Playing biology's name game: identifying protein names in scientific text

Publication Type		Conference Paper
Authors		Daniel Hanisch, Juliane Fluck, Heinz-Theodor Mevissen, Ralf Zimmer
Year of Publication		2003
Editors		Russ B. Altman, Keith A. Dunker, Lawrence Hunter, Teri E. Klein
Proceedings Title		Proceedings of the 8th Pacific Symposium on Biocomputing (PSB 2003)
Pages		403-414
Keywords		textmining
Conference Date/Location		Lihue, Hawaii, USA, January 3-7, 2003
Citation Key		bioinflmu-281
Document visibility		Global publication list
Export		BibTex

Abstract

A growing body of work is devoted to the extraction of protein or gene interaction information from the scientific literature. Yet, the basis for most extraction algorithms, i.e. the specific and sensitive recognition of protein and gene names and their numerous synonyms, has not been adequately addressed. Here we describe the construction of a comprehensive general purpose name dictionary and an accompanying automatic curation procedure based on a simple token model of protein names. We designed an efficient search algorithm to analyze all abstracts in MEDLINE in a reasonable amount of time on standard computers. The parameters of our method are optimized using machine learning techniques. Used in conjunction, these ingredients lead to good search performance. A supplementary web page is available at http://cartan.gmd.de/ProMiner/.