The ELIXIR Core Data Resource ChEBI is a dictionary of molecular entities and, currently, is able to handle all possible forms of a given chemical structure (E.g. neutral, tautomeric, protonated, isotopic, zwitterionic forms). Each form is assigned its own unique ChEBI identifier, which enables inter-relations within ChEBI via the ontology.
Within the biological community, different database resources represent chemical structures in different ways. The ELIXIR resource, Rhea, uses only the physiological pH 7.3 form of a given molecule, whereas Reactome requires both neutral and protonated forms of a given molecule. This inconsistency between resources in the mapping of chemical structures was highlighted in a recent ChEBI user workshop held in May 2019 (EMBL-EBI, UK), where it was agreed that a unification of the methodology, and consistency in the mapping of chemical structures would allow easier mapping across the different ELIXIR resources.
Here we propose a set of meetings and working groups between the resources ChEBI (EMBL-EBI) and Rhea (SIB), with the aim of streamlining the link between chemicals (ChEBI), reactions (Rhea) and pathways (Reactome) and to provide guidelines on the representation of chemical entities to the metabolic modelling community. We anticipate that the development of closer interactions and working relationships between core staff from the different resources during the course of this project will enable further streamlining and increased levels of interoperability between these ELIXIR resources. It will lead to a greater degree of understanding of the
underlying workflows of each resource and to more efficient coordination of their development.