chebi

Access to Biological Web Services from Python.

Schema for chemistry ontology classes

LLM-generated CHEBI classifiers

Always hungry SDF chemical file format parser with many output formats

CHEBI Integrated Role Ontology

Access online services of chemical identifiers from Python

Python tools for ChEBI database: subgraph extraction and molecular entity standardization for metabolomics

metabolomicsDB is a collection of three open-source command-line tools and an API. The tools create a meta-database of HMDB and ChEBI, while the API allows others to read the meta-database and use it on their own projects.

A Bio2BEL package for converting Chemical Entities of Biological Interest (ChEBI) to BEL

A spec-complete OBO 1.4 format parser for TypeScript and JavaScript.

Integrate metabolomics datasets that do not share the same measured metabolites, by grouping metabolites into shared chemical classes (through the ChEBI ontology, RefMet, or ClassyFire) and scoring each class per sample.

Systematic expansion of R-group for ChEBI molecules from the RHEA database

ssCCA: single-sample chemical class analysis for cross-dataset LC-MS metabolomics integration (analysis code for the accompanying report).

Classify, cluster, and extract data using structured LLM outputs with validated models, consensus voting, and multithreading for efficient batch processing.

Predicting whether disease pathways are associated with Alzheimer's disease using data from UniProt, CheBi, KEGG and Reactome.

SMILES validation and diagnosis, molecular identity, SMARTS auditing, and multi-database compound lookup (PubChem, ChEMBL, ChEBI, KEGG)

Calls BioPortal API to look for matches in ChEBI to DrOn ingredient terms derived from RxNorm

Agent Skill for querying, traversing, and visualizing 250+ biomedical ontologies (GO, DOID, HP, MONDO, CHEBI, CL, UBERON) via the EMBL-EBI Ontology Lookup Service (OLS4) REST API with interactive 3D network, D3.js 2D DAG hierarchy, and lineage tree HTML5 dashboards.