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skills/hmdb-database/SKILL.md
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skills/hmdb-database/SKILL.md
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name: hmdb-database
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description: "Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification."
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---
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# HMDB Database
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## Overview
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The Human Metabolome Database (HMDB) is a comprehensive, freely available resource containing detailed information about small molecule metabolites found in the human body.
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## When to Use This Skill
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This skill should be used when performing metabolomics research, clinical chemistry, biomarker discovery, or metabolite identification tasks.
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## Database Contents
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HMDB version 5.0 (current as of 2025) contains:
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- **220,945 metabolite entries** covering both water-soluble and lipid-soluble compounds
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- **8,610 protein sequences** for enzymes and transporters involved in metabolism
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- **130+ data fields per metabolite** including:
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- Chemical properties (structure, formula, molecular weight, InChI, SMILES)
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- Clinical data (biomarker associations, diseases, normal/abnormal concentrations)
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- Biological information (pathways, reactions, locations)
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- Spectroscopic data (NMR, MS, MS-MS spectra)
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- External database links (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, GenBank)
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## Core Capabilities
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### 1. Web-Based Metabolite Searches
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Access HMDB through the web interface at https://www.hmdb.ca/ for:
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**Text Searches:**
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- Search by metabolite name, synonym, or identifier (HMDB ID)
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- Example HMDB IDs: HMDB0000001, HMDB0001234
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- Search by disease associations or pathway involvement
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- Query by biological specimen type (urine, serum, CSF, saliva, feces, sweat)
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**Structure-Based Searches:**
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- Use ChemQuery for structure and substructure searches
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- Search by molecular weight or molecular weight range
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- Use SMILES or InChI strings to find compounds
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**Spectral Searches:**
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- LC-MS spectral matching
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- GC-MS spectral matching
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- NMR spectral searches for metabolite identification
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**Advanced Searches:**
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- Combine multiple criteria (name, properties, concentration ranges)
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- Filter by biological locations or specimen types
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- Search by protein/enzyme associations
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### 2. Accessing Metabolite Information
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When retrieving metabolite data, HMDB provides:
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**Chemical Information:**
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- Systematic name, traditional names, and synonyms
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- Chemical formula and molecular weight
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- Structure representations (2D/3D, SMILES, InChI, MOL file)
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- Chemical taxonomy and classification
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**Biological Context:**
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- Metabolic pathways and reactions
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- Associated enzymes and transporters
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- Subcellular locations
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- Biological roles and functions
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**Clinical Relevance:**
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- Normal concentration ranges in biological fluids
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- Biomarker associations with diseases
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- Clinical significance
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- Toxicity information when applicable
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**Analytical Data:**
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- Experimental and predicted NMR spectra
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- MS and MS-MS spectra
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- Retention times and chromatographic data
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- Reference peaks for identification
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### 3. Downloadable Datasets
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HMDB offers bulk data downloads at https://www.hmdb.ca/downloads in multiple formats:
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**Available Formats:**
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- **XML**: Complete metabolite, protein, and spectra data
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- **SDF**: Metabolite structure files for cheminformatics
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- **FASTA**: Protein and gene sequences
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- **TXT**: Raw spectra peak lists
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- **CSV/TSV**: Tabular data exports
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**Dataset Categories:**
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- All metabolites or filtered by specimen type
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- Protein/enzyme sequences
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- Experimental and predicted spectra (NMR, GC-MS, MS-MS)
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- Pathway information
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**Best Practices:**
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- Download XML format for comprehensive data including all fields
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- Use SDF format for structure-based analysis and cheminformatics workflows
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- Parse CSV/TSV formats for integration with data analysis pipelines
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- Check version dates to ensure up-to-date data (current: v5.0, 2023-07-01)
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**Usage Requirements:**
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- Free for academic and non-commercial research
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- Commercial use requires explicit permission (contact samackay@ualberta.ca)
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- Cite HMDB publication when using data
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### 4. Programmatic API Access
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**API Availability:**
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HMDB does not provide a public REST API. Programmatic access requires contacting the development team:
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- **Academic/Research groups:** Contact eponine@ualberta.ca (Eponine) or samackay@ualberta.ca (Scott)
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- **Commercial organizations:** Contact samackay@ualberta.ca (Scott) for customized API access
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**Alternative Programmatic Access:**
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- **R/Bioconductor**: Use the `hmdbQuery` package for R-based queries
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- Install: `BiocManager::install("hmdbQuery")`
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- Provides HTTP-based querying functions
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- **Downloaded datasets**: Parse XML or CSV files locally for programmatic analysis
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- **Web scraping**: Not recommended; contact team for proper API access instead
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### 5. Common Research Workflows
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**Metabolite Identification in Untargeted Metabolomics:**
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1. Obtain experimental MS or NMR spectra from samples
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2. Use HMDB spectral search tools to match against reference spectra
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3. Verify candidates by checking molecular weight, retention time, and MS-MS fragmentation
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4. Review biological plausibility (expected in specimen type, known pathways)
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**Biomarker Discovery:**
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1. Search HMDB for metabolites associated with disease of interest
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2. Review concentration ranges in normal vs. disease states
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3. Identify metabolites with strong differential abundance
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4. Examine pathway context and biological mechanisms
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5. Cross-reference with literature via PubMed links
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**Pathway Analysis:**
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1. Identify metabolites of interest from experimental data
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2. Look up HMDB entries for each metabolite
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3. Extract pathway associations and enzymatic reactions
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4. Use linked SMPDB (Small Molecule Pathway Database) for pathway diagrams
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5. Identify pathway enrichment for biological interpretation
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**Database Integration:**
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1. Download HMDB data in XML or CSV format
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2. Parse and extract relevant fields for local database
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3. Link with external IDs (KEGG, PubChem, ChEBI) for cross-database queries
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4. Build local tools or pipelines incorporating HMDB reference data
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## Related HMDB Resources
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The HMDB ecosystem includes related databases:
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- **DrugBank**: ~2,832 drug compounds with pharmaceutical information
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- **T3DB (Toxin and Toxin Target Database)**: ~3,670 toxic compounds
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- **SMPDB (Small Molecule Pathway Database)**: Pathway diagrams and maps
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- **FooDB**: ~70,000 food component compounds
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These databases share similar structure and identifiers, enabling integrated queries across human metabolome, drug, toxin, and food databases.
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## Best Practices
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**Data Quality:**
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- Verify metabolite identifications with multiple evidence types (spectra, structure, properties)
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- Check experimental vs. predicted data quality indicators
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- Review citations and evidence for biomarker associations
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**Version Tracking:**
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- Note HMDB version used in research (current: v5.0)
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- Databases are updated periodically with new entries and corrections
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- Re-query for updates when publishing to ensure current information
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**Citation:**
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- Always cite HMDB in publications using the database
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- Reference specific HMDB IDs when discussing metabolites
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- Acknowledge data sources for downloaded datasets
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**Performance:**
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- For large-scale analysis, download complete datasets rather than repeated web queries
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- Use appropriate file formats (XML for comprehensive data, CSV for tabular analysis)
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- Consider local caching of frequently accessed metabolite information
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## Reference Documentation
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See `references/hmdb_data_fields.md` for detailed information about available data fields and their meanings.
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