The ChEMBL database as linked open data

Willighagen, Egon L., Waagmeester, Andra, Spjuth, Ola, Ansell, Peter, Williams, Antony J., Tkachenko, Valery, Hastings, Janna, Chen, Bin and Wild, David J. (2013) The ChEMBL database as linked open data. Journal of Cheminformatics, 5 5: . doi:10.1186/1758-2946-5-23

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Author Willighagen, Egon L.
Waagmeester, Andra
Spjuth, Ola
Ansell, Peter
Williams, Antony J.
Tkachenko, Valery
Hastings, Janna
Chen, Bin
Wild, David J.
Title The ChEMBL database as linked open data
Journal name Journal of Cheminformatics   Check publisher's open access policy
ISSN 1758-2946
Publication date 2013-05
Year available 2013
Sub-type Article (original research)
DOI 10.1186/1758-2946-5-23
Open Access Status DOI
Volume 5
Issue 5
Total pages 12
Place of publication London, United Kingdom
Publisher Chemistry Central
Collection year 2014
Language eng
Formatted abstract
Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis.

This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples. Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying.

We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support.
Keyword ChEMBL
Semantic web
Resource description framework
Linked data
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article number 23.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Information Technology and Electrical Engineering Publications
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Citation counts: TR Web of Science Citation Count  Cited 22 times in Thomson Reuters Web of Science Article | Citations
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