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2016 ; 8
(ä): 11
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libChEBI: an API for accessing the ChEBI database
#MMPMID26933452
Swainston N
; Hastings J
; Dekker A
; Muthukrishnan V
; May J
; Steinbeck C
; Mendes P
J Cheminform
2016[]; 8
(ä): 11
PMID26933452
show ga
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.