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RXNO is the name reaction ontology. It contains more than 500 classes representing organic name reactions such as the Diels–Alder cyclization and the Cannizzaro reaction to their roles in an organic synthesis.

The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modelling. It consists of seven orthogonal vocabularies defining: reaction participants roles (e.g. „substrate“), quantitative parameters (e.g. „Michaelis constant“), classification of mathematical expressions describing the system (e.g. „mass action rate law“), modelling framework used (e.g. „logical framework“), the nature of the entity (e.g. „macromolecule“), the type of interaction (e.g. „process“), as well as a branch to define the different types of metadata that may be present within a model.

The Chemical Analysis Ontology (CAO) is organized using the BFO framework with entries primarily under concepts (not complete by any means), material entities, information content entities (data items), roles, and processes. Currently, the ontology is more of a vocabulary in that development of predicates (ontology properties) that relate subjects to objects has not been a focal point.

The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.

The Chemical Information Ontology (CHEMINF) aims to establish a standard in representing chemical information. In particular, it aims to produce an ontology to represent chemical structure and to richly describe chemical properties, whether intrinsic or computed.

ChEBI is a freely available, open source bioinformatics and cheminformatics resource that provides manually annotated information on ‘small’ chemical entities – constitutionally or isotopically distinct atoms, molecules, ion pairs, radicals, radical ions, complexes, conformers, or anything else that is a distinguishable entity. In biology, metabolites are a typical example of small molecules. Molecules directly encoded by the genome (e.g. nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI.

CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).

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