ChemFOnt Project

The Chemical Functional Ontology (ChemFOnt) is a hierarchical, OWL-compatible ontology describing the functions and actions of more than 341,000 biologically important chemicals. These include primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals.

ChemFOnt is a FAIR-compliant resource intended to bring the same rigor, standardization and formal structure to the terms and terminology used in biochemistry, food chemistry and environmental chemistry as the gene ontology (GO) has brought to molecular biology. ChemFOnt is available as both a freely accessible, web-enabled database and a downloadable Web Ontology Language (OWL) file. Users may download and deploy ChemFOnt within their own chemical databases or integrate ChemFOnt into their own analytical software to generate machine readable relationships that can be used to make new inferences, enrich their omics data sets or make new, non-obvious connections between chemicals and their direct or indirect effects. The web version of the ChemFOnt database has been designed to be easy to search, browse and navigate.

Currently ChemFOnt contains data on 341,627 chemicals, including 515,332 terms or definitions. The functional hierarchy for ChemFOnt consists of four functional “aspects”, 12 functional super-categories and a total of 173,705 functional terms. In addition, each of the chemicals are classified into 4825 structure-based chemical classes. ChemFOnt currently contains 3.9 million protein-chemical relationships and ~10.3 million chemical-functional relationships. The long-term goal for ChemFOnt is for it to be adopted by databases and software tools used by the general chemistry community as well as the metabolomics, exposomics, metagenomics, genomics and proteomics communities.

To contribute to ChemFOnt, please contact the ChemFOnt team at (preferred) or via the contact/Feedback page. Before submitting a contribution, please ensure the term does not already exist by using the searches or the Browse page. Then, provide the invormation on the change or addition to the ontology, such as the term to be added, and as much information as possible. If you are suggesting any changes, please include the ChemFOnt identifiers for the terms along with the changes. For each request, please provide as much background information as possible to help the team process your request as efficiently as possible.

Citing ChemFOnt:

  1. Wishart DS, Girod S, Peters H, Oler E, Jovel J, Budinski Z, Milford R, Lui VW, Sayeeda Z, Mah R, Wei W, Badran H, Lo E, Yamamoto M, Djoumbou-Feunang Y, Karu N, Gautam V. ChemFOnt: the chemical functional ontology resource. Nucleic Acids Res. 2023 Jan 6;51(D1):D1220-D1229. PMID: 36305829