ChemFOnt (the Chemical Functional Ontology) is a hierarchical, OWL-compatible ontology describing the functions and actions of more than 319,000 biologically important chemicals. It is intended to bring the same rigor, standardization and formal structure to the 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 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 metabolomic set data (metabolite set enrichment) or make new, non-obvious connections.

In general terms, an ontology comprises a series of named entities, their descriptions or definitions, their relationships to each other and a series of hierarchical categories that group those entities according to various criteria.
ChemFOnt’s top layer in its hierarchy consists of 12 major categories:

• 1) Environmental processes
• 2) Biological processes
• 3) Industrial processes
• 4) Adverse biological roles
• 5) Normal biological roles
• 6) Environmental roles
• 7) Industrial applications
• 8) Health effects
• 9) Organoleptic effects
• 10) Sources
• 11) Biological locations
• 12) Routes of exposure

These major categories are subdivided into another 384 subcategories which are divided into thousands of other branches or leaf nodes for a maximum depth of up 7 layers. The entire ontological hierarchy for ChemFOnt currently comprises a total of 394,000 fully defined terms and over 11 million chemical/functional relationships. All terminal leaf nodes in the ChemFOnt hierarchy contain a fact supported by a citeable reference. The information for constructing ChemFOnt was built from many pre-existing ontologies and definitions (GO, FOBI, FoodOnt, ChemOnt, Disease Ontology), handwritten definitions (where no prior ontology or definitions existed) and structured facts/references acquired from hand-curated databases maintained in the Wishart lab (FooDB, HMDB, MiMeDB, DrugBank, MarkerDB, PathBank). To ensure uniformity, consistency and compliance, additions, corrections and improvements to ChemFOnt are done through a moderated process and strict standard operating protocols (SOPs) maintained by designated ChemFOnt editors. Requests to join the ChemFOnt editorial team and suggestions from external users can be emailed to the ChemFOnt editors and will be handled as a first-come-first-served basis. This is the first release of ChemFOnt and it is expected that annual or bi-annual updates will continue over many years.

The use of text mining tools such as PolySearch2 is expected to facilitate the continued expansion and updating of ChemFOnt’s contents. The long-term goal is to fully annotate the nearly 1 million detectable compounds known to exist in the human and natural environment using the ChemFOnt structure.