2003 ExtractingSynonymousGeneProteinTerms

(Yu & Agichtein, 2003) ⇒ Hong Yu, Eugene Agichtein. (2003). “Extracting Synonymous Gene and Protein Terms from Biological Literature.” In: Proceedings of the 11th Int. Conference on Intelligent Systems for Molecular Biology (ISMB-2003).

Subject Headings: Relation Recognition, Word Normalization.

Notes

Cited By

2004

(Krauthammer & Nenadic, 2004) ⇒ Michael Krauthammer, and Goran Nenadic. (2004). “Term Identification in the Biomedical Literature.” In: Journal of Biomedical Informatics, 37(6). doi:10.1016/j.jbi.2004.08.004

Quotes

Abstract

Motivation: Genes and proteins are often associated with multiple names. More names are added as new functional or structural information is discovered. Because authors can use any one of the known names for a gene or protein, information retrieval and extraction would benefit from identifying the gene and protein terms that are synonyms of the same substance.

Results: We have explored four complementary approaches for extracting gene and protein synonyms from text, namely the unsupervised, partially supervised, and supervised machine-learning techniques, and the manual knowledge-based approach. We report results of a large scale evaluation of these alternatives over an archive of biological journal articles. Our evaluation shows that our extraction techniques could be a valuable supplement to resources such as SWISSPROT, as our systems were able to capture gene and protein synonyms not listed in the SWISSPROT database.

Data Availability: The extracted gene and protein synonyms are available at http://synonyms.cs.columbia.edu/

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BibTeX

@inproceedings{DBLP:conf/ismb/YuA03,

 author    = {Hong Yu and
              Eugene Agichtein},
 title     = {Extracting synonymous gene and protein terms from biological
              literature.},
 booktitle = {ISMB (Supplement of Bioinformatics)},
 year      = {2003},
 pages     = {340-349},
 ee        = {http://bioinformatics.oupjournals.org/cgi/content/abstract/19/suppl_1/i340?etoc},
 crossref  = {DBLP:conf/ismb/2003},
 bibsource = {DBLP, http://dblp.uni-trier.de}

}
@proceedings{DBLP:conf/ismb/2003,

 title     = {Proceedings of the Eleventh International Conference on
              Intelligent Systems for Molecular Biology, June 29 - July
              3, 2003, Brisbane, Australia},
 booktitle = {ISMB (Supplement of Bioinformatics)},
 year      = {2003},
 bibsource = {DBLP, http://dblp.uni-trier.de}

}

,

	Author	volume	Date Value	title	type	journal	titleUrl	doi	note	year
2003 ExtractingSynonymousGeneProteinTerms	Hong Yu Eugene Agichtein			Extracting Synonymous Gene and Protein Terms from Biological Literature		Proceedings of the 11th Int	http://www.cs.columbia.edu/~eugene/papers/ismb2003.pdf			2003