The ChEBI ontology has two separate classification hierarchies: structure and role. The enrichment analysis can be performed on either of these hierarchies, or on both simultaneously.

ChEBI structure classification: The structure classification describes a molecular entity based on its composition and/or the connectivity between its constituent atoms.

ChEBI role classification: The role classification describes the role of a molecular entity within a biological context and/or its intended use by humans.

ChEBI structure and role classification ("Both"): The structure and role classification is the union of both classifications. Note that the structure classification is significantly larger than the role classification.

When using SMILES, the enrichment analysis will be performed on the ChEBI entities that are mapped to the input SMILES. If a SMILES is not mapped to any ChEBI entity, its direct parent classes can be predicted (this is done with Chebifier) and used for the enrichment analysis. Alternatively, the unmapped SMILES can be completely excluded, depending on the option you select.

Homo sapiens-based background 1

Based on data derived from the Human Metabolome Database (HMDB) and Lotus (taxonomy = Homo sapiens) and is thus only based on entities that have been measured in human samples.

Homo sapiens-based background 2

Based on data derived from Recon3D (from BiGG Models) that only contains metabolites that are guaranteed to have genetic machinery to be synthesised in the human body, unlike the broader Homo sapiens background, which also includes externally-sourced human-associated compounds (eg drugs, diet).

Arabidopsis thaliana-based background

Based on data from Lotus (taxonomy = Arabidopsis thaliana) which is based on entities that have been measured in Arabidopsis thaliana samples.

Since the ChEBI ontology is continuously updated, monthly re-downloads of the data is automatically executed on the first of each month. The date of the last update is stated at the bottom right of the page. Observe that each update may affect the enrichment analysis results.

Data used to build the narrow backgrounds

The Lotus data that is used for two of the narrow backgrounds is also re-downloaded together with the ontology. The data used from HMDB was released on 2021-11-17, and the Recon3D model is from 2019-10-31.