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.
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.
Authors: Francisco-Javier Gamo; Laura M Sanz; Jaume Vidal; Cristina de Cozar; Emilio Alvarez; Jose-Luis Lavandera; Dana E Vanderwall; Darren V S Green; Vinod Kumar; Samiul Hasan; James R Brown; Catherine E Peishoff; Lon R Cardon; Jose F Garcia-Bustos Journal: Nature Date: 2010-05-20 Impact factor: 49.962
Authors: Janna Hastings; Leonid Chepelev; Egon Willighagen; Nico Adams; Christoph Steinbeck; Michel Dumontier Journal: PLoS One Date: 2011-10-03 Impact factor: 3.240
Authors: Martijn P van Iersel; Alexander R Pico; Thomas Kelder; Jianjiong Gao; Isaac Ho; Kristina Hanspers; Bruce R Conklin; Chris T Evelo Journal: BMC Bioinformatics Date: 2010-01-04 Impact factor: 3.169
Authors: Lauren B Becnel; Smita Hastak; Wendy Ver Hoef; Robert P Milius; MaryAnn Slack; Diane Wold; Michael L Glickman; Boris Brodsky; Charles Jaffe; Rebecca Kush; Edward Helton Journal: J Am Med Inform Assoc Date: 2017-09-01 Impact factor: 4.497
Authors: Frederic B Bastian; Marcus C Chibucos; Pascale Gaudet; Michelle Giglio; Gemma L Holliday; Hong Huang; Suzanna E Lewis; Anne Niknejad; Sandra Orchard; Sylvain Poux; Nives Skunca; Marc Robinson-Rechavi Journal: Database (Oxford) Date: 2015-05-09 Impact factor: 3.451