Taxonomies and ontologies organize complex knowledge about concepts and their relationships. Currently, in contrast to biology, pharmacology, geology, and many other scientific disciplines, the world of chemistry still lacks a standard taxonomy/ontology. Moreover, the manual or semi-automated classification attempts that have been presented so far have proven cost-expensive, error-prone, or not comprehensive enough to provide detailed classifications for the tens of millions of compounds that are publicly available.
ClassyFire is a web-based application for automated rule-based structural classification of chemical entities (including peptide and nucleotide sequences). This application uses a rule-based classification approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy named ChemOnt.
ChemOnt is comphrehensive, computable, and manually curated. It covers 4825 chemical classes of organic and inorganic compounds. The set of classes was created and extended by extracting common terms from the scientific literature (e.g.: IUPAC) and available databases. The flexibility The taxonomy is currently mapped to the ChEBI and LIPID MAPS ontologies in collaboration with the respective teams. Moreover, ChemOnt has been partially mappped to the MeSH thesaurus. The mapping effort in this regard is ongoing. Thanks to the flexibility and simplicity of its structure as well as its chemo-taxonomic definition, ClassyFire is meant to easily evolve to cover the increasing number of newly discovered scaffolds of natural and synthetic chemical entities, facilitating biochemical research.
ClassyFire automatically provides a hierarchical chemical classification for all known chemical compounds (including small molecules, peptides and peptide sequences), as well as a structure-based textual description. When available, it also provides descriptors from some external databases such as ChEBI and LIPID MAPS. The chemical entities, sequences, and their classifications are then stored in a database that can be easily accessed through the RESTful application. Moreover, ClassyFire offers for text-based search capabilities via its web interface.
ClassyFire has been already to annotated several of the most popular and comprehensive databases including DrugBank, HMDB, PubChem, ECMDB, YMDB, T3DB, ChEBI, LIPID MAPS, and MoNA - MassBank of North America, among others. Moreover, ClassyFire and ChemOnt have found application in many cheminformatics related tasks as described in the paper below.
ClassyFire can be accessed via the web-interface or via the ClassyFire API.
ClassyFire is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (ClassyFire) and the original publication (see below). We ask that users who download portions of the database, or use the service (via the server or the API), to cite the ClassyFire paper in any resulting publications.
- Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.