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libChEBI: an API for accessing the ChEBI database
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, co...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772646/ https://www.ncbi.nlm.nih.gov/pubmed/26933452 http://dx.doi.org/10.1186/s13321-016-0123-9 |
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author | Swainston, Neil Hastings, Janna Dekker, Adriano Muthukrishnan, Venkatesh May, John Steinbeck, Christoph Mendes, Pedro |
author_facet | Swainston, Neil Hastings, Janna Dekker, Adriano Muthukrishnan, Venkatesh May, John Steinbeck, Christoph Mendes, Pedro |
author_sort | Swainston, Neil |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-016-0123-9) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4772646 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-47726462016-03-02 libChEBI: an API for accessing the ChEBI database Swainston, Neil Hastings, Janna Dekker, Adriano Muthukrishnan, Venkatesh May, John Steinbeck, Christoph Mendes, Pedro J Cheminform Software 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-016-0123-9) contains supplementary material, which is available to authorized users. Springer International Publishing 2016-03-01 /pmc/articles/PMC4772646/ /pubmed/26933452 http://dx.doi.org/10.1186/s13321-016-0123-9 Text en © Swainston et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Swainston, Neil Hastings, Janna Dekker, Adriano Muthukrishnan, Venkatesh May, John Steinbeck, Christoph Mendes, Pedro libChEBI: an API for accessing the ChEBI database |
title | libChEBI: an API for accessing the ChEBI database |
title_full | libChEBI: an API for accessing the ChEBI database |
title_fullStr | libChEBI: an API for accessing the ChEBI database |
title_full_unstemmed | libChEBI: an API for accessing the ChEBI database |
title_short | libChEBI: an API for accessing the ChEBI database |
title_sort | libchebi: an api for accessing the chebi database |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772646/ https://www.ncbi.nlm.nih.gov/pubmed/26933452 http://dx.doi.org/10.1186/s13321-016-0123-9 |
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