title: libChEBI: an API for accessing the ChEBI database.
abstract: BACKGROUND
  ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software.
  
  
  RESULTS
  To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications.
  
  
  CONCLUSIONS
  libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.
authors.affiliation: Manchester Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN UK ; European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD UK.
authors.forename: Neil
authors.identifier: 0000-0001-7020-1236
authors.initials: N
authors.lastname: Swainston
authors.affiliation: European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD UK.
authors.forename: Janna
authors.initials: J
authors.lastname: Hastings
authors.affiliation: European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD UK.
authors.forename: Adriano
authors.initials: A
authors.lastname: Dekker
authors.affiliation: European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD UK.
authors.forename: Venkatesh
authors.initials: V
authors.lastname: Muthukrishnan
authors.affiliation: European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD UK ; NextMove Software Ltd., Innovation Centre, Science Park, Milton Road, Cambridge, CB4 0EY UK.
authors.forename: John
authors.initials: J
authors.lastname: May
authors.affiliation: European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD UK.
authors.forename: Christoph
authors.initials: C
authors.lastname: Steinbeck
authors.affiliation: Manchester Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN UK ; School of Computer Science, University of Manchester, Manchester, M13 9PL UK ; Center for Quantitative Medicine, UConn Health, Farmington, CT 06030 USA.
authors.forename: Pedro
authors.initials: P
authors.lastname: Mendes
keywords: API; ChEBI; Cheminformatics; Database; Java; Library; MATLAB; Python