The ChEMBL database as linked open data

By Egon Willighagen, A. Waagmeester, O. Spjuth, P. Ansell, Antony J. Williams, Valery Tkachenko, Janna Hastings, Bin Chen, D. Wild. 2013

123 citations recorded by the source corpus.

BackgroundMaking 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.ResultsThis 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.ConclusionsWe 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.

Subfields: Artificial Intelligence, Information Systems and Management, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Artificial Intelligence

1. Samuel Madden
2. M. Stonebraker
3. Evan E. Bolton
4. Ziawasch Abedjan
5. Sanjay Krishnan
6. M. Franklin
7. Eugene Wu
8. Ihab F. Ilyas

In Information Systems and Management

1. Samuel Madden
2. M. Stonebraker
3. Axel Drefahl

In Molecular Biology

1. Stephen H. Bryant
2. Sunghwan Kim
3. Evan E. Bolton
4. Bo Yu
5. Lianyi Han
6. Jian Zhang
7. Siqian He
8. Benjamin A. Shoemaker

Citations in the corpus

• PubChem Substance and Compound databases (2015, background): “uk/rdf/services/chembl/) (36,38); and compound to WikiData RDF (https: //meta.”
• PubChemRDF: towards the semantic annotation of PubChem compound and substance databases (2015, methodology): “…PubChem substance and the PDB record is exposed: If a PubChem substance was deposited by ChEMBL, it is cross-linked to EBI RDF [21] and ChEMBL RDF [27]: If a PubChem depositor provided the PubMed references for a given substance, the literature mentioning of a given substance is exposed: where…”
• Aurum: A Data Discovery System (2018, methodology): “C H EMBL is a well known public chemical database [9] with around 70 tables.”