Detection of IUPAC and IUPAC-like Chemical Names

Klinger R, Kolarik C, Fluck J, Hofmann-Apitius M, Friedrich CM (2008)
Bioinformatics 24(13): i268-i276.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Autor*in
Klinger, RomanUniBi; Kolarik, Corinna; Fluck, Juliane; Hofmann-Apitius, Martin; Friedrich, Christoph M.
Erscheinungsjahr
2008
Zeitschriftentitel
Bioinformatics
Band
24
Ausgabe
13
Seite(n)
i268-i276
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/2603465

Zitieren

Klinger R, Kolarik C, Fluck J, Hofmann-Apitius M, Friedrich CM. Detection of IUPAC and IUPAC-like Chemical Names. Bioinformatics. 2008;24(13):i268-i276.
Klinger, R., Kolarik, C., Fluck, J., Hofmann-Apitius, M., & Friedrich, C. M. (2008). Detection of IUPAC and IUPAC-like Chemical Names. Bioinformatics, 24(13), i268-i276. doi:10.1093/bioinformatics/btn181
Klinger, R., Kolarik, C., Fluck, J., Hofmann-Apitius, M., and Friedrich, C. M. (2008). Detection of IUPAC and IUPAC-like Chemical Names. Bioinformatics 24, i268-i276.
Klinger, R., et al., 2008. Detection of IUPAC and IUPAC-like Chemical Names. Bioinformatics, 24(13), p i268-i276.
R. Klinger, et al., “Detection of IUPAC and IUPAC-like Chemical Names”, Bioinformatics, vol. 24, 2008, pp. i268-i276.
Klinger, R., Kolarik, C., Fluck, J., Hofmann-Apitius, M., Friedrich, C.M.: Detection of IUPAC and IUPAC-like Chemical Names. Bioinformatics. 24, i268-i276 (2008).
Klinger, Roman, Kolarik, Corinna, Fluck, Juliane, Hofmann-Apitius, Martin, and Friedrich, Christoph M. “Detection of IUPAC and IUPAC-like Chemical Names”. Bioinformatics 24.13 (2008): i268-i276.

38 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Improving Biochemical Named Entity Recognition Using PSO Classifier Selection and Bayesian Combination Methods.
Akkasi A, Varoglu E., IEEE/ACM Trans Comput Biol Bioinform 14(6), 2017
PMID: 28113438
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning.
Zhang Y, Xu J, Chen H, Chen H, Wang J, Wu Y, Prakasam M, Xu H., Database (Oxford) 2016(), 2016
PMID: 27087307
Chemical entity recognition in patents by combining dictionary-based and statistical approaches.
Akhondi SA, Pons E, Afzal Z, van Haagen H, Becker BF, Hettne KM, van Mulligen EM, Kors JA., Database (Oxford) 2016(), 2016
PMID: 27141091
Recognizing chemicals in patents: a comparative analysis.
Habibi M, Wiegandt DL, Schmedding F, Leser U., J Cheminform 8(), 2016
PMID: 27843493
Enhancing of chemical compound and drug name recognition using representative tag scheme and fine-grained tokenization.
Dai HJ, Lai PT, Chang YC, Tsai RT., J Cheminform 7(suppl 1 text mining for chemistry and the chemdner trac), 2015
PMID: 25810771
CheNER: a tool for the identification of chemical entities and their classes in biomedical literature.
Usié A, Cruz J, Comas J, Solsona F, Alves R., J Cheminform 7(suppl 1 text mining for chemistry and the chemdner trac), 2015
PMID: 25810772
tmChem: a high performance approach for chemical named entity recognition and normalization.
Leaman R, Wei CH, Lu Z., J Cheminform 7(suppl 1 text mining for chemistry and the chemdner trac), 2015
PMID: 25810774
LeadMine: a grammar and dictionary driven approach to entity recognition.
Lowe DM, Sayle RA., J Cheminform 7(suppl 1 text mining for chemistry and the chemdner trac), 2015
PMID: 25810776
A document processing pipeline for annotating chemical entities in scientific documents.
Campos D, Matos S, Oliveira JL., J Cheminform 7(suppl 1 text mining for chemistry and the chemdner trac), 2015
PMID: 25810778
A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature.
Tang B, Feng Y, Wang X, Wu Y, Zhang Y, Jiang M, Wang J, Xu H., J Cheminform 7(suppl 1 text mining for chemistry and the chemdner trac), 2015
PMID: 25810779
Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.
Clark AM, Dole K, Coulon-Spektor A, McNutt A, Grass G, Freundlich JS, Reynolds RC, Ekins S., J Chem Inf Model 55(6), 2015
PMID: 25994950
Many InChIs and quite some feat.
Warr WA., J Comput Aided Mol Des 29(8), 2015
PMID: 26081259
An Overview of Biomolecular Event Extraction from Scientific Documents.
Vanegas JA, Matos S, González F, Oliveira JL., Comput Math Methods Med 2015(), 2015
PMID: 26587051
A survey on annotation tools for the biomedical literature.
Neves M, Leser U., Brief Bioinform 15(2), 2014
PMID: 23255168
CheNER: chemical named entity recognizer.
Usié A, Alves R, Solsona F, Vázquez M, Valencia A., Bioinformatics 30(7), 2014
PMID: 24227678
Annotated chemical patent corpus: a gold standard for text mining.
Akhondi SA, Klenner AG, Tyrchan C, Manchala AK, Boppana K, Lowe D, Zimmermann M, Jagarlapudi SA, Sayle R, Kors JA, Muresan S., PLoS One 9(9), 2014
PMID: 25268232
Chemical name extraction based on automatic training data generation and rich feature set.
Yan S, Spangler WS, Chen Y., IEEE/ACM Trans Comput Biol Bioinform 10(5), 2013
PMID: 24384710
Silver threads.
Warr WA., J Comput Aided Mol Des 26(1), 2012
PMID: 22160657
Chemical Entity Recognition and Resolution to ChEBI.
Grego T, Pesquita C, Bastos HP, Couto FM., ISRN Bioinform 2012(), 2012
PMID: 25937941
ChemSpot: a hybrid system for chemical named entity recognition.
Rocktäschel T, Weidlich M, Leser U., Bioinformatics 28(12), 2012
PMID: 22500000
Mining the pharmacogenomics literature--a survey of the state of the art.
Hahn U, Cohen KB, Garten Y, Shah NH., Brief Bioinform 13(4), 2012
PMID: 22833496
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.
Kim S, Kim W, Wei CH, Lu Z, Wilbur WJ., Database (Oxford) 2012(), 2012
PMID: 23160415
ChemEx: information extraction system for chemical data curation.
Tharatipyakul A, Numnark S, Wichadakul D, Ingsriswang S., BMC Bioinformatics 13 Suppl 17(), 2012
PMID: 23282330
Mining metabolites: extracting the yeast metabolome from the literature.
Nobata C, Dobson PD, Iqbal SA, Mendes P, Tsujii J, Kell DB, Ananiadou S., Metabolomics 7(1), 2011
PMID: 21687783
Challenges in integrating Escherichia coli molecular biology data.
Lourenço A, Carneiro S, Rocha M, Ferreira EC, Rocha I., Brief Bioinform 12(2), 2011
PMID: 21059604
Using workflows to explore and optimise named entity recognition for chemistry.
Kolluru B, Hawizy L, Murray-Rust P, Tsujii J, Ananiadou S., PLoS One 6(5), 2011
PMID: 21633495
Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications.
Vazquez M, Krallinger M, Leitner F, Valencia A., Mol Inform 30(6-7), 2011
PMID: 27467152
Cross-species gene normalization by species inference.
Wei CH, Kao HY., BMC Bioinformatics 12 Suppl 8(), 2011
PMID: 22151999
OSCAR4: a flexible architecture for chemical text-mining.
Jessop DM, Adams SE, Willighagen EL, Hawizy L, Murray-Rust P., J Cheminform 3(1), 2011
PMID: 21999457
Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining.
Hettne KM, Williams AJ, van Mulligen EM, Kleinjans J, Tkachenko V, Kors JA., J Cheminform 2(1), 2010
PMID: 20331846
Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy.
Alexopoulou D, Andreopoulos B, Dietze H, Doms A, Gandon F, Hakenberg J, Khelif K, Schroeder M, Wächter T., BMC Bioinformatics 10(), 2009
PMID: 19159460
Identification of histone modifications in biomedical text for supporting epigenomic research.
Kolárik C, Klinger R, Hofmann-Apitius M., BMC Bioinformatics 10 Suppl 1(), 2009
PMID: 19208128
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 25(22), 2009
PMID: 19759196

48 References

Daten bereitgestellt von Europe PubMed Central.

ACDName. Software
AUTHOR UNKNOWN, 2007
Reconstruction of chemical molecules from images
Algorri M-E., 2007
Identifying and classifying terms in the life sciences: the case of chemical terminology
Anstein S., 2006

Bishop CM., 2006
Name=struct. Software
AUTHOR UNKNOWN, 2007
Marvin. Software
AUTHOR UNKNOWN, 2007
High-throughput identification of chemistry in life science texts
Corbett P, Murray-Rust P., 2006
Annotation of chemical named entities
Corbett P., 2007
Oscar3. Software
Corbett P., 2007

Efron B, Tibshirani RJ., 1993
Mining, storage, retrieval: the challenge of integrating chemoinformatics with chemical structure recognition in text and images
Eigner-Pitto V., 2007
Biomedical and chemical named entity recognition with conditional random fields: the advantage of dictionary features
Friedrich CM., 2006
ProMiner: rule-based protein and gene entity recognition
Hanisch D., 2005

AUTHOR UNKNOWN, 2007
Top 50 drugs brand-name prescribed
Humana I., 2005
The extraction of information from the text of chemical patents. 1. identification of specific chemical names
Kemp N, Lynch M., 1998
Classical Probabilistic Models and Conditional Random Fields
Klinger R, Tomanek K., 2007
Identifying gene specific variations in biomedical text
Klinger R., 2007
Named entity recognition with combinations of conditional random fields
Klinger R., 2007
Identification of new drug classification terms in textual resources.
Kolarik C, Hofmann-Apitius M, Zimmermann M, Fluck J., Bioinformatics 23(13), 2007
PMID: 17646305
Chemical names: terminological resources and corpora annotation
Kolářik C., 2008
Factor graphs and the sum-product algorithm
Kschischang F., 2001
Conditional random fields: probabilistic models for segmenting and labeling sequence data
Lafferty JD., 2001
MALLET: a machine learning for language toolkit
McCallum AK., 2002
An entity tagger for recognizing acquired genomic variations in cancer literature.
McDonald RT, Winters RS, Mandel M, Jin Y, White PS, Pereira F., Bioinformatics 20(17), 2004
PMID: 15180929
Identifying gene and protein mentions in text using conditional random fields.
McDonald R, Pereira F., BMC Bioinformatics 6 Suppl 1(), 2005
PMID: 15960840

McNaught AD, Wilkinson A., 1997
Chemical markup language: a simple introduction to structured documents
Murray-Rust P., 1997
A biological named entity recognizer
Narayanaswamy M., 2003
Pubchem data. Online
AUTHOR UNKNOWN, 2007
Updating Quasi-Newton matrices with limited storage
Nocedal J., 1980
Lexichem. Software
AUTHOR UNKNOWN, 2007
A tutorial on hidden Markov models and selected applications in speech recognition
Rabiner LR., 1989
Ebimed – text crunching to gather facts for proteins from medline. newblock
Rebholz-Schuhmann D., 2007
Understanding chemical terminology
Reyle U., 2006
Mining patents using molecular similarity search
Rhodes J., 2007

Schölkopf B, Smola AJ., 2002
The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics.
Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E., J Chem Inf Comput Sci 43(2), 2003
PMID: 12653513
Extraction and search of chemical formulae in text documents on the web
Sun B., 2007
A reappriasal of sentence and token splitting for life science documents
Tomanek K., 2007
Medlineplus
AUTHOR UNKNOWN, 2007
Smiles, a chemical language and information system. 1. introduction to methodology and encoding rules
Weininger D., 1988
Biocreative 2. gene mention task
Wilbur J., 2007
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. 34(Database issue), 2006
PMID: 16381955
Combating illiteracy in chemistry: towards computer-based chemical structure reconstruction
Zimmermann M., 2005

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 18586724
PubMed | Europe PMC

Suchen in

Google Scholar