Reports limit to first 10 metabolites; consider batching for >20 metabolites
Tool Parameter Reference
HMDB Tools (SOAP)
Tool
Required Parameters
Optional Parameters
Response Format
Notes
HMDB_search
operation="search", query
-
{status, data: []}
SOAP tool - operation required
HMDB_get_metabolite
operation="get_metabolite", hmdb_id
-
{status, data: {}}
SOAP tool - operation required
MetaboLights Tools (REST)
Tool
Required Parameters
Optional Parameters
Response Format
Notes
metabolights_list_studies
-
size (default: 10)
{status, data: []} or [...]
May return direct list
metabolights_search_studies
query
-
{status, data: []}
Returns study IDs
metabolights_get_study
study_id
-
{status, data: {}}
Full study metadata
Metabolomics Workbench Tools (REST)
Tool
Required Parameters
Optional Parameters
Response Format
Notes
MetabolomicsWorkbench_get_study
study_id
output_item (default: "summary")
{status, data: {}}
Data may be text
MetabolomicsWorkbench_search_compound_by_name
compound_name
-
{status, data: {}}
Compound information
PubChem Tools (REST)
Tool
Required Parameters
Optional Parameters
Response Format
Notes
PubChem_get_CID_by_compound_name
compound_name
-
{status, data: {cid}}
Returns CID
PubChem_get_compound_properties_by_CID
cid
-
{status, data: {}}
Chemical properties
Important: All parameter names and requirements apply to both Python SDK and MCP implementations.
Summary
The Metabolomics Research skill provides comprehensive metabolomics analysis through a 4-phase pipeline that:
Identifies metabolites using HMDB (primary) and PubChem (fallback) databases
Retrieves study details from MetaboLights and Metabolomics Workbench repositories
Searches studies by keywords across metabolomics databases
Generates structured reports with all findings in readable markdown format
