# ChEBI: re-engineered for a sustainable future

**Authors:** Adnan Malik, Muhammad Arsalan, Carlos Moreno, Juan Mosquera, Eloy Félix, Tevfik Kizilören, Venkatesh Muthukrishnan, Barbara Zdrazil, Andrew R Leach, Noel M O’Boyle

PMC · DOI: 10.1093/nar/gkaf1271 · Nucleic Acids Research · 2025-11-28

## TL;DR

ChEBI, a database of biologically relevant chemicals, has been modernized to ensure its sustainability and continued utility for researchers.

## Contribution

A complete overhaul of ChEBI's infrastructure, enabling new features and improved maintenance.

## Key findings

- ChEBI's outdated codebase was replaced with a modernized infrastructure.
- New features and tools were introduced to enhance the database's functionality.
- The overhaul ensures the long-term availability and growth of ChEBI.

## Abstract

Chemical Entities of Biological Interest (ChEBI) is a high-quality, manually curated, and open-access database and ontology of chemical entities available online at https://www.ebi.ac.uk/chebi/. The chemical entities in question are either naturally occurring compounds or synthetic compounds that play a vital role in the processes of living organisms. ChEBI was launched in 2004, and over the years the original codebase has become increasingly difficult to maintain. Here, we describe the complete overhaul and modernization of ChEBI’s infrastructure, including its codebase and associated tools (website, web services, and submission tool) to ensure the continued availability and growth of this critical resource for the global bioinformatics community and beyond. The infrastructure overhaul also enabled us to introduce new features and capabilities into ChEBI as well as to update or deprecate redundant ones.

Graphical Abstract

## Full-text entities

- **Genes:** BCAR1 (BCAR1 scaffold protein, Cas family member) [NCBI Gene 9564] {aka CAS, CAS1, CASS1, CRKAS, P130Cas}
- **Diseases:** inflammatory (MESH:D007249), ChEBI (MESH:D019966)
- **Chemicals:** 2-(acetyloxy)benzoic acid (MESH:D001241), glycans (MESH:D011134), ChEBI (-), Carbohydrate (MESH:D002241), fatty acid (MESH:D005227)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]
- **Cell lines:** BALB/c — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0184)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12807787/full.md

## References

40 references — full list in the complete paper: https://tomesphere.com/paper/PMC12807787/full.md

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Source: https://tomesphere.com/paper/PMC12807787