Abstract
BackgroundScientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, the world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at chemical classification have been made; but they have mostly been limited to either manual, or semi-automated proof-of-principle applications. This is regrettable as comprehensive chemical classification and description tools could not only improve our understanding of chemistry but also improve the linkage between chemistry and many other fields. For instance, the chemical classification of a compound could help predict its metabolic fate in humans, its druggability or potential hazards associated with it, among others. However, the sheer number (tens of millions of compounds) and complexity of chemical structures is such that any manual classification effort would prove to be near impossible.ResultsWe have developed a comprehensive, flexible, and computable, purely structure-based chemical taxonomy (ChemOnt), along with a computer program (ClassyFire) that uses only chemical structures and structural features to automatically assign all known chemical compounds to a taxonomy consisting of >4800 different categories. This new chemical taxonomy consists of up to 11 different levels (Kingdom, SuperClass, Class, SubClass, etc.) with each of the categories defined by unambiguous, computable structural rules. Furthermore each category is named using a consensus-based nomenclature and described (in English) based on the characteristic common structural properties of the compounds it contains. The ClassyFire webserver is freely accessible at http://classyfire.wishartlab.com/. Moreover, a Ruby API version is available at https://bitbucket.org/wishartlab/classyfire_api, which provides programmatic access to the ClassyFire server and database. ClassyFire has been used to annotate over 77 million compounds and has already been integrated into other software packages to automatically generate textual descriptions for, and/or infer biological properties of over 100,000 compounds. Additional examples and applications are provided in this paper.ConclusionClassyFire, in combination with ChemOnt (ClassyFire’s comprehensive chemical taxonomy), now allows chemists and cheminformaticians to perform large-scale, rapid and automated chemical classification. Moreover, a freely accessible API allows easy access to more than 77 million “ClassyFire” classified compounds. The results can be used to help annotate well studied, as well as lesser-known compounds. In addition, these chemical classifications can be used as input for data integration, and many other cheminformatics-related tasks.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0174-y) contains supplementary material, which is available to authorized users.
Highlights
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci 28:31–3613
Taxonomies and ontologies are widely used in many scientific fields, including biology [4], geology [5], subatomic physics [6], astronomy [7, 8] and pharmacology [9]
We describe a comprehensive, flexible, computable, chemical taxonomy along with a fully annotated chemical ontology (ChemOnt) and a Chemical Classification Dictionary
Summary
Introduction to methodology and encoding rulesJ Chem Inf Comput Sci 28:31–3613. Fahy E, Subramaniam S, Murphy RC, Nishijima M, Raetz CRH, Shimizu T et al (2009) Update of the LIPID MAPS comprehensive classification system for lipids. Taxonomies are simplistic schemes that help in the hierarchical classification of concepts or objects [1]. They are usually limited to a specific domain and to a single relationship type connecting one node to another. They often have multiple relationship types and are really designed to provide a formal naming of the types, properties and interrelationships of entities or concepts in a specific discipline, domain or field of study [2, 3]. Ontologies provide a system to create relationships between concepts across different domains Both taxonomies and ontologies can be used to help scientists explain, organize or improve their understanding of the natural world. Because PLA2G4A is annotated with the GO term “phospholipid catabolic process”, it could be inferred that PC[14:0/22:1(13Z)] is a product of this biological process
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