LINNAEUS: a species name identification system for biomedical literature.

ABSTRACT:

Background

The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles.

Results

In this paper we describe an open-source species name recognition and normalization software system, LINNAEUS, and evaluate its performance relative to several automatically generated biomedical corpora, as well as a novel corpus of full-text documents manually annotated for species mentions. LINNAEUS uses a dictionary-based approach (implemented as an efficient deterministic finite-state automaton) to identify species names and a set of heuristics to resolve ambiguous me

SUBMITTER: Gerner M 

PROVIDER: S-EPMC2836304 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature