Which ChEBIs are used in Rhea?


The ChEBI ontology

Rhea uses the chemical ontology ChEBI (Chemical Entities of Biological Interest) to describe reaction participants in a computationally tractable manner. The ChEBI ontology is subdivided into three separate sub-ontologies that are organized in separate namespaces. The individual concepts (aka classes) of the ontology are linked with various types of relationships to form a directed graph where a child class may have several parent classes and some relationships are cyclic in nature.

Figure 1: The ChEBI ontology

Rhea uses the three ChEBI sub-ontologies to varying degrees:

  • Most ChEBI concepts that are used in Rhea belong to the chemical entity sub-ontology (CHEBI:24431).
  • Rhea uses two concepts of the role sub-ontology (CHEBI:50906):
    • AH2: hydrogen donor (CHEBI:17499)
      A molecular entity that can undergo oxidation by the loss of hydrogen atom(s).
    • A: hydrogen acceptor (CHEBI:13193)
      A molecular entity that can undergo reduction by the gain of hydrogen atom(s).

Figure 2: Examples of ChEBI concepts used in Rhea

The major microspecies at pH 7.3

Most chemical compounds contain functional groups that are likely to lose or gain protons under specific conditions (pH, temperature, pressure). The ChEBI ontology describes each protonation state of a given compound (neutral, protonated, zwitterionic, tautomeric) with a separate class and links related classes by specific relationships (is conjugate acid of, is conjugate base of, is tautomer of). D-alanine, for instance, has two groups, an amino group and a carboxylic acid group, that each can be (de)protonated. The different protonation states are described by 4 linked ChEBI entities (CHEBI:15570, CHEBI:32435, CHEBI:32436, CHEBI:57416).