Protein names and how to find them

Franzén, Kristofer and Eriksson, Gunnar and Olsson, Fredrik and Asker, Lars and Lidén, Per and Cöster, Joakim (2002) Protein names and how to find them. Journal of Medical Informatics, 67 (1-3). pp. 49-61. ISSN 1386-5056


Official URL:


A prerequisite for all higher level information extraction tasks is the identification of unknown names in text. Today, when large corpora can consist of billions of words, it is of utmost importance to develop accurate techniques for the automatic detection, extraction and categorization of named entities in these corpora. Although named entity recognition might be regarded a solved problem in some domains, it still poses a significant challenge in others. In this work we focus on one of the more difficult tasks, the identification of protein names in text. This task presents several interesting difficulties because of the named entities' variant structural characteristics, their sometimes unclear status as names, the lack of common standards and fixed nomenclatures, and the specifics of the texts in the molecular biology domain in which they appear. We describe how we approached these and other difficulties in the implementation of Yapex, a system for the automatic identification of protein names in text. We also evaluate Yapex under four different notions of correctness and compare its performance to that of another publicly available system for protein name recognition.

Item Type:Article
Uncontrolled Keywords:Knowledge; Linguistics; Natural Language Processing; Medical Information Science; Computational Molecular Biology; Information Extraction; Protein Names
ID Code:957
Deposited On:02 Oct 2007
Last Modified:18 Nov 2009 15:58

Repository Staff Only: item control page