Automatic vs. manual curation of a multi-source chemical dictionary: The impact on text mining

Journal of Cheminformatics

Volumn 2, Issue 1, 2010, Pages

  Hettne, Kristina M ^a,b   Williams, Antony J ^c   Van Mulligen, Erik M ^a   Kleinjans, Jos ^b   Tkachenko, Valery ^c   Kors, Jan A ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b MAASTRICHT UNIVERSITY   (Netherlands)

^c ROYAL SOCIETY OF CHEMISTRY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77954173513     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-2-3     Document Type: Article

References (28)

1. Mining chemical structural information from the drug literature. DL Banville, Drug Discov Today 2006 11 35 42 10.1016/S1359-6446(05)03682-2 16478689
2. Status of text-mining techniques applied to biomedical text. RAA Erhardt R Schneider C Blaschke, Drug Discov Today 2006 11 315 325 10.1016/j.drudis.2006. 02.011 16580973
3. Extraction of Information from the Text of Chemical Patents. 1. Identification of Specific Chemical Names. N Kemp L Michael, J Chem Inf Comput Sci 1998 38 544 551
4. Chemistry for everyone. P Murray-Rust, Nature 2008 451 648 651 10.1038/451648a 18256659
5. Internet-based tools for communication and collaboration in chemistry. AJ Williams, Drug Discov Today 2008 13 502 506 10.1016/j.drudis.2008.03.015 18549976
6. A perspective of publicly accessible/open-access chemistry databases. AJ Williams, Drug Discov Today 2008 13 495 501 10.1016/j.drudis.2008.03.017 18549975
7. DrugBank: a knowledgebase for drugs, drug actions and drug targets. DS Wishart C Knox AC Guo D Cheng S Shrivastava D Tzur B Gautam M Hassanali, Nucleic Acids Res 2008 36 901 906 10.1093/nar/gkm958 18048412
8. The Unified Medical Language System (UMLS): integrating biomedical terminology. O Bodenreider, Nucleic Acids Res 2004 32 267 D270 10.1093/nar/gkh061 14681409
9. Identification of new drug classification terms in textual resources. C Kolarik M Hofmann-Apitius M Zimmermann J Fluck, Bioinformatics 2007 23 264 272 10.1093/bioinformatics/btm196 17646305
10. Drug name recognition and classification in biomedical texts. A case study outlining approaches underpinning automated systems. I Segura-Bedmar P Martinez M Segura-Bedmar, Drug Discov Today 2008 13 816 823 10.1016/j.drudis. 2008.06.001 18602492
11. Literature mining in support of drug discovery. P Agarwal DB Searls, Brief Bioinform 2008 9 479 492 10.1093/bib/bbn035 18820304
12. Cascaded classifiers for confidence-based chemical named entity recognition. P Corbett A Copestake, BMC Bioinformatics 2008 9 Suppl 11 4 10.1186/1471-2105-9-S11-S4 19025690
13. A Dictionary to Identify Small Molecules and Drugs in Free Text. KM Hettne RH Stierum MJ Schuemie PJ Hendriksen BJ Schijvenaars EM van Mulligen J Kleinjans JA Kors, Bioinformatics 2009 25 2983 2991 10.1093/bioinformatics/ btp535 19759196
14. ChemSpider. http://www.chemspider.com/
15. ChemMantis. http://www.chemspider.com/blog/welcome-chemmantis-to-chemzoo- and-a-call-for-contributions-to-the-community.html
16. Chemical names: terminological resources and corpora annotation. C Kolarik R Klinger CM Friedrich M Hofmann-Apitius J Fluck, Workshop on Building and evaluating resources for biomedical text mining (6th edition of the Language Resources and Evaluation Conference) 2008
17. Name=Struct: A Practical Approach to the Sorry State of Real-Life Chemical Nomenclature. J Bretcher, J Chem Inf Comput Sci 1999 39 943 950
18. Medical Subject Headings (MeSH). CE Lipscomb, Bull Med Libr Assoc 2000 88 265 266 10928714
19. ChEBI: a database and ontology for chemical entities of biological interest. K Degtyarenko P de Matos M Ennis J Hastings M Zbinden A McNaught R Alcantara M Darsow M Guedj M Ashburner, Nucleic Acids Res 2008 36 344 350 10.1093/nar/gkm791 17932057
20. From genomics to chemical genomics: new developments in KEGG. M Kanehisa S Goto M Hattori KF Aoki-Kinoshita M Itoh S Kawashima T Katayama M Araki M Hirakawa, Nucleic Acids Res 2006 34 354 D357 10.1093/nar/gkj102 16381885
21. LIGAND: database of chemical compounds and reactions in biological pathways. S Goto Y Okuno M Hattori T Nishioka M Kanehisa, Nucleic Acids Res 2002 30 402 404 10.1093/nar/30.1.402 11752349
22. HMDB: a knowledgebase for the human metabolome. DS Wishart C Knox AC Guo R Eisner N Young B Gautam DD Hau N Psychogios E Dong S Bouatra, et al. Nucleic Acids Res 2009 37 603 610 10.1093/nar/gkn810 18953024
23. ChemIDplus Fact Sheet. http://www.nlm.nih.gov/pubs/factsheets/ chemidplusfs.html
24. CAS REGISTRY and CAS Registry Numbers. http://www.cas.org/expertise/ cascontent/registry/regsys.html
25. Beilstein database. http://en.wikipedia.org/wiki/Beilstein-database
26. EINECS numbers. http://en.wikipedia.org/wiki/EINECS
27. Peregrine: Lightweight gene name normalization by dictionary lookup. MJ Schuemie R Jelier JA Kors, Proceedings of the Biocreative 2 workshop 2007 April 23-25, Madrid 131 140
28. Detection of IUPAC and IUPAC-like chemical names. R Klinger C Kolarik J Fluck M Hofmann-Apitius CM Friedrich, Bioinformatics 2008 24 268 276 10.1093/bioinformatics/btn181 18586724