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Creating taxonomically-informed metabolome libraries for any species using the pubchem.bio R package.

Corey D Broeckling1

  • 1Colorado State University, Analytical Resources Core - Bioanalysis and Omics Center, Fort Collins, CO, 80523, USA. cbroeckl@colostate.edu.

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Summary
This summary is machine-generated.

The pubchem.bio R package simplifies metabolomics by providing a curated PubChem subset for building custom metabolite libraries. It aids in the crucial metabolite annotation process for diverse species.

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Area of Science:

  • Metabolomics
  • Bioinformatics
  • Cheminformatics

Background:

  • Metabolomics annotation is challenging due to the vast structural diversity of small molecules.
  • PubChem is a large chemical structure database with extensive biological metadata.
  • Many PubChem structures are not relevant for typical metabolomics experiments.

Purpose of the Study:

  • Introduce the R package, pubchem.bio, designed to address challenges in metabolomics.
  • Enable users to download a metabolomics-focused subset of PubChem.
  • Facilitate the creation of custom metabolite structure libraries for specific species.

Main Methods:

  • The pubchem.bio R package allows downloading a metabolomics-centric subset of PubChem.
  • It enables building structured metabolomic libraries and custom species-specific libraries.
  • A lowest-common-ancestor chemotaxonomy approach is used, linking PubChem CIDs to NCBI Taxonomy.

Main Results:

  • Users can create tailored metabolite libraries for any species or group of species.
  • The package facilitates the definition of a core biological metabolome.
  • It allows extrapolation of taxonomic ranges beyond reported species.

Conclusions:

  • The pubchem.bio package simplifies metabolite annotation in metabolomics research.
  • It integrates biological metadata into the annotation workflow.
  • The package enhances the discoverability and utility of PubChem data for metabolomics.