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

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.

Access online services of chemical identifiers from Python

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.

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

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.

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

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.

Data Manipulation and neo4j imports for Analysis

Search genomes by chemical compounds

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