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Protein names and how to find them》.pdf
International Journal of Medical Informatics 67 (2002) 49/ 61
/locate/ijmedinf
Protein names and how to find them
Kristofer Franze´na,, Gunnar Eriksson a, Fredrik Olsson a, Lars Asker b,
Per Lide´nb, Joakim Coster b
¨
a Swedish Institute of Computer Science, Box 1263, SE-164 29 Kista, Sweden
b Virtual Genetics Laboratory AB, SE-171 77 Stockholm, Sweden
Abstract
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
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