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ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.

Yannick Djoumbou Feunang1, Roman Eisner2, Craig Knox3

  • 1Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8 Canada.

Journal of Cheminformatics
|November 22, 2016
PubMed
Summary

A new automated chemical classification system, ClassyFire, and its associated chemical taxonomy, ChemOnt, have been developed. This system classifies millions of chemical compounds based on their structures, enabling better data integration and property prediction.

Keywords:
AnnotationData integrationDatabaseInferenceOntologyStructure-based classificationTaxonomyText-based search

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Area of Science:

  • Cheminformatics
  • Computational Chemistry
  • Chemical Taxonomy

Background:

  • The scientific community lacks a standardized chemical taxonomy, hindering chemistry's integration with other fields.
  • Manual classification of millions of chemical compounds is infeasible due to sheer numbers and complexity.
  • Existing classification attempts are limited to manual or semi-automated proof-of-principle applications.

Purpose of the Study:

  • To develop a comprehensive, computable, and structure-based chemical taxonomy (ChemOnt).
  • To create a software tool (ClassyFire) for automated chemical classification.
  • To enable large-scale annotation and property inference for chemical compounds.

Main Methods:

  • Developed ChemOnt, a hierarchical taxonomy with >4800 categories defined by computable structural rules.
  • Created ClassyFire, a program that assigns compounds to ChemOnt categories using only structural features.
  • Built a webserver and Ruby API for accessible use of ClassyFire and its database.

Main Results:

  • ClassyFire automatically classifies compounds into a >4800 category taxonomy with up to 11 levels.
  • The system has been used to annotate over 77 million chemical compounds.
  • ClassyFire has been integrated into other software for automated description generation and property inference.

Conclusions:

  • ClassyFire and ChemOnt enable rapid, large-scale, automated chemical classification.
  • A freely accessible API provides access to over 77 million classified compounds.
  • These classifications facilitate data integration and cheminformatics tasks for both well-studied and lesser-known compounds.