Display Settings:


Send to:

Choose Destination
See comment in PubMed Commons below
Int J Med Inform. 2002 Dec 4;67(1-3):49-61.

Protein names and how to find them.

Author information

  • 1Swedish Institute of Computer Science, Box 1263, SE-164 29, Kista, Sweden. franzen@sics.se


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.

[PubMed - indexed for MEDLINE]
PubMed Commons home

PubMed Commons

How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Elsevier Science
    Loading ...
    Write to the Help Desk