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Items: 1 to 20 of 104

1.

ChEBI: a database and ontology for chemical entities of biological interest.

Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D344-50. Epub 2007 Oct 11.

2.

Chemical Entities of Biological Interest: an update.

de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C.

Nucleic Acids Res. 2010 Jan;38(Database issue):D249-54. doi: 10.1093/nar/gkp886. Epub 2009 Oct 23.

3.

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D456-63. doi: 10.1093/nar/gks1146. Epub 2012 Nov 24.

4.

ChEBI: an open bioinformatics and cheminformatics resource.

Degtyarenko K, Hastings J, de Matos P, Ennis M.

Curr Protoc Bioinformatics. 2009 Jun;Chapter 14:Unit 14.9. doi: 10.1002/0471250953.bi1409s26.

PMID:
19496059
5.

A database for chemical proteomics: ChEBI.

de Matos P, Adams N, Hastings J, Moreno P, Steinbeck C.

Methods Mol Biol. 2012;803:273-96. doi: 10.1007/978-1-61779-364-6_19.

PMID:
22065232
6.

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J.

BMC Genomics. 2013 Jul 29;14:513. doi: 10.1186/1471-2164-14-513.

7.

ChEBI in 2016: Improved services and an expanding collection of metabolites.

Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1214-9. doi: 10.1093/nar/gkv1031. Epub 2015 Oct 13.

8.

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

Moreno P, Beisken S, Harsha B, Muthukrishnan V, Tudose I, Dekker A, Dornfeldt S, Taruttis F, Grosse I, Hastings J, Neumann S, Steinbeck C.

BMC Bioinformatics. 2015 Feb 21;16:56. doi: 10.1186/s12859-015-0486-3.

9.

libChEBI: an API for accessing the ChEBI database.

Swainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C, Mendes P.

J Cheminform. 2016 Mar 1;8:11. doi: 10.1186/s13321-016-0123-9. eCollection 2016.

10.

Self-organizing ontology of biochemically relevant small molecules.

Chepelev LL, Hastings J, Ennis M, Steinbeck C, Dumontier M.

BMC Bioinformatics. 2012 Jan 6;13:3. doi: 10.1186/1471-2105-13-3.

11.

Rhea--a manually curated resource of biochemical reactions.

Alcántara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, Cao H, de Matos P, Ennis M, Turner S, Owen G, Bougueleret L, Xenarios I, Steinbeck C.

Nucleic Acids Res. 2012 Jan;40(Database issue):D754-60. doi: 10.1093/nar/gkr1126. Epub 2011 Dec 1.

12.

A dictionary to identify small molecules and drugs in free text.

Hettne KM, Stierum RH, Schuemie MJ, Hendriksen PJ, Schijvenaars BJ, Mulligen EM, Kleinjans J, Kors JA.

Bioinformatics. 2009 Nov 15;25(22):2983-91. doi: 10.1093/bioinformatics/btp535. Epub 2009 Sep 16.

PMID:
19759196
13.

Updates in Rhea--a manually curated resource of biochemical reactions.

Morgat A, Axelsen KB, Lombardot T, Alcántara R, Aimo L, Zerara M, Niknejad A, Belda E, Hyka-Nouspikel N, Coudert E, Redaschi N, Bougueleret L, Steinbeck C, Xenarios I, Bridge A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D459-64. doi: 10.1093/nar/gku961. Epub 2014 Oct 20.

14.

OntoQuery: easy-to-use web-based OWL querying.

Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C.

Bioinformatics. 2013 Nov 15;29(22):2955-7. doi: 10.1093/bioinformatics/btt514. Epub 2013 Sep 5.

15.

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

Blank CE, Cui H, Moore LR, Walls RL.

J Biomed Semantics. 2016 Apr 12;7:18. doi: 10.1186/s13326-016-0060-6. eCollection 2016.

16.

A rule-based ontological framework for the classification of molecules.

Magka D, Krötzsch M, Horrocks I.

J Biomed Semantics. 2014 Apr 15;5:17. doi: 10.1186/2041-1480-5-17. eCollection 2014.

17.

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.

Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W372-6. doi: 10.1093/nar/gkn252. Epub 2008 May 8.

18.

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.

Côté RG, Jones P, Apweiler R, Hermjakob H.

BMC Bioinformatics. 2006 Feb 28;7:97.

19.

Accessing and using chemical property databases.

Hastings J, Josephs Z, Steinbeck C.

Methods Mol Biol. 2012;929:193-219.

PMID:
23007431
20.

DrugBank: a comprehensive resource for in silico drug discovery and exploration.

Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D668-72.

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