ChEBI ontology

Introduction to ChEBI ontology - part 1

ChEBI entities are annotated using standard vocabularies or ontologies. These consist of three sub-ontologies: (see Figure 11)

  1. Molecular structure, in which molecular entities or parts of entities are classified according to their structure;
  2. Role, in which entities are classified on the basis of their role within a biological context, e.g. as antibiotics, antiviral agents, coenzymes, enzyme inhibitors, or on the basis of their intended use by humans, e.g. as pesticides, detergents, healthcare products, fuel; 
  3. Subatomic particle, in which entities are classified as particles that are smaller than atoms.
Figure 11 ChEBI ontology for (R)-adrenaline.

Introduction to ChEBI ontology - part 2

The ChEBI ontology uses two generic plus several chemistry-specific relationships (Figure 12).

Various ontology relationships in ChEBI

Figure 12 Various ontology relationships in ChEBI.

  • Is a: Entity A is an instance of Entity B. For example, ethanol is a primary alcohol;
  • Has part: Indicates a relationship between a part and the whole;
  • Is conjugate base of and is conjugate acid of: Relationships used to connect acids with their conjugate bases. For example, L-cysteine is conjugate base of L-cysteinium (Figure 13A);
  • Is tautomer of: Cyclic relationship used to show the relationship between two tautomers (Figure 13B);
  • Is enantiomer of: Cyclic relationship used in instances when two entities are non-superposable mirror images of each other. For example, D-cysteine is enantiomer of L-cysteine (Figure 13C);
  • Has functional parent: Denotes the relationship between two molecular entities or classes, one of which possesses one or more characteristic groups from which the other can be derived by functional modification. For example, S-(4-bromophenyl)-L-cysteine has functional parent L-cysteine (Figure 13D).

Figure 13 Ontology relationships (I).

  • Has parent hydride: Denotes the relationship between an entity and its parent hydride (Figure 14E);
  • Is substituent group from: Indicates the relationship between a substituent group/atom and its parent molecular entity (Figure 14F);
  • Has role: Denotes the relationship between a molecular entity and the particular behaviour which the entity may exhibit either by nature or by human application, for example, morphine has role as an opioid analgesic.

Figure 14 Ontology relationships (II).