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Chemical Compound Annotations

Source: R/compound_annotation.R
compound_annotation.Rd

A curated annotation table for small molecules and chemical compounds used in pharmacological, biochemical, or research contexts. It has one row per Compound node of tkoi_net, with the node's identifier (an InChIKey, a ChEBI ID, or a ChEMBL ID) and the compound name, when available. This dataset is used within the tKOI framework to annotate nodes representing chemical entities or drugs in biological knowledge graphs.

Usage

compound_annotation

Format

A data frame with 554,526 rows and 2 columns:

identifier

Character. The compound ID, in one of three forms: an InChIKey (530,612 rows, e.g. "inchikey:NZLJDTKLZIMONR-UHFFFAOYSA-N"), a ChEBI ID (22,652 rows, e.g. "CHEBI:85476"), or a ChEMBL compound accession (1,262 rows, e.g. "chembl.compound:CHEMBL5219790").

name

The human-readable compound name, when available (e.g., "ACRIFLAVINE"). Missing values indicate uncharacterized or unnamed entries.

Source

Data compiled from chemical databases such as ChEMBL, ChEBI, and the InChI registry.

Details

This dataset enables mapping of compound-level features in biomedical networks, including chemical perturbagens, drug candidates, or environmental exposures. It can be joined to tKOI network results using the identifier field to enrich nodes of type "Compound" with interpretable names.

run_tkoi reports only Compound nodes whose identifier is in human_metabolites. That vector matches Compound nodes only through InChIKeys, so the Compound table of a run_tkoi() result lists InChIKey compounds only; the ChEBI and ChEMBL rows of this table annotate Compound nodes that run_tkoi() does not report.

See also

complex_annotation, clinicallab_annotation, run_tkoi

Examples

data(compound_annotation)
subset(compound_annotation, grepl("CETRIMIDE", name))
#>                      identifier      name
#> 3 chembl.compound:CHEMBL5219790 CETRIMIDE
#> 4 chembl.compound:CHEMBL5219942 CETRIMIDE

# Identifier forms
table(sub(":.*", "", compound_annotation$identifier))
#> 
#>           CHEBI chembl.compound        inchikey 
#>           22652            1262          530612 
head(subset(compound_annotation, startsWith(identifier, "CHEBI:")))
#>         identifier                            name
#> 527390 CHEBI:85476   O-hydroxyvaleroyl-L-carnitine
#> 527391 CHEBI:48679                   sorbopyranose
#> 527392 CHEBI:60592 poly(fluorene-2,7-diyl) polymer
#> 527393 CHEBI:46687                     diazaalkane
#> 527394 CHEBI:53104                            <NA>
#> 527395 CHEBI:64840                            <NA>