CHEMINFORMATICS TOOLS FOR ENABLING METABOLOMICS

• Author / Creator

  DJOUMBOU FEUNANG, YANNICK

• Metabolites are small molecules (4,800 chemical categories, as well as their textual descriptions and mappings to other ontologies. ClassyFire was used to classify and annotate >80 million compounds. The webserver also integrates a text-based search engine. These features make ClassyFire unique in the sphere of publicly available computational tools. ClassyFire and ChemOnt are available at http://classyfire.wishartlab.com. Second, I developed BioTransformer and BioTransformerDB. BioTransformer is a software tool for the prediction of small molecule metabolism in mammals. It uses a hybrid approach that partly relies on BioTransformerDB, a unique database of biotransformations containing experimentally confirmed metabolic reactions that transform >1,000 drugs, pesticides, cosmetics, and food compounds, among others. The current version of BioTransformer, which is available at https://bitbucket.org/djoumbou/biotransformer, focuses on the human species, but is easily expandable to other species. Third, I developed CFM-ID 3.0, an extension of CFM-ID (1.0, and 2.0), originally developed by Felicity Allen et al. CFM-ID 3.0 is a software tool and webserver for the prediction and annotation of MS spectra, as well as the identification of metabolites. With the integration of a rule-based fragmentation approach for spectra prediction, the development of new ranking functions, and the expansion of the spectral database, CFM-ID 3.0 showed a significant improvement, in terms of speed and accuracy, compared to previous versions. CFM-ID 3.0 is currently available as we web server at http://cfmid-staging.wishartlab.com/. ClassyFire, BioTransformer, and CFM-ID have found applications in various fields including chemical information management, metabolomics, and exposomics, among others. Together, they build a cheminformatics platform that can enable metabolomics, and contribute to the understanding of our environment as well as the advancement of science.

• Subjects / Keywords

  • MASS SPECTRA PREDICTION
  • CLASSYFIRE
  • AUTOMATED CHEMICAL CLASSIFICATION
  • CHEMINFORMATICS
  • METABOLOMICS
  • METABOLISM
  • CHEMICAL ONTOLOGIES
  • METABOLISM PREDICTION
  • BIOTRANSFORMER
  • CHEMONT
  • METABOLITE IDENTIFICATION
  • CFM-ID

• Graduation date

  Fall 2017

• Type of Item

  Thesis

• Degree

  Doctor of Philosophy

• DOI

  https://doi.org/10.7939/R3VD6PJ8B

• License

  This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.