The ChEMBL database as linked open data

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


Background 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.

Results 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.

Conclusions 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.

You already know about the fragility of ontologies so no need to repeat that rant here.

Having material encoded with an ontology, on the other hand, after vetting, can be a source that you wrap with a topic map.

So all that effort isn’t lost.

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