The ChEMBL database as linked open data

被引:85
作者
Willighagen, Egon L. [1 ]
Waagmeester, Andra [1 ]
Spjuth, Ola [2 ]
Ansell, Peter [3 ]
Williams, Antony J. [4 ]
Tkachenko, Valery [4 ]
Hastings, Janna [5 ]
Chen, Bin [6 ]
Wild, David J. [6 ]
机构
[1] Maastricht Univ, Dept Bioinformat BiGCaT, NL-6200 MD Maastricht, Netherlands
[2] Uppsala Univ, Dept Pharmaceut Biosci, SE-75124 Uppsala, Sweden
[3] Univ Queensland, Sch Informat Technol & Elect Engn, Brisbane, Qld 4072, Australia
[4] Royal Soc Chem, Wake Forest, NC 27587 USA
[5] Cheminformat & Metab European Bioinformat Inst, Hinxton CB10 1SD, Cambs, England
[6] Indiana Univ, Sch Informat & Comp, Bloomington, IN USA
来源
JOURNAL OF CHEMINFORMATICS | 2013年 / 5卷
关键词
ChEMBL; Bioactivity; Semantic web; Resource Description Framework; Linked Data; CHEMICAL BIOLOGY DATA; ONTOLOGY; SYSTEMS; PROTEIN; FRAMEWORK; LINKING;
D O I
10.1186/1758-2946-5-23
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
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.
引用
收藏
页数:12
相关论文
共 34 条
[1]   Model and prototype for querying multiple linked scientific datasets [J].
Ansell, Peter .
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE, 2011, 27 (03) :329-333
[2]   The Universal Protein Resource (UniProt) in 2010 [J].
Apweiler, Rolf ;
Martin, Maria Jesus ;
O'Donovan, Claire ;
Magrane, Michele ;
Alam-Faruque, Yasmin ;
Antunes, Ricardo ;
Barrell, Daniel ;
Bely, Benoit ;
Bingley, Mark ;
Binns, David ;
Bower, Lawrence ;
Browne, Paul ;
Chan, Wei Mun ;
Dimmer, Emily ;
Eberhardt, Ruth ;
Fedotov, Alexander ;
Foulger, Rebecca ;
Garavelli, John ;
Huntley, Rachael ;
Jacobsen, Julius ;
Kleen, Michael ;
Laiho, Kati ;
Leinonen, Rasko ;
Legge, Duncan ;
Lin, Quan ;
Liu, Wudong ;
Luo, Jie ;
Orchard, Sandra ;
Patient, Samuel ;
Poggioli, Diego ;
Pruess, Manuela ;
Corbett, Matt ;
di Martino, Giuseppe ;
Donnelly, Mike ;
van Rensburg, Pieter ;
Bairoch, Amos ;
Bougueleret, Lydie ;
Xenarios, Ioannis ;
Altairac, Severine ;
Auchincloss, Andrea ;
Argoud-Puy, Ghislaine ;
Axelsen, Kristian ;
Baratin, Delphine ;
Blatter, Marie-Claude ;
Boeckmann, Brigitte ;
Bolleman, Jerven ;
Bollondi, Laurent ;
Boutet, Emmanuel ;
Quintaje, Silvia Braconi ;
Breuza, Lionel .
NUCLEIC ACIDS RESEARCH, 2010, 38 :D142-D148
[3]   Bio2RDF: Towards a mashup to build bioinformatics knowledge systems [J].
Belleau, Francois ;
Nolin, Marc-Alexandre ;
Tourigny, Nicole ;
Rigault, Philippe ;
Morissette, Jean .
JOURNAL OF BIOMEDICAL INFORMATICS, 2008, 41 (05) :706-716
[4]  
Bilder G., 2011, CONTENT NEGOTIATION
[5]  
Bizer C., 2008, P LINK DAT WEB WORKS
[6]  
Bradley JC, 2009, BEAUTIFYING DATA REA
[7]   Assessing Drug Target Association Using Semantic Linked Data [J].
Chen, Bin ;
Ding, Ying ;
Wild, David J. .
PLOS COMPUTATIONAL BIOLOGY, 2012, 8 (07)
[8]   Improving integrative searching of systems chemical biology data using semantic annotation [J].
Chen, Bin ;
Ding, Ying ;
Wild, David J. .
JOURNAL OF CHEMINFORMATICS, 2012, 4
[9]   Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data [J].
Chen, Bin ;
Dong, Xiao ;
Jiao, Dazhi ;
Wang, Huijun ;
Zhu, Qian ;
Ding, Ying ;
Wild, David J. .
BMC BIOINFORMATICS, 2010, 11
[10]   Thousands of chemical starting points for antimalarial lead identification [J].
Gamo, Francisco-Javier ;
Sanz, Laura M. ;
Vidal, Jaume ;
de Cozar, Cristina ;
Alvarez, Emilio ;
Lavandera, Jose-Luis ;
Vanderwall, Dana E. ;
Green, Darren V. S. ;
Kumar, Vinod ;
Hasan, Samiul ;
Brown, James R. ;
Peishoff, Catherine E. ;
Cardon, Lon R. ;
Garcia-Bustos, Jose F. .
NATURE, 2010, 465 (7296) :305-U56