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human_metabolites: Parsed Human Metabolite Metadata from HMDB

human_metabolites.Rd

A data frame containing key chemical identifiers for metabolites curated from the Human Metabolome Database (HMDB). This dataset was constructed by parsing the official HMDB XML export and selecting metabolite-level identifiers relevant for downstream bioinformatics and network biology analyses.

Usage

human_metabolites

Format

A data frame with rows and 4 columns:

name

Metabolite name (character)

inchikey

Standard InChIKey identifier (character)

chebi_id

ChEBI ID with "CHEBI:" prefix, or NA (character)

chembl_id

ChEMBL compound ID, or NA (character)

Details

Description

Each row corresponds to a unique metabolite entry from HMDB. The following columns are included:

  • name: The primary name of the metabolite as recorded in HMDB

  • inchikey: The standard InChIKey chemical structure identifier

  • chebi_id: The corresponding ChEBI identifier (when available), prefixed with "CHEBI:"

  • chembl_id: The corresponding ChEMBL compound ID (when available)

All values are character strings. Missing values are represented as NA.

Use Cases

This table is useful for:

  • Mapping metabolites across chemical databases (InChIKey, ChEBI, ChEMBL)

  • Filtering knowledge graph nodes to retain only human-relevant compounds

  • Cross-referencing with metabolomics datasets or annotations

Construction

This object was created by parsing hmdb_metabolites.xml using the xml2 package. Chemical identifiers were extracted using XPath queries for <inchikey>, <chebi_id>, and <chembl_id>. ChEBI identifiers were post-processed to include the standard "CHEBI:" prefix when present.

Examples

data(human_metabolites)
head(human_metabolites)
#> [1] "inchikey:BRMWTNUJHUMWMS-LURJTMIESA-N"
#> [2] "inchikey:XFNJVJPLKCPIBV-UHFFFAOYSA-N"
#> [3] "inchikey:TYEYBOSBBBHJIV-UHFFFAOYSA-N"
#> [4] "inchikey:AFENDNXGAFYKQO-VKHMYHEASA-N"
#> [5] "inchikey:WHEUWNKSCXYKBU-QPWUGHHJSA-N"
#> [6] "inchikey:WHBMMWSBFZVSSR-GSVOUGTGSA-N"