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human_metabolites: Parsed Human Metabolite Metadata from HMDB

Source: R/human_metabolites.R
human_metabolites.Rd

A character vector of compound identifiers for metabolites curated from the Human Metabolome Database (HMDB), written like the identifier of Compound nodes in tkoi_net: InChIKeys (for example "inchikey:BRMWTNUJHUMWMS-LURJTMIESA-N"), ChEBI IDs (for example "CHEBI:50599"), and ChEMBL IDs (for example "chembl.compound:CHEMBL4159192"). run_tkoi reports only Compound nodes whose identifier is in this vector, and these nodes form the multiple-testing family of the Compound table.

Usage

human_metabolites

Format

A character vector of 231,466 unique identifiers (217,895 InChIKeys, 13,562 ChEBI IDs, and 9 ChEMBL IDs).

Details

In tkoi 1.1.0 the identifiers were repaired: ChEBI IDs had a doubled prefix ("CHEBI:CHEBI:50599"), ChEMBL IDs lacked the "CHEMBL" prefix, placeholder entries ("CHEBI:NA", a bare "inchikey:") were removed, and duplicates were dropped. As a result, 45 Compound nodes identified by ChEBI ID are now reported in addition to the 24,099 InChIKey-identified compounds.

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>, and prefixed with their namespace.

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"