HMDB Data Fields Reference

This document provides detailed information about the data fields available in HMDB metabolite entries.

Metabolite Entry Structure

Each HMDB metabolite entry contains 130+ data fields organized into several categories:

Chemical Data Fields

Identification: - accession: Primary HMDB ID (e.g., HMDB0000001) - secondary_accessions: Previous HMDB IDs for merged entries - name: Primary metabolite name - synonyms: Alternative names and common names - chemical_formula: Molecular formula (e.g., C6H12O6) - average_molecular_weight: Average molecular weight in Daltons - monoisotopic_molecular_weight: Monoisotopic molecular weight

Structure Representations: - smiles: Simplified Molecular Input Line Entry System string - inchi: International Chemical Identifier string - inchikey: Hashed InChI for fast lookup - iupac_name: IUPAC systematic name - traditional_iupac: Traditional IUPAC name

Chemical Properties: - state: Physical state (solid, liquid, gas) - charge: Net molecular charge - logp: Octanol-water partition coefficient (experimental/predicted) - pka_strongest_acidic: Strongest acidic pKa value - pka_strongest_basic: Strongest basic pKa value - polar_surface_area: Topological polar surface area (TPSA) - refractivity: Molar refractivity - polarizability: Molecular polarizability - rotatable_bond_count: Number of rotatable bonds - acceptor_count: Hydrogen bond acceptor count - donor_count: Hydrogen bond donor count

Chemical Taxonomy: - kingdom: Chemical kingdom (e.g., Organic compounds) - super_class: Chemical superclass - class: Chemical class - sub_class: Chemical subclass - direct_parent: Direct chemical parent - alternative_parents: Alternative parent classifications - substituents: Chemical substituents present - description: Text description of the compound

Biological Data Fields

Metabolite Origins: - origin: Source of metabolite (endogenous, exogenous, drug metabolite, food component) - biofluid_locations: Biological fluids where found (blood, urine, saliva, CSF, etc.) - tissue_locations: Tissues where found (liver, kidney, brain, muscle, etc.) - cellular_locations: Subcellular locations (cytoplasm, mitochondria, membrane, etc.)

Biospecimen Information: - biospecimen: Type of biological specimen - status: Detection status (detected, expected, predicted) - concentration: Concentration ranges with units - concentration_references: Citations for concentration data

Normal and Abnormal Concentrations: For each biofluid (blood, urine, saliva, CSF, feces, sweat): - Normal concentration value and range - Units (μM, mg/L, etc.) - Age and gender considerations - Abnormal concentration indicators - Clinical significance

Pathway and Enzyme Information

Metabolic Pathways: - pathways: List of associated metabolic pathways - Pathway name - SMPDB ID (Small Molecule Pathway Database ID) - KEGG pathway ID - Pathway category

Enzymatic Reactions: - protein_associations: Enzymes and transporters - Protein name - Gene name - Uniprot ID - GenBank ID - Protein type (enzyme, transporter, carrier, etc.) - Enzyme reactions - Enzyme kinetics (Km values)

Biochemical Context: - reactions: Biochemical reactions involving the metabolite - reaction_enzymes: Enzymes catalyzing reactions - cofactors: Required cofactors - inhibitors: Known enzyme inhibitors

Disease and Biomarker Associations

Disease Links: - diseases: Associated diseases and conditions - Disease name - OMIM ID (Online Mendelian Inheritance in Man) - Disease category - References and evidence

Biomarker Information: - biomarker_status: Whether compound is a known biomarker - biomarker_applications: Clinical applications - biomarker_for: Diseases or conditions where used as biomarker

Spectroscopic Data

NMR Spectra: - nmr_spectra: Nuclear Magnetic Resonance data - Spectrum type (1D ¹H, ¹³C, 2D COSY, HSQC, etc.) - Spectrometer frequency (MHz) - Solvent used - Temperature - pH - Peak list with chemical shifts and multiplicities - FID (Free Induction Decay) files

Mass Spectrometry: - ms_spectra: Mass spectrometry data - Spectrum type (MS, MS-MS, LC-MS, GC-MS) - Ionization mode (positive, negative, neutral) - Collision energy - Instrument type - Peak list (m/z, intensity, annotation) - Predicted vs. experimental flag

Chromatography: - chromatography: Chromatographic properties - Retention time - Column type - Mobile phase - Method details

External Database Links

Database Cross-References: - kegg_id: KEGG Compound ID - pubchem_compound_id: PubChem CID - pubchem_substance_id: PubChem SID - chebi_id: Chemical Entities of Biological Interest ID - chemspider_id: ChemSpider ID - drugbank_id: DrugBank accession (if applicable) - foodb_id: FooDB ID (if food component) - knapsack_id: KNApSAcK ID - metacyc_id: MetaCyc ID - bigg_id: BiGG Model ID - wikipedia_id: Wikipedia page link - metlin_id: METLIN ID - vmh_id: Virtual Metabolic Human ID - fbonto_id: FlyBase ontology ID

Protein Database Links: - uniprot_id: UniProt accession for associated proteins - genbank_id: GenBank ID for associated genes - pdb_id: Protein Data Bank ID for protein structures

Literature and Evidence

References: - general_references: General references about the metabolite - PubMed ID - Reference text - Citation - synthesis_reference: Synthesis methods and references - protein_references: References for protein associations - pathway_references: References for pathway involvement

Ontology and Classification

Ontology Terms: - ontology_terms: Related ontology classifications - Term name - Ontology source (ChEBI, MeSH, etc.) - Term ID - Definition

Data Quality and Provenance

Metadata: - creation_date: Date entry was created - update_date: Date entry was last updated - version: HMDB version number - status: Entry status (detected, expected, predicted) - evidence: Evidence level for detection/presence

XML Structure Example

When downloading HMDB data in XML format, the structure follows this pattern:

<metabolite>
  <accession>HMDB0000001</accession>
  <name>1-Methylhistidine</name>
  <chemical_formula>C7H11N3O2</chemical_formula>
  <average_molecular_weight>169.1811</average_molecular_weight>
  <monoisotopic_molecular_weight>169.085126436</monoisotopic_molecular_weight>
  <smiles>CN1C=NC(CC(=O)O)=C1</smiles>
  <inchi>InChI=1S/C7H11N3O2/c1-10-4-8-3-5(10)2-7(11)12/h3-4H,2H2,1H3,(H,11,12)</inchi>
  <inchikey>BRMWTNUJHUMWMS-UHFFFAOYSA-N</inchikey>

  <biospecimen_locations>
    <biospecimen>Blood</biospecimen>
    <biospecimen>Urine</biospecimen>
  </biospecimen_locations>

  <pathways>
    <pathway>
      <name>Histidine Metabolism</name>
      <smpdb_id>SMP0000044</smpdb_id>
      <kegg_map_id>map00340</kegg_map_id>
    </pathway>
  </pathways>

  <diseases>
    <disease>
      <name>Carnosinemia</name>
      <omim_id>212200</omim_id>
    </disease>
  </diseases>

  <normal_concentrations>
    <concentration>
      <biospecimen>Blood</biospecimen>
      <concentration_value>3.8</concentration_value>
      <concentration_units>uM</concentration_units>
    </concentration>
  </normal_concentrations>
</metabolite>

Querying Specific Fields

When working with HMDB data programmatically:

For metabolite identification: - Query by accession, name, synonyms, inchi, smiles

For chemical similarity: - Use smiles, inchi, inchikey, molecular_weight, chemical_formula

For biomarker discovery: - Filter by diseases, biomarker_status, normal_concentrations, abnormal_concentrations

For pathway analysis: - Extract pathways, protein_associations, reactions

For spectral matching: - Compare against nmr_spectra, ms_spectra peak lists

For cross-database integration: - Map using external IDs: kegg_id, pubchem_compound_id, chebi_id, etc.

Field Completeness

Not all fields are populated for every metabolite:

Highly complete fields (>90% of entries): accession, name, chemical_formula, molecular_weight, smiles, inchi
Moderately complete (50-90%): biospecimen_locations, tissue_locations, pathways
Variably complete (10-50%): concentration data, disease associations, protein associations
Sparsely complete (<10%): experimental NMR/MS spectra, detailed kinetic data

Predicted and computational data (e.g., predicted MS spectra, predicted concentrations) supplement experimental data where available.

references/hmdb_data_fields.md