HMDB Data Fields Reference

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.